单词句型汇总

A

as to 关于 至于 就…而论

• The boxes were marked in such a way as to permit the repeated location of each seed throughout stratification , germi- nation , and subsequent germinant growth.
• Also, these can give yield criteria for the decision as to whether clones should stay or be moved (or replaced) because of overly large or small reproductive efficiency (Muller-Starck and Ziehe 1984).
• There was some uncertainty as to whether Fisher should try for a Cambridge scholarship in mathematics or in biology, but in the end mathematics won.
• We all have our pet ideas as to what are important sources of variation or covariation, and fit models accordingly, but typically many different models can fit almost as well (e.g. full sib common environment and dominance).

albeit, although

• Recent work in P. lambertiana has confirmed the existence of a 24-nt DCL3 pathway in conifers, albeit with distinct spatial and/or temporal characteristics (40).
• However, while yield and wood quality are known to act in antagonizing fashion, the results based on PC2 and PC3, albeit collectively accounting for 42% of the total variation, created interesting opportunities for the concurrent selection for both traits without any adverse effect associated with the known negative correlations.
• In support of this observation, surveys of natural variation in DNA methylation have repeatedly demonstrated that the correlation of methylation variation with differential gene expression is low, albeit significant [15,22,40,41].

ambiguous unambiguous (distinct clear evident explicit)

• In such situations where spatial patterns are ambiguous about competition, the correlation between tree size and neighborhood density provides a useful measurement (Shackleton 2002).
• Fibre length is also highly heritable however the nature of genetic correlations is ambiguous in this study.
• MEAGHER(1986) discussed the implications of the answers to these questions in the context of ambiguous determination of paternity and their relevance to the extent and spread of genes in a well-defined geographical area.
• Therefore, this figure also establishes that unambiguous assignment of paternity in a natural population is not generally feasible, based solely on exclusionary events.
• We could not resolve unambiguously the question of the origin of the thirteenth chromosome pair in Douglas fir, but our data allow some speculation.
• The SAR regression approach was not unambiguously superior to other spatial regression approaches.
• Our observation of the greater influence of variation in female than in male flowering was not unambiguously supported by the results for these pine seed orchards.

allow （见permit）

• The availability of cheap and abundant molecular markers in maize (Zea mays L.) has allowed breeders to ask how molecular markers may best be used to achieve breeding progress, without conditioning the question on how breeding has traditionally been done.

at best 在最好的情况下；即便作最乐观的估计，就最乐观的一面看，从最好的角度来看；充其量，至多；说得再好也只是

• Thus, Drake’s 0.003 rule is at best a rough approximation for microorganisms.
• If empiricists have been a bit slow to embrace this, opting more commonly to focus on single traits or at best pairs of traits
• However, the first results on DNA sequence variation for conifers showed, at best, moderate estimates of nucleotide diversity
• Because of the low mutation rate and due to the fact that a mutation must occur in a predominant parent to cause significant LD, we assume that mutation is at best a marginal factor causing LD in elite maize germplasm.

anti.cip.ate -to expect that something will happen and be ready for it预期，预料

• The un.pre.ced.ent.ed rates of climate changes anticipated to occur in the future, coupled with land use changes that im.ped.e gene flow, can be expected to disrupt the interplay of adaptation and migration, likely affecting productivity and threatening the persistence of many species.
• The empirical results are supported by theoretical expectations demonstrating anticipated minimum genetic response compared with conventional approaches.
• Most of the genetic architecture underlying susceptibility to the disease remains to be defined and is anticipated to require the analysis of sample sizes that are beyond the numbers currently available to individual research groups.
• When applied to hybrid breeding, genomic selection is anticipated to be evenmore efficient because genotypes of hybrids are predetermined by their inbred parents.
• Hence, tree improve- ment efforts must select for more favourable juvenile wood properties to counterbalance anticipated negative effects on wood quality.
• This is among the first of many examples of how sequencing of the Populus genome is revolutionizing tree biotechnology and forest ecology research, and we anticipate a flurry of such studies to follow the publication of the sequence this year.
• Phenotype predictions for unobserved individuals that both anticipate sampling variation and incorporate all posterior uncertainty are easily obtained from MCMC output.
• It is widely anticipated that a gene-by-gene engineering approach will enable enhanced efficiency in plant breeding

ac.com.mod.ate 适应

• Here we build on recently developed methods for linkage-disequilibrium mapping of quan- titative traits to construct a general approach that can accommodate nuclear families of any size, with or with- out parental information.
  
  • a general approach
• The approach is sufficiently general to accommodate individuals with partial or no marker information.
• These include the need to accommodate replicate plants for each line, consider spatial variation in field trials, address line by environment interactions, and capture nonadditive effects.
• Therefore, sta- tistical models of species response to the environment not only need to accommodate spatial structure, but need to distinguish between components due to exogeneous and endogeneous processes rather than discarding all spatial variance.
• Even when traditional analysis methods accommodate the design, choice about which parameters (e.g., explicit models of dominance, SCA, etc.) should be included in the model can alter the estimates and interpretation of the other parameters.
• To increase its applicability in clinical genomics, GWAS could further accommodate irregular longitudinal data measured at subject-specific time points.
• A positive feature of categorical allocation is that the use of likelihoods or posterior probabilities results in a framework in which scoring errors or mutations can be accommodated very easily by modifying the transition probabilities accordingly
• Here, we derive a robust statistical approach for QTL mapping that accommodates a certain degree of misspecification of the true model by incorporating integrated square errors into the genetic mapping framework
• Likelihood methods can also be adjusted to accommodate genotyping error, mutation, and null alleles and are helpful in compensating for some of the errors in genotyping caused by microsatellites

a surge of……的涌现

• Recently, a surge of interest has also been exploded in solving the mixture models by Bayesian approaches
• For this reason, an understanding of biological curvature and texture has received a surge of interest in structural biology.
• Recently, with the surge of “omics” technologieswehave been able to generate amore comprehensive panorama of the genome-wide expression profiles during SE
• This is arguably the most important factor that drives the recent surge of popularity of Bayesian inference in most branches of science.
• During the last five years there has been a surge of work involving SilviScan (or similar tools) data for DEN and MFA at the ring level.

address- solve problems

• address
  
  • ~ questions /issue uncertainty /problems
• We conclude by briefly summarizing more complex applications of the animal model, and by highlighting key pitfalls and dangers for the researcher wanting to begin using quantitative genetic tools to address ecological and evolutionary questions.
• We address this issue in a study of two 10-year-old genetic field trials of Eucalyptus globulus Labill. in Australia.
• Integrating functional mapping into a full-sib family requires a model selection procedure capable of addressing these uncertainties.
• Phenotypic competition addresses largely the same source of variation as the autoregressive parameters.

appraise; to officially judge how successful, effective, or valuable something is 评定；鉴定；估价

• evaluate = to appraise; to assess
• Monitoring programs should be included as part of the breeding program in order to appraise coancestry levels in new orchards and inbreeding levels in seed crops.
• As part of this section, the authors critically appraise a putative alternative solution namely “land sparing,” which is the spatial separation of biodiversity conservation and agriculture.
• Longitudinal growth strain at the stem surface is **appraise**d on the basis of stress released on the stem periphery by drilling into wood under the cambium.
• Given the rapid growth of genomic resources available for studies of non-model organisms, now is an excellent time to appraise the future prospects for molecular genetic- and pedigree-based studies of inbreeding and inbreeding depression in the wild.
• Note that (1) and (2) can only be **appraise**d precisely for a specific model,(3) for two or more alternative models, and (4) for the appropriateness for the data in hand of the various models
• The assumption that forest protection and management should be based on central policy and planning within an authoritative and hierarchical forest service, having important territorial and policing functions, was re**appraise**d.
• However, Peri and Pandey (2001) and others have recently re**appraise**d this convention, finding that more than 40 per cent of known transcripts contain in-frame AUG codons upstream of the actual initiator codon, some of which conform more closely to the Kozak motif than the authentic initiator codon.
• Discrepancies should, however, cause us to critically reappraise the model, the data, and our preconceptions.
• Such risks include assessing: the `gain’ projections; the markets’ ability to model the improvements with respect to future potential buyers of the timberland and appraisers who periodically value the timberland; and susceptibility to catastrophic loss due to reduced genetic diversity.
• Tubby look at their land holdings and reappraise whether the current land use is providing them with the greatest long term benefit.
• Note that the membership of clusters may change each cycle, so we have to repeatedly re-appraise the memberships.

appreciable很大的 considerable，great，hugely； large

• Grain angle under bark exhibited non-significant genetic correlations, close to zero, with growth traits, stem form, and branch traits in both species, and with pilodyn penetration in Norway spruce, suggesting that genetic selection for this trait would not generate any appreciable response in the other traits.
• Some of these mutations can reach an appreciable frequency in the population, for example by random drift or by natural selection.
• However, using less than 500 markers led to an appreciable loss in accuracy for all four traits.
• For instance, Daniels [273] studied the effect of eight different pollination regimes, including SMP, on filled seed production of one selected Douglas-fir parent, but found no appreciable increase as compared with the wind-pollinated control.
• The level of variation found in different wood properties in this study indicated that good genetic gain could be achieved via conventional breeding, subject to these traits showing appreciable genetic control.

B

bear

1. 忍受，忍耐，具有，支撑

   • It also identified a chromosomal region bearing a semi-lethal recessive allele and demonstrated the genetic variability of recombination rate over the genome.
   • First, following on from the discussion above, if recombination occurs in hotspots and these hotspots bear most of the genes, then differential sequencing efforts will be required to obtain data for all of the genes in conifer genome sequencing programs.
   • Therefore, their genetic background may have been indirectly selected toward generalists bearing a plastic adaptability to local conditions.
   • The application of the genomic tools to plant breeding, besides improving the selection process, offers the possibility of planning and developing novel varieties bearing pre-defined traits (breeding by design).

2. 结果实，开花

   • This can explain why, applying growth regulator to control vegetative vigour, the `Dongkui’ cultivar is prone to bear male flowers [28], as well as provide evidence that male and female of Chinese bayberry may share common ancestors and co-evolved.
   • In plant species that bear both male and female flowers, the same individuals can be used both as females and as males in breeding; this mating design is called a diallel.

3. bearing on 对…有影响

   • PNAS does not take responsibility for or endorse these services, and their use has no bearing on acceptance of a manuscript for publication.
   • Chlorite holocellulose, its fractionation and bearing on summative wood analysis and on studies on the hemicelluloses.
   • Most of the attention devoted to identification of variables that have a bearing on resin production, however, has concentrated on environmental attributes and cultural practices aimed at stimulating tree growth.
   • A comparison of these results with those in Table 3 suggested that use of different models would not have appreciable bearing on the estimates of h2.
   • Wood properties of the tree have a major bearing on the final quality and strength of veneer and in turn performance of the final engineered product.
   • Considering the constraints of breeding cycles over several generations also brings into focus practical aspects of GS that have a bearing on its potential for success.
4. bearing/keep/ in mind that 记住
   
   • Such an approach could be useful since breeders of autogamous species are primarily interested in selecting progenies that, during homozygosis, accumulate a higher quantity of favorable alleles that associate the best additive genetic values (AGV), bearing in mind that the ultimate aim is the establishment of lines (Fehr, 1987).
   • We must bear in mind that, in breeding procedures using GS, the unintended fixation of deleterious mutations might occur in a short time span because the cycles of selection is turned over rapidly.
   • It is also useful to keep in mind that in a large randomly mating population with no linkage between loci influencing different characters, genetic correlations are soon dissipated (Lande, 1984).
   • One caveat to bear in mind is that many demographic processes, such as population expansion, bottlenecks or population subdivision, can result in patterns of polymorphism that mimic signatures of natural selection.
   • Moreover, we did not standardize the data as in Waldmann and Ericsson (2006), and comparison with their results should be done bearing this in mind.

C

cull 选择 剔除不好的

• It is better to cull undesirable individuals (selfed and related progenies) during the nursery stage prior to planting.
• It is possible that grafts with better flowering are favoured as complements, and it is likely that grafts with inferior flowering are culled at orchard thinning.
• RKER and LIBBY (1974) suggest that the correlation between self performance and outcross per- formance may be improved by culling the lower .50% of each self family to reduce the bias that may occur due to the segre- gation of rare, recessive, deleterious alleles.
• With independent culling levels, all genotypes are discarded which have a phenotypic value below the culling level for at least one trait; for example, low yield, poor quality or poor disease resistance.

corollary推论

• An important corollary to the gene balance hypothesis is balanced gene drive, which predicts, e.g., that multiple tetraploidies will naturally drive up the relative gene content of genes encoding transcription factors, protein kinases, multisubunit proteins like ribosomes and proteasomes, and other subunits of life’s most complicated machines (40).
• A corollary is that obtaining GS model accuracy beyond that of pedigree-based models would likely necessitate increasing genome coverage by a factor of at least 10X to 100X of that used herein, resulting in the use of a very large number of markers, likely in the hundreds of thousands.
• In parallel, inbreeding experiments have been conducted as a corollary with an interpretation as being the opposing effect of heterosis.
• A corollary of the hypothesis is that the chromosomal state most similar to the paleohexaploid progenitor is present in extant members of the genus Vitis, where chromosomes are still assorted in triplets due to an unexpected maintenance of gene order along tens of millions of years13.
• Falconer (1989) presents the correlated response equation, a corollary to the predicted gain equation, as:
• An important corollary is that the form of E(Y |X), the regression function, is unaffected by selection operating on X, this being true for any distribution.
• A corollary of this analysis is that relatively high amounts of resources must be absorbed by the crop to achieve high yields.
• A corollary of this problem is that lack of dynamic consistency makes any kind of individual differences analysis uninterpretable.

contemplate 考虑

• Some of the specific changes adopted or **contemplate**d are:
• The estimates do provide a useful benchmark for breeders interested in the potential for correlated responses in meat quality from selection on growth and yield and for breeders who contemplate the estimation of heritabilities in their breeding lines and/or adding these traits to their breeding objectives.
• Thus, the simple nested treatment model cross/DH could be **contemplate**d for analysis, where cross codes the particular cross and the DH nested within a cross is coded by DH.
• However, the lack of repetitive grouping along the orchard’s grid might affect the optimal nature of the design if practices such as systematic thinning are **contemplate**d.
• Among approaches now being **contemplate**d to raise further the yield ceiling, the exploitation of hybrid vigour (heterosis) is considered widely, the most prospective one.
• As we learn more about the detail of the genetic architecture of quantitative traits, it is interesting to contemplate whether this dominance will continue or whether some form of resolution of the two models will emerge.

coupled with/together with 加上，与…结合

• We pinpoint several future directions in which functional mapping can be coupled with systems biology to unravel the genetic and metabolic machinery of drug response.
• The evolution of body shape is thought to be tightly coupled to changes in regulatory sequences, but specific molecular events associated with major mor- phological transitions in vertebrates have remained elusive.
• Breeding in raspberry is time-consuming due to the highly heterozygous nature of this perennial fruit crop, coupled with relatively long periods of juven.ility童期长.
• The availability of reliable, informative molecular markers coupled with paternity assignment methods [13] created an opportunity whereby the breeding phase of tree breeding could be effectively eliminated.
• This inbreeding depression coupled with variation in outcrossing rates in the wild (Hardner et al. 1998) is believed to be a major factor driving differences in the performance of open-pollinated families in common-garden trials of E. globulus

com.pelling 令人信服的；极为有趣的；令人激动的；引人入胜的

• compelling

  • ~association /candidate /gene /method /(experimental) evidence /advantage /benefit /consequence /signal /approach /study /question /efficiency /results /reason /need /support /case /example /

• For systolic blood pressure收缩压, the most compelling association involved chromosome 12q21 and variants near the ATP2B1 gene.

• The most compelling regional candidate gene is ATP2B1
• This is encouraging because it suggests the commonly-used argument for using more resource-intensive and less readily accessible Bayesian methods may be less compelling than suggested by some authors.
• For all models except pine crown radius, we found compelling evidence for species-specific differences in competitive effects, as has been demonstrated in previous neighborhood analyses of tree growth
• A particularly compelling advantage of this RI set is that the two parental strains, C57BL/6J and DBA/2J, are sequenced
• This marker, which is a highly polymorphic gene, is a compelling candidate for regulation of these transcript abundances.
• This generative modelling approach offers several compelling benefits.
• The differentiation of the marker-allele which is in linkage to low extractives content was a compelling consequence, to make it useable for MAS.
• Appropriately, the most compelling candidate genes in the regions we identified have well- established effects in cartilage and bone differentiation and have been shown to impact on craniofacial development in animal models.
• Prior to the GWAS era, the only compelling association signal for fasting glucose levels was known at GCK (MIM 138079) (glucokinase), but GWAS in European samples (46,000 GWAS and 76,000 replication samples) have expanded that number to 16
• This approach is compelling, in that it addresses two important elements of post-GWAS prioritization: the selected pathway provides a biological vehicle for statistically combining GWAS association results, and an implicated pathway provides a biological interpretation.
• Nevertheless, this study is compelling in its use of natural genetic variation instead of engineered gene knockouts, suggesting that its profound genetic effects may be more widely generalized.
• Accounting for the external factors would move them closer to the proposed ‘intrinsic’ line, further supporting the conjecture that the intrinsic line is mainly defined by cancers without compelling known epidemiological risk, whereas those above are at higher risks owing to extrinsic factors.
• Two compelling questions arise from the discovery of these large gene families in pine
• The corresponding arguments are no less compelling for EWASs, but the relevant parameters are even more diffi- cult to predict because of the paucity of data and relevant theory.
• Sequence redundancy of about twofold (rather than the eightfold that is typical of whole-genome efforts) is suggested to offer compelling efficiency in yielding new information69, although it also suffers various limitations as detailed below.

circum.vent v. 包围；智取；绕行，规避更多还是用避免这个意思

• Hence, measure- ments should be taken to circumvent the problem in trade- offs between gain in selection and keeping diversity
• To circumvent this problem, a closed-form expression for an upper bound to R2 is obtained instead.
• The use of CBCS to efficiently capture the complex- ity of repetitive elements33,44— the largest constituent in most angiosperm genomes — might circumvent some problems and create new opportunities.
• One way to circumvent this limitation is to draw a profile of LD that decays over an extended genomic region
• To circumvent the limitations of QTL-based models, Meuwissen et al. (2001) proposed using whole genome regression (WGR) methods (also known as models for genomic selection, GS) where information about poten- tially hundreds of thousands of markers is jointly consid- ered.
• If we can further understand the genetic basis of these negative genetic correlations using molecular tools (e.g., identifying pleiotropic alleles or genes associated with antagonistically correlated traits), more efficient breeding strategies may be developed to circumvent these antagonistic genetic correla- tions by crossing genotypes with a desirable suite of al- leles.
• The rapid development of high-throughput and cost-effective genotyping technologies is making genome-wide studies in non- model organisms more feasible, which may circumvent the need for associations with known genes.

championed支持；拥护

• This was in part made possible by the overlap layout consensus (OLC) as- sembly paradigm championed by Myers [13] and ubiquitously implemented in first-generation WGS assemblers.
• On the one end of the spectrum, Lamb and Jablonka have championed the notion概念见解 that inherited epigenetic variation plays an important role in evolution, adding a complementary Lamarckian dimension to neo- Darwinian mechanisms

commit to 致力于 不及devote用的多

• The consortium represented by the authorship list hold long-term data that represent a considerable investment in scientific endeavour. Whilst we are committed to sharing these data for scientific research, users are requested to collaborate before publication of these data to ensure accurate biological interpretation.
• In contrast, relatively meager effort has been committed to determining how strongly genetic effects influence pheno- typic variation for resin yield in loblolly pine.

contribute

• We collected and sequenced 1,495 diverse varieties of hybrid rice (F1), which are grown on 415 million hectares per annum and contribute greatly to the agricultural production.
  
  • rice ~to production - diverse varieties - hectares - per annum每年 - greatly - agricultural production
• Cosegregation information from half sibs contributes little to accuracy of GEBVs in current dairy cattle breeding schemes but from full sibs it contributes considerably to accuracy within family in corn breeding.
  
  • cosegregation information - breeding schemes - considerably - information ~ to accuracy
• These results present the first step in the application of marker- assisted selection (MAS) to the Western Gulf Forest Tree Improvement Program (WGFTIP) for loblolly pine and will contribute to the knowledgebase necessary for genomic selection technology.
  
  • present the first step in the application of - knowledgebase - necessary for - genomic selection technology - results ~ to knowledgebase
• Statistical models play a pivotal role in mapping specific quantitative trait loci (QTLs) that contribute to biological shape and its developmental trajectories.
  
  • developmental trajectories - qtl ~ to shape and trajectories
• Currently, the genetic worth of a seedlot is estimated by the mean breeding value of all the parents, including those that contribute to pollen contamination and supplemental mass pollination, weighted by their proportional gamete contributions
  
  • the genetic worth of a seedlot - pollen contamination - supplemental mass pollination - parents ~ to pollen contamination
• The advancement made in the procedures described in this document should contribute to superior decisions in many aspects of forest management.
  
  • advancement ~ to decision
• A Bayesian analysis using 2 different sets of prior distributions for the variance components showed that inferences differed only when the relative amount of information contributed by the data was small.
  
  • inferences differed - the relative amount of - information ~ by data
• Forest managers may endeavor 努力 to understand and explore how competition and spatial dependence contribute to the growth of a forest stand and affect stand dynamics and forest health.
  
  • endeavor to - explore - competition and spatial dependence ~ to growth
• Internode length and leaf number contributed substantially to the heterosis of stem volume
  
  • length and leaf number ~ to heterosis
• Although much progress has been made in identifying the genes (and, in rare cases, mutations) that contribute to phenotypic variation, less is known about the effects that these genes have on fitness.
  
  • much process - gene ~ to variation
• Genetic effects contributed more than nongenetic parental effects to variation in traits measured at the adult stage
  
  • genetic effects ~ to variation
• Epistasis has been found to contribute significantly to life-history traits in many studies (reviewed
  
  • been found to - epistasis ~ to traits
• Integration of this complex expression data might contribute to improve our understanding of the molecular basis of heterosis.
  
  • integration ~ to improve our understanding of / a better understanding

cornerstone基石/milestone 里程碑

• Parentage analysis is a cornerstone of research in molecu- lar ecology.
• Given their undomesticated state, and difficulty in produc- ing suitable pedigrees as a result of high heterozygosity and long generation cycles [1,39,40], the OP family design should provide a cornerstone for the inevitable next wave of dis- secting complex phenotypes in forest trees.
• We can thus perceive (9) as the cornerstone of the NOIA model.
• We will not enter into details, but just note that the sparse structure of the left hand side matrix in (9) is the cornerstone for the fast computation of the AI-matrix used in the numerical maximisation of the REML likelihood.
• Although it remains the cornerstone approach, cost-per-unit yield gain has risen substantially.
• Arabidopsis research has also been an important cornerstone in the bid to describe how plants respond to chewing pests.
• That the lumber sector will remain the cornerstone of the competitiveness of the traditional and emerging forest products industry in Canada is one of the key findings of the Bio-pathways Project

D

deregulate 放松管制

• a transgenic construct-driven system for production of non-genetically modified hybrid maize has been deregulated

devote 致力于

• devote
  
  • ~ much/ substantial /major /considerable /initial/increasing /more effort to
  • ~ sth. to
  • ~ attention /discussion /energy /interest /resources /research /publications /to
• The increasing research effort devoted to IGEs suggests that they are a widespread phenomenon, probably particularly in natural populations and plants.
• This kind of design has the desirable feature that entries need not be replicated, but suffers from the fact that a considerable proportion of plots may need to be devoted to controls.
• This combining of cycles for testing improves the efficiency of the testing procedure and decreases the percentage of plots devoted to standard check treatments.
• Acreage devoted to growing longleaf pine has diminished to less than three percent of that at the time of European settlement
• MUCH effort in genetics has been devoted to revealing the underlying genetic architecture of
  quantitative or complex traits.
• Variation in drought resistance in conifers has long been recognized to have a genetic basis [61,62], and substantial effort has previously been devoted to attempts at using molecular and genomic tools to uncover the responsible genetic determinants [63-65].
• How- ever, the REML approach requires an iterative technique that usually tends to be computationally very demanding, especially for multivariate data sets, and much effort has therefore been devoted to development of more efficient algorithms
• Major efforts devoted to sequencing ESTs in various species are also multiplying 增加 越来越多
• Therefore, considerable effort has been devoted to develop new statistical methods that estimate the breeding values and heritability in the linear mixed model context
• Evolutionary change is usually driven by natural selection, and evolutionary biologists have devoted considerable energy to classifying and quantifying patterns of selection
• Ernst Mayr devoted an extended discussion to the origins of the modern neo- Darwinian consensus in evolutionary biology and the concep- tual unity it forged out of often-conflicting perspectives of the biometrically oriented “naturalist” and Mendelian camps
• Most of the attention devoted to identification of variables that have a bearing on resin production, however, has concentrated on environmental attributes and cultural practices aimed at stimulating tree growth.
  
  • have a bearing on与…有关系；对…有影响 - environmental attribute - cultural practice
• Much less attention has been devoted to the fact that phenotypes may also be correlated.

depleted耗尽的

• depleted
  
  • ~ sth/variation /resources
• Direct sunlight contains a high proportion of red light, whereas light reflected from neighboring vegeta- tion is depleted in red and relatively rich in far red
• When IGEs differ systematically between relatives and strangers, evolution by kin selection should not fully deplete heritable variation which could be expressed under interactions among strangers.

diminish- reduce /decrease

• Rapid germination and large seeds resulted in significantly larger seed- lings in the nursery, but these carryover effects diminished with age.
• Additive genetic correlations with height and stem diameter were negative with the simplest statistical model (r
  A = –0.425 and 0.511, respectively) but vanished or diminished when ring width was added as covariate.
• Simulations of growth under various scenarios (situation) of climate change indicated that it would be diminished tangibly under more intense warming.

de.fer- delay

• Some technical derivations are deferred to Appendices A

document

• Atkin et al. (2009) have also documented the impact of depth of pedigree and inclusion of historical data on the estimation of additive variance and breeding values in a sugarcane breeding program.
• Although well-documented software often exists for
  the fixed analog of the additive genetic model, and in some cases also a simple mixed model, the applicability of such software in animal breeding is often limited.
• Potential criteria for deciding which traits to pursue aggressively in this way might include the strength and robustness of detected associations, evidence that asso- ciations are disrupted by varying linkage disequilibrium patterns, documented associations of identified loci with multiple traits, and public health importance of the traits to be studied.
  
  • potential criteria - pursue aggressively - strength and robustness - disrupted - public health improtance
• Site effects have been shown in many studies to be important in heartwood content but genotype by site (GxE) interactions are poorly documented.
  
  • have been shown in many studies
• Despite considerable range in data describing current distribution, several studies have documented that the abundance of shortleaf pine in the Missouri Ozarks has diminished
  
  • the abundance of - has diminished
• Relationships between wood properties and profitability of kraft pulp production are well documented
  
  • wood properties - pfofitability of craft pulp production
• The involvement of NHX1, SOS1 and other CPA1 genes in plant response to NaCl stress has been well documented (An et al., 2007; Ma et al., 2015).
  
  • the involvement … in … - response to
• Although the ecological consequences of climate change are increasingly well documented, the effects of climate on the key evolutionary process driving adaptation— natural selection—are largely unknown.
  
  • ecological consequences - key evolutionary process - driving adaptation

depict- to describe something or someone in writing or speech, or to show them in a painting, picture etc【正式】 描写，描述，描绘

• The familial relatedness axis depicts the relationships among individuals from recent coancestry.
  -familial relatedness

• The degree and nature of polymorphism revealed by SRAP primerc combination Me4Em4 is depicted in Fig.2.

• Figure 2 depicts scatter plots of relationships among G, D,and GD that are taken from four randomly sampled animals.

• Figure 2 depicts the progress of breeding and deployment populations and method of breeding value prediction in the STBA radiata pine breeding history.

• Signal boundaries, depicted by vertical dotted lines, were chosen using the recombination hot spots flanking the strongest signal.

• Principal coordinate analysis (PCA) implemented in SAS and the unrooted neighbor- joining (N-J) tree based on the Nei’s distance using MEGA 4.0 (Tamura et al. 2007) were employed to depict genetic relationship between the 192 rapeseed inbred lines.

（un）duly 不适当地 过度地 不适当的

• In light of these weaknesses it was natural that an alternative would be sought, and so maximum likelihood estimation duly came to be considered.
• Breeding should therefore focus on improving adaptation, productivity, and stem and branch quality without unduly reducing wood density or adversely affecting fibre traits.
• Our conclusion is that haying-off is scientifically plausible, but the concept has been unduly extrapolated and might have influenced farmers’ practices in true Mediterranean environments where it is unlikely.
• The challenge for future yield improvement is to devise strategies that will enhance the scope for PWG to respond to availability of assimilates without unduly enhancing the risk of incomplete grain filling.
• concerns that an unduly high level of uniformity would be required; and (4) the need to establish standardized protocols and to demonstrate that laboratories around the globe can generate data of sufficient quality and consistency.

E

event.ual 最终的 last

• Over the course of evolution, many duplicate genes lose their function and are eventually removed by deletion.
• Cross-validation (CV) is an essential tool to achieve this goal, where a sample is partitioned into K parts of roughly equal size, one part is predicted using parameters estimated from the remaining K – 1 parts and eventually every part is predicted using a sample excluding that part.
• The ancestral angiosperm-wide genome duplica- tion apparent in the Amborella genome not only serves as a genetic marker for the origin of extant angiosperms, but it may also have set inmotion a series of events as numerous genes evolved novel functions, eventually leading to modern flowering plants.
• Further decreasing nc by increasing nr will eventually reduce family selection gains by increasing the contribution of within-family genetic variance components to the family gain denominators.
• As the position of the endogenous cline is not con- strained by selection, it can move, and eventually comes to rest where the gradient in exogenous allele frequency is locally maximal

ex.plic.it- very clear and direct 明确的

• explicit
  
  • ~ attention /description /framework
  • ~ly indicate /examine /account for
• Such determination requires explicit attention to the prior probability of particular findings, as well as appropriate correction for multiple comparisons.
• Journals could improve the reporting of gene association results by requiring explicit, critical and standardized descriptions of pre- vious evidence for candidate genes.
• Neighbour-joining trees based on SNP data provide an explicit framework for investigating hypotheses of breed history and the genesis of phenotypic diversity.
• Authors should indicate explicitly the phenotype combinations that yield negative mapping results and state how they use phenotypic infor- mation to guide the extension of pedigrees.
• Although this type of variation has not been explicitly examined in most GWAS until now
• Alternatively, common environmental variation can be explicitly accounted for by taking replicate measurements of flies of the same genotype emerging from different vials, and at different times.
• Although neither prediction has yet been explicitly demonstrated in crops, patterns of residual heterozygosity in the maize genome support the first prediction14, and evidence from humans128 bears out the
  second.
• Like GC, this approach does not explicitly model the population structure and is com- putationally fast, but it is much more flexible than GC because epistatic and covariate effects can be included in the regression model.
• Alternatively, a mixed-model approach that involves estimated kinship, with or without an explicit subpopulation effect, has recently been found to outperform GC in many settings
• Alternative approaches can be based on the estimated haplotype proportions among cases and controls, without an explicit haplotype assignment for individuals
• a Bayesian analysis requires explicit assumptions about effect sizes at truly associated SNPs.
• Indeed, some frequentist approaches to controlling the FDR, which are popular in microarray analyses, do not involve explicit consideration of the number of tests but do involve treating π as a parameter to be estimated41
• The posterior probability of association depends on modelling assumptions that should be made explicit in a careful analysis.
• no field experiment can investigate all of the factors that are important for adaptation, but the hope is that by conducting empirical studies in nature, the single or few factors that are explicitly manipulated and tested will be subject to all of the interactions that occur under natural conditions.
  
  • factors be subjected to all of the interactions

engage 从事，吸引 attract

• Once molecular markers are cost-effective and applica- ble in plant breeding, it is often straightforward to engage plant breeders to apply them in breeding programs.
• The Bayesian approach is well suited to the needs of a scientist engaged in the disinterested无私的 pursuit of knowledge, but its greater flexibility can make it more difficult for referees and edi- tors to perform a gatekeeper role in maintaining high publication standards.
• This recently funded proposal will engage community members over the next 5 yr in activities to capitalize upon the excellence in Arabidopsis research and facilitate new training directions for the next generation of diverse Arabidopsis research scientists.

en.dure 持续的

• Competition for canopy space is a fundamental structuring feature of forest ecosystems and remains an enduring focus of research attention.
• Thanks to acclimation, trees overcome envi- ronmental changes and endure for centuries.
• I sincerely thank my partner Warwick for his enduring love, ongoing support and encouragement, for listening, and for tolerating my crazy hours, odd work practices, and periodic absences.
• Shortleaf pine grows more slowly but endures competition longer than loblolly pine (Lawson 1990).
• My deepest gratitude, however, is due to the Thai branch of my family for their enduring support in hard times.
• In plant and animal breeding, the recipient parent is usually an enduring variety or inbred line/strain that has thrived for decades despite the introduction of new varieties in the field.
• Most tree species are genetically diverse and much of the variation in genetically-controlled traits is associated with evolu- tionary adaptation of populations to their enduring local growth conditions.
• An enduring goal of evolutionary biology is to understand the forces that govern how populations and species evolve.
• However, given the enduring appeal of h2 as a summary statistic, perhaps the most important point to note is that the values of h2 need to be interpreted in the context not just of the biological system (trait and population) in which they were estimated, but also in the context of the model used to determine them.
• The reason for this number is that the whole genome has endured three duplications.
• However, the effec- tive number of traits may easily exceed the upper limit of endurable genetic load.
• Selection criteria are endurance of summer drought, stem quality and wood density

(dis)entangle 〔用绳、网等〕缠住，套住；使卷入；使陷入

• How can we get accurate information about social issues, collected consistently over time, and yet not entangle the government with sex, reli- gion, and other touchy subjects?
• This is an effect of predicting the values of individuals, which have only one observation each, such that the genetic value of the individual is entangled with the residual effect of that observation.
• In contrast, the implemented genomic pairwise realized relationship models allowed the disentanglement of additive from all nonadditive factors through genetic variance decomposition.
• We show that the use of genome-wide SNP information can disentangle confounding factors to estimate genetic variances by separating genetic and non-genetic effects.
• Trees are often found in large populations that are connected by extensive gene flow, an ideal context for disentangling selective from stochastic evolutionary forces.
• The interrelationship between parent material, topographic position, and pine remnants is complex, and cannot be easily disentangled.
• Disentangling the contributions of shared environment and genetic dominance effects requires additional data from, for example, twins reared apart, half- sibs, or non-biological relatives reared together.
• Further research is needed to disentangle the biological role of rapid gene evolution from statistical artifacts of small sequence lengths
• Specifically, we high- light how these three spatial approaches can provide new insights about landscape spatial pattern and to what degree these methods can disentangle the patterns due to species response to a spatially structured en- vironment and those due to ecological spatial process- es.

enhance (improve)

• For trials with enhanced designs (RIB or RRC) there was usually an improvement in LogL for all trait types from the simplified design (RCB) model to the design model (using all within-replicate design features)

• In particular, we clarify the role of the sample variogram and present a range of enhanced graphical diagnostics to aid the spatial modeling process.

  • the role of - sample variogram - a range of - graphical diagnostics - aid - spatial modeling process

• Second, functional mapping is based on parsimonious modeling of mean-covariance structures, which enhances the statistical power of QTL detection.

  • functional mapping - parsimonious modeling 简约建模 - statistical power

• This approach, embedded within a mixture likelihood framework, leads to enhanced accuracy, precision, and flexibility of functional mapping while preserving its biological relevance.

  • embedde within
  • flexibility - preserving -biological relevance

• Results promise 预示 to enhance a fundamental understanding of evolutionary changes of tree architecture under domestication and to design sound silvicultural and breeding measures for improving plant productivity.

  • promise, allow, indicate - fundamental understanding - evolutionary changes - domestication

• Enhanced forest inventories and silvicultural practices are essential to produce high-quality wood and to meet the growing demand for wood products.

  • forest inventories - silvicultural practices - growing demand

• Genetic benefits can enhance the fitness of poly.andr.ous 多雄蕊的；一妻多夫的 females through the high intrinsic genetic quality of females’ mates or through the interaction between female and male genes.

  • genetic benefit - polyandrous - high intrinsic genetic quality

• DNA microarray analysis has emerged as a leading technology to enhance our understanding of gene regulation and function in cellular mechanism controls on a genomic scale.

  • dna microarray analysis - leading technoloty - gene regulation and function - on a genomic scale

• The integration of game theory into QTL mapping opens new opportunities to enhance the precision and resolution of QTL identification for complex phenotypes.

  • the integration of … into融入 - open new opportunities

• Management practices are reviewed including those implemented during the establishment phase (orchard size, design, number of parents and their representation) and those implemented for enhanced crop management (crown management, supplemental mass pollination 人工辅助授粉, bloom delay, selective seed harvesting and the production of designer crops).

• Careful marker annotation using a variety of references further enhances the utility of the integrated SSR map.

  • marker annotation - a variety of - the utility of

• Pinus taeda also is considered one of the major bioenergy feedstocks [4] and recently was selected as the first pine species for complete genome sequencing with the intent of using genome information to enhance its bioenergy potential

  • one of the major - bioenergy feedstocks 生物能源原料 - with the intent of 怀有… 的目的 - bioenergy potential

• We conclude that it is advantageous for prediction of single-cross hybrids to enhance a GCA- based model with SCA effects estimated from molec- ular marker data, if SCA variances are of similar or larger importance as GCA variances.

  • advantageous

• Marker selection will also be enhanced if pairs of tightly-linked markers flanking the QTL can be identified.

  • markers flanking the qtl

en.capsul.ate: to express or show something in a short way概括，压缩; to completely cover something with something else, especially in order to prevent a substance getting out封装，密封

• The prior encapsulates information about the values of a parameter before examining the data in the form of a probability distribution.
• We focus on aridity because it encapsulates water availability as a function of temperature and precipitation.
• At the same time, more research is needed to encapsulate the effect of historical population structure (e.g., IBD vs. IBS: Powell et al. 2010), type, number, and informativeness of markers and sample size.
• For example, leading principle coordinates of genome-wide methylation states may encapsulate unmeasured confounders, so if these are also correlated with phenotype, then it may be appropriate to include them as covariates in a regression analysis, as is common for GWAS analyses.
• Bayesian: A statistical school of thought that, in contrast to the frequentist school, holds that inferences about any unknown parameter or hypothesis should be encapsulated in a probability distribution, given the observed data.

emerge - appear or come out

• emerge
• has recently emerged as a vital area of public health
• It should be applicable for rapidly improving the output quality of seed orchards, especially when an emergency demand for improved seed is faced by the breeder.
• genetics has emerged as the central theme of biology.
• Since the mathematical parameters that define the emergent properties of the met- abolic system can be estimated and tested for different mQTL genotypes, the framework allows the dynamic pattern of genetic effects to be quantified on metabolic capacity and efficacy across a time-space scale.

exert 施加影响

• One QTL on chromosome 7 that may be expressed in both the embryo and endosperm exerted a pleiotropic effect on two different parameters of endoreduplication.
• This was not significantly different from –1, indicating that competition is almost exactly proportion- al to 成比例 the direct genetic effect and that a tree will exert a competitive effect which is closely related to its own genetic merit for size在size上与相关.
• We have successfully identified a quan- titative trait locus that exerts a significant maternal-offspring interac- tion effect on amino acid contents of the endosperm in maize
• Nonetheless, QTL PVE distributions for most individual studies and traits were similarly skewed to the right, indicating that the experimental setup exerted little influence over the allele effect size distri- bution
• These positive coeffi- cients can be interpreted as the intensity of competition (IC) that each neighbor exerts over the phenotype of the ith tree
• trees that are truly superior will exert their superiority over others due to an inherent higher growth rate and/or a stronger competitive advantage (Stoehr
• These polymorphisms exert widespread pleiotropic effects on phenotypes ranging from simple steady-state transcript abundance to complex behaviors.

equip- provide

• equip
  
  • ~ with a capacity /functionality/
• The new model is equipped with a capacity to characterize the genetic effects ofQTLs on seasonal alternation at different ages and then to better elucidate the genetic architecture of development.

exceed- to be more than a particular number or amount超过，超出

• exceed
  
  • ~ 90%/level /value
• Survival of both stock types was excellent, exceeding 90 percent after 10 years.
• However, polymorphism levels greatly exceeding that needed for markers can result in inefficiencies in identifying causal variants within QTL harboring a great many polymorphisms, as there may be too many candidates.
• Boldface denotes values for forwards selection exceeding those from backwards selection.
• the approach can be exceedingly inefficient极其
• we observed exceedingly large epistatic additive · additive genetic variance

endeavor v.attempt by employing effort; n.a purposeful or industrious undertaking 努力尽力渴望勤奋

• Methods to incorporate social association information into quantitative genetic analysis are currently an area of much endeavor (seeWalsh and Lynch 2009).
  
  • incorporate information into analysis
• The magnitude of prediction accuracies found is encouraging, suggesting that genomic prediction in rye is a worthwhile endeavor.
  
  • magnitude of accuracy - a worthwhile endeavor
• Obviously, the completion of a single breeding–testing–selection cycle is a protracted拖延的 延长的 持久 endeavor due to several uncontrollable biological factors; namely, the time needed for reaching sexual maturity for structured pedigree production and reproductive phenology and fertility variation that hinder the mating design completion
  
  • uncontrollable biological factors - structured pedigree production - protract
• Increasing productivity while growing crops in increasingly stressful environments is a challenging endeavor.
• Their support in this endeavor is gratefully acknowledge
  
  • Forest tree breeding is a long-term endeavor often adopting the recurrent selection scheme [1] where hundreds of parents are rigorously tested through the performance of several thousands of their offspring planted over vast geographic territories known as breeding zones
  • geographic territories - breeding zones

embed- put something firmly and deeply into something else

• The MER gene appears to be embedded in such a cluster, making it difficult to identify the particular resistance gene of interest from among the many closely linked candidates

  • appear to be - making it difficult - resistance gene - among the many closely linked candidates

• Second, given that phenotypic data are observed in a longitudinal time series, a step of embedding the multiple re- sponse structure in a biologically meaningful way is essential.

  • in a longitudinal time series - in a biologically meaningful way

• Kernel regression and reproducing kernel Hilbert spaces regression procedures are embedded into standard mixed-effects linear models, retaining additive genetic effects under multivariate normality for operational reasons.

• Functional mapping that embeds the developmental mechanisms of complex traits shows great power to study the dynamic pattern of genetic effects triggered by individual quantitative trait loci (QTLs).

  • developmental mechanisms - great power - dynamic pattern - trigger

• All functions are embedded within the framework of a single, unified data object.

F

for a while

• In view of its complexity, it therefore seems likely that the black box will remain cloudy for a while, even though fed information on, inter alia, myriads of genetic markers, levels of gene expressions and trait phenotypes.
• American crayfish may be yet another example of a species that after an introduction and low numbers with accompanying low genetic variation fared well for a while.
• Finding a bad record somewhere in a huge plain-text BLAST file One really ugly problem that happens to me is that I’ll be parsing a huge blast file for a while, and the parser will bomb out with a ValueError.

fraught with充满

• Non- consumptive use value and non-use value of the forest therefore have appeared in the mainstream economic literature only recently, although attempts at assessment of these values are fraught with great uncertainty.
• It should be stated that wind-pollinated testing is fraught with assumptions that cannot be either tested or fulfilled, and often leads to inaccuracies in estimates of individual breeding values (Namkoong 1966).
• The whole area of gene symbols and aliasing can be fraught with confusion, and it is probably fair to say that this is one of the commonest sources of error in bioinformat- ics searches.
• In these situations the error rate concept may be fraught with definitional difficulties and is conveniently replaced by the dichotomy between zero and nonzero numbers of errors.
• . Unfortunately, the interpretation of such plots is fraught with difficulties, as the empirical covariances can be biased, correlated, and heteroscedast

furnish- supply or provide提供

• Currently, however, availability of whole-genome SNPs arrays has improved the accuracy of genomic studies and furnished knowledge of the current status of cattle
• The availability of geo-referenced data means that it is always possible technically to furnish some analysis using geostatistical methods genetic resources (Gibbs et al. 2009).

G

guarantee

• in order to guarantee a suffi- cient exclusion power (> 0.97) to exclude non-pollen parents of sampled seeds, paternity analysis requires loci markers with a high level of polymorphism in terms of number of alleles per locus (Ashley, 2010).

H

har.nessed –to control and use the natural force or power of something控制[利用]〔自然力等〕

• harness
  
  • ~ mutations /data /heterosis /genetic variation/gene /diversity
• We propose that harnessing mutations in the florigen pathway to customize plant architecture and flower production offers a broad toolkit to boost crop productivity.
  
  • customize - boost
• The expanded population genomics functions in Stacks will make it a useful tool to harness the newest generation of massively parallel genotyping data for ecological and evolutionary genetics.
  
  • expanded functions - make it a useful tool
• In agricultural settings, there are numerous examples in which heterosis has been harnessed to create more productive and more uniform products including livestock [7–11]
  
  • in agricultural settings 在农业环境 - numerous example - more productive
• The key question is how to harness the marked recent improvements in our knowledge of the genome sequence and its variation in populations,together with advances in genotyping technologies, to accelerate susceptibility-locus discovery at the lowest cost
  
  • the key question - marked improvements - at the lowest cost - accelerate discovery
• Harnessing the genetic variation contained in crop germplasm collections for mapping QTL through GWA has been found successfully conducted in several crop species, including barley
• The P transposable element has been harnessed as a transformation vector and modified for efficient inser- tional mutagenesis, analysis of tissue-specific expression patterns, general and targeted overexpression, and,most recently,homologous recombination

hinge on取决于 depends entirely on

• The success of reforestation hinges on, among other things, a continuous supply of high-quality seeds for growing the desired stock in nurseries or for direct sowing out in the field.
• Efforts to understand the links between evolutionary and ecological dynamics hinge on our ability to measure and understand how genes influence phenotypes, fitness and population dynam- ics.
  
  • phenotype - fitness - population dynamics
• Quantitative genetics provides a range of theoretical and empirical tools with which to achieve this when the relatedness between individuals within a population is known.
  
  • a range of 一些 a number of - theoretical and empirical tools - relatedness between individuals
• Although the amount of genomic data continues to increase, resolution of the debate may hinge on both the development of more sensitive models to estimate selection and demography jointly and the development of experimental studies to provide functional validation for the genomic extent of selection
  
  • So, the utility of QTL mapping for identifying human disease loci, as a functional genomics tool and for understanding evolutionary processes hinges on our ability to confirm the existence of QTL by an independent method that relies less on sophisticated statistical models,and to map QTL to the level of genetic loci40,41.

therein

herein

thereinafter

thereinto

I

in view of 鉴于

• It is not yet clear how the new genomic data will help, in view of the many genes identified for height, for example.
• The wide range in oleoresin yields among progeny groups and between trees within groups, the wide range in stem vol- -ume between trees within progeny groups, and the moder -ate range in wood specific gravity between trees is espe cially noteworthy in view of the high economic importance of these traits.
• In such a case, which, in view of the actual variability of every organism, and of the parts of related organisms, must be regarded as somewhat ideal, we are really only concerned with the question whether the actual variability in different members of the species concerned, does or does not reach as far as the critical point.
• For all purposes of this kind, however, in view of the actual relationships to be dis- cussed it is more useful to use a scale on which the ratio between the two frequencies increases in geometric progression.

invoke 调用

• Hamilton’s 1964 works on inclusive fitness,” Hamilton (1964) had pointed out, with a quotation, that Fisher had invoked the idea of inclusive fitness in The Genetical Theory, “Mimicry” (Chap. 8), to explain the evolution of distastefulness in insects.
• Some traits, such as litter size or lifespan, are clearly not normally distributed, but adequate transformations can be invoked or departures ignored. (c) The infinitesimal model Response to the first generation of selection can be predicted from the breeder’s equation Response

inter alia 除…外 也 还

• In view of its complexity, it therefore seems likely that the black box will remain cloudy for a while, even though fed information on, inter alia, myriads of genetic markers, levels of gene expressions and trait phenotypes.
• Since they are compared inter alia, multiplication by 2 is not necessary.
• Such a series of well-planned field trials would enable estimates of costs and of various popUlation parameters to be made, estimates which are required inter alia for developing appropriate breeding and propagation strategies.
• Relatively strong correlations have been reported between juvenile and mature wood properties inter alia for density in spruce (Blouin et al. 1994); nevertheless, a detailed determination of wood properties and their variation with cambial age remains crucial for the estimation of genetic parameters.
• Modern information systems can capture large volumes of environmental information such as, inter alia, temperature, radiation, soil fertility, or moisture, thus coinciding with the developmental phases of a crop.
• The concept of biological diversity is defined in Article 2 of the CBD as follows: `Biological diversity’ means the variability among living organisms from all sources including, inter alia, terrestrial, marine and other aquatic ecosystems and the ecological complexes of which they are part; this includes diversity within species, between species and of ecosystems.
• The speed of subsequent symptom development down the branch and into the rest of the tree will depend, inter alia, on the species of host and pathogen involved.
• This chapter deals with the 1-way classification more generally, introducing inter alia many topics concerning variance components that re-occur in subsequent chapters in more complicated situations and with more detail than is needed here.
• The three Scots pine international provenance trials initiated by IUFRO are described by Giertych (1991) and Giertych and Oleksyn (1992) inter alia.
• The situation on the southern distribution limit is considered inter alia by Sabat

identification 确定 发现 鉴定

• simplifies the identification of superior single crosses 鉴定
• the identification of a high-yielding heterotic pattern 确定

increasingly

• increasingly
  
  • ~ used to /applied to /become /developed /available /affordable /well documented /greater portion /more productive /considered vital /important /powerful /recognized /impact/common /attractive /popular
• Haplotype analysis has been increasingly used to study the genetic basis of human dis- eases, but models for characterizing genetic interactions between haplotypes from dif- ferent chromosomal regions have not been well developed in the current literature.
• Although covariance structure analysis is used increasingly to analyze nonex- perimental data, important statistical requirements for its proper use are fre- quently ignored.
• Simple-sequence repeats (SSRs) have increasingly become the marker of choice for population genetic analyses.
• Genetic linkage maps have been increasingly developed for a wide variety of plants, using segregating populations such as F2s or backcrosses between inbred lines.
• With the recent advent of high-throughput genotyping techniques, genetic data for genome-wide association studies (GWAS) have become increasingly available
• Genomic selection is increasingly considered vital to accelerate genetic improvement.
• Nonetheless, as large- scale genotyping becomes increasingly affordable, the genome-wide approach association mapping will likely be the preferred method as it does not suffer from the candidate gene selection constraints.
• Although the ecological consequences of climate change are increasingly well documented, the effects of climate on the key evolutionary process driving adaptation— natural selection—are largely unknown.
• It can be anticipated that over the next decade the genetic basis of complex trait variation will be gradually uncovered in loblolly pine and other conifers, explain- ing an increasingly greater portion of the phenotypic variance.

irrespective of - regardless 不考虑without being affected or influenced by something

• These processes are complex and still poorly understood — irrespective of which marker is studied.
• The qualitative type of climate– phenology correlation (positive or negative) may remain consistent, irrespective of when in the year climatic change occurs.
• The PPA can be interpreted directly as a probability,
  irrespective of power, sample size or how many other SNPs were tested.
• For each facial feature we show the results that achieved strongest statistical significance **regardless of **the type of variable analysed
• The definition of imperfection was strictly observed regardless of the size of the repeat and implied that a 12- base microsatellite might also include up to one mismatch.
• Mapping strat- egies cannot uncover loci that are responsible for phenotypes that have not been measured, regardless of the evolutionary importance of the phenotypes, and the view that domestication involves few loci51is prob-ably a result of this limitation.
• Regardless of imprinting, only one system of genes has been discov- ered so far that has an important role in growth of the fetus as a whole.
• The general tests (Pearson 2 df and Fisher) have reason- able power regardless of the underlying risks, but if the genotype risks are additive they will not be as powerful as tests that are tailored to this scenario.

integrate （使）合并，（使）结合〔从而变得更有效〕

• Here, we address this problem by developing a statistical model that integrates the principle of shape analysis into a mixture-model-based likelihood formulated for QTL mapping.

  • address this problem 解决这个问题

• The model is founded on functional mapping, a statistical framework to map developmental dynamics, which is reformed to integrate a seasonally adjusted growth function.

  • founded on - statistical framework - developmental dynamics - be reformed to

• We integrated a complementary database comprising 25 years of legacy phenotypic data 遗留数据 on these strains.

  • legacy data on

• Here we describe how functional mapping and studies of plant ontology can be integrated so as to elucidate the expression mechanisms of QTLs that control plant growth, morphology, development, and adaptation to changing environments.

  • so as to 以便 - adaptation to changing environments

• We integrate the Markov chain properties of dynamic data into the model to facilitate the estimation of parameters that define virus dynamics.

  • parameters define virus dynamics

• More recently, a new mapping strategy has been designed to integrate the advantages of linkage analysis and linkage disequilibrium analysis for genome mapping in outcrossing populations.

  • more recently - strategy be designed

im.plic.ate vt. 使卷入；涉及；暗指；影响

• As the consequence of complex interactions between different parts of an organ, shape can be used as a predictor of structural–functional relationships implicated in changing environments.

  • as the consequence of - complex interactions - can be used as

• Notable among these was the QTL for five wax esters, which co-located with a gene from the KCS family, previously implicated in the biosynthesis of cuticular waxes in Arabidopsis.

  • a gene inplicated in biosynthesis/variation …

• The putative eucalypt homologs of well characterized genes implicated in variation in cuticular wax compounds in Arabidopsis were also mapped in this study.

  • putative 推定的，假定的, 公认的，被普遍认可的

• Increasing evidence suggests that specific genes are implicated in heterochrony [胚] 异时性, guiding the process of developmental divergence, but no quantitative models have been instrumented to map such heterochrony genes.

  • heterochrony - increasing evidence - developmental/evolutionary divergence - models have been instrumented to …

• One question that naturally arises from these evolutionary divergences is what mechanisms are implicated for heterochrony and the change of biological clock.

  • divergences - question that naturally arises from …

• The most interesting genes from the perspective of understanding the relationship between natural genotypic and phenotypic variation are those that are implicated using both quantitative and population genetic approaches.

J

K

L

lacuna gap

• I will address some of the background and some of these questions in this personal perspective, which is inevitably uneven in coverage and references, and reflects my interests, biases, knowledge and lacunae.
• This lacuna of understanding is also present in pedigree-based calculations of IBD coefficients, which, despite over a hundred years of use, can only be calculated from truncated pedigrees.
• Conclusions Although patterns in forest plant diversity at large spatial scales are now well described, there are still substantial lacunae in the record that can only be resolved by additional botanical exploration.

lever.age 充分利用〔资源、观点等〕

• For overcoming that barrier, we proposed an idea to leverage a seed orchard system, which has been used commonly in conifers, because some degree of LD exists in progenies derived from the limited number of elite trees in a seed orchard.
• For spatial effects, we outline two approaches for circumventing the prohibitively expensive matrix decompositions: the first leverages analytical results from Ornstein–Uhlenbeck processes that yield computationally efficient tridiagonal structures, whereas the second derives a modified predictive process model from the original model by projecting its realizations to a lower-dimensional subspace, thereby reducing the computational burden.
• However, to better leverage the vast number of discoveries made in the last couple of decades, we constructed a second “expanded allele panel” (EAP) that included all disease- associated variants in HGMD classified as disease causing, “DM”, and with overall minor allele frequency (MAF) < 0.5% according to the 1000 Genomes and ESP databases, for those genes contained within the gene panel defined above.
• it is entirely appropriate to leverage ancestry information to the fullest extent possible, and this inflation is not a pitfall (because discovery, validation and target samples are similarly stratified)
• As a result, breeders are looking for ways to leverage genotypic information, which is relatively fast, cheap, and easy to generate, to inform them about the phenotypic potential of their materials.
• Once devel- opment stages are known, agronomy and plant physiology knowledge can be leveraged to define stress covariates by stage.
• A wide variety of assays were leveraged in these different studies to score DNA variants, from genotyping of comprehensive SNP panels capturing all com- mon small-nucleotide variation in the genome, to whole exome and genome sequencing
• Our study therefore informs future study design in ALS genetics, promoting the combina- tion of larger sample sizes, full genome coverage and targeted genome editing experiments, leveraged together to fine-map new loci, identify rare causal variants and thereby elucidate the biology of ALS.
• The benefits of such a model are hopefully clear for small breeding programs, which, with their limited resources would benefit from an enhanced ability to leverage data from programs beyond their own.
• One possibility is a large multibreed reference population, which would leverage the fact that the extent of linkage disequilibrium is less between than within breeds
• Our experimental de- sign leveraged a unique feature of the conifer life cycle and new computational approaches to reduce the assem- bly problem to a tractable scale [9,11].
• First, it should leverage the large numbers of SNPs deposited in public data- bases by TSC.
• To take advantage of the sustainably managed forests that already exist in Canada, producers need to continue to promote the sustainable forest brand and to leverage their established environmental records (Lazar

lie in 在于

• Through examples we show that the framework can be furnished with general statistical packages whose great advantage lies in simplicity and flexibility to study both genetic and environmental effects.
• The merit of functional mapping lies in its biological relevance to study the tempo-spatial pattern of change for the trait and further predict the physiological or pathological status of trait phenotype.
• The complexity of biology lies in the fact that no bio-
  logical trait is isolated, rather every trait is affected by other traits through genes and environmental factors.

lend … to 有助于（facilitate），适用于，给予

• It provides first-hand results and lends confidence to long-term population management decisions
• Experimental inbred populations will provide timely, first-hand knowledge and lend confidence to decision-making in large operational programs.
• This lends empirical support to the hypothesis that the small scale spatial variation may be partially a result of cultural and agronomic practices which have been used in this field for many years.
• Although these results do not rule out the possibility put forth by Price & Schluter, they suggest that selection on traits closely associated with fitness will tend to change the relative contribution of additive and dominance variance in the genetic architecture of traits, and therefore lend support to Fisher’s theory.
• The empirical date from the Pioneer breeding program as shown in the Era experiments also lends support to the actions of the breeders in the 1950s.
• This approach has limitations; for example, it does not lend itself easily to the notion of averaging over particular factors in the model to form predictions.
• It lends itself well to reforestation and sylviculture for timber production.
• It could, however, be argued that such approaches, although useful and commercially advantageous, are technical fixes that do not easily lend themselves to scientific enquiry
• Moreover, a steep, highly dissected landscape lends itself to small-scale events because fi res are not perpetuated in topographically complex areas.
• While this expression is useful, h2a does not lend itself to the computation of a response to selection by standard equations, because breeding values in a population will be correlated and heteroscedastic due to the pedigree.

M

moot

a moot point/question 争论未决的论点/问题
be mooted 被提出供考虑
- Again some caution is required: physiological predictors of performance, e.g. use of hormone levels, have been much mooted but produced little of practical benefit in livestock improvement.
- Whether this can be brought about by natural selection alone is a moot question.
- In some cases, this decision is moot because only one propagule type is available.
- Whether such complexes retain their adaptive advantage in an agricultural environment is, however, a moot point (Lawrence, Marshall and Davies, 1995a).
- In this sense, learning the material in the rest of this textbook is to some extent a moot point unless one understands the issues in this chapter.
- This renders the results for the A and B main effects moot.

myrid 大量 无数的 a myrid of

• In view of its complexity, it therefore seems likely that the black box will remain cloudy for a while, even though fed information on, inter alia, myriads of genetic markers, levels of gene expressions and trait phenotypes.
• From the myriad of candidate genes that were identified for the individual resistance traits (Table S4; Figure 4), our study also identified an array of single genes that were associated with both resistance and growth phenotype (Table S6 and Table S4).
• An enlightened implementation of the ESA therefore requires that more explicit concern be devoted to the viability of entire ecosystems, whereby not only keystone endangered species but also their myriad ecological associates would simultaneously benefit.
• Population viability analysis is used to assess the combined impacts of all these factors on extinction risk, and to evaluate alternative management options to recover species `It’s a hard world out there’: stylized scenario of the myriad risks faced by species in natural habitats.
• Zooplankton gorge on these small plants and themselves are eaten by myriad coastal fish and invertebrates.
• Modern uses of biodiversity involve the many varieties of plants, animals, and microorganisms now being used worldwide for farming and myriad other human activities.
• Genetic collections are being lost worldwide from myriad causes, including insufficient funding and infrastructure support, a deficit of trained taxonomists and curators, natural disasters, accidents, wars and civil strife, and vandalism.
• A second factor sparking increasing interest in the conservation of farmland biodiversity is that a myriad of species declines has been documented in farmland in a wide range of nations (Attwood, et al., 2009; Brown et al., 2008; Conrad et al., 2006; Kleijn et al., 2009; Murphy, 2003).

N

not least, especially notably

• The models and summary quantities defined by Fisher and Wright have remained at the heart of the subject not least because they provide ways to make predictions of quantities such as the response to artificial and natural selection.
• We can be optimistic about the prospects for future improvement, not least because the input of molecular and high-throughput technologies to livestock improvement has so far been tiny.
• Infectious disease has had large effects on feral populations when a disease to which there is no resistance has been introduced, not least in our own species.
• Undoubtedly, the progress in sequencing technologies, availability of reference genome in major crops, rapid evolution in high-throughput polymorphism detection platforms and bioinformatics tools and last, but not least, the development of accurate phenotypic data collection methodology will increase the precision of QTL mapping in major and orphan crops bringing us closer to the discovery of the Holy Grail of molecular geneticists, causative mutations, that will be subsequently translated into robust diagnostic tools to implement marker-assisted selection.

O

outwith

• Statistical methods were invented by Fisher (1918) and Wright (1921), the analysis of variance and path coefficients, respectively, to partition the variation and describe the resemblance between relatives, and such tools and methods developed in quantitative genetics have had widespread application in disciplines way outwith their original targets.
• There have been some advances in parentage analysis outwith and since the Jones & Ardren (2003) review of parentage inference methods.
• Resistance can potentially be improved by altering the intensity of the land use adjacent to the forest or by planting different vegetation between wooded patches, but often such intervention is outwith the scope of a forest manager.
• Traceability of former seed transfer between regions within Spain is unrealistic, so both successful and unsuccessful plantations outwith the natural range are difficult to trace in terms of seed origin.

out of

• Out of the 155 detected alleles, 115 (73.2%) alleles were common to both B and R lines, 11 alleles at 9 loci were unique to B lines, while 29 alleles at 14 lociwere unique in R lines.
• Dutkowski et al. (2002) found that the variograms in two out of five trials were not stationary, implying that large-scale covariance was still present in the spatial errors.
• According to Michael and Van Buren [45], over 100 plants genomes have been sequenced since 2000, out of which 63% are genomes from various crop species.

outperform

• There is evidence that specific hybrid families are produced that outperform most of the pure species families for one or other of the traits examined; however, there is no reliable quantitative genetic method of predicting which parents should be used.
• Most hybrids outperformed the parental lines for fruit yield, earliness and plant height.
• Yield stability of hybrids is expected to outperform that of inbred lines because of general vigor and fitness advan- tages.
• We find that EMMAX outperforms both principal component analysis and genomic control in correcting for sample structure.
• Simulations suggest that our method outperforms existing methods in terms of power as well as false discovery rate.

P

pre.mis.e 前提

• On the premise that many genes and the environment act and interact to determine the trait, founders recognized that it would be difficult if not impossible to determine the action of individual trait genes.
• Under this general premise, even the previous models of asynchrony of sexual maturity (section 7.1) and individual self-mating (chapter 5) can be conceived of as special cases of the present concept of mating predisposition.
• The premise behind these models is that environmental conditions are the primary determinant of realized species niches, and that the future preferred range distribution of species can be predicted by transferring the environmental parameters associated with the present distribution onto maps representing future climate scenarios (Pearson and Dawson 2003).
• One premise of GBS applications is the development of genome-wide molecular markers with high density and low cost (Heffner et al., 2009, 2010; Jannink et al., 2010).

project 预计

• it is projected that the barriers to economically feasible hybrid wheat production can be overcome in the next 10–15 years

pinpoint -to discover or explain exactly the real facts about something or the cause of a problem查明，准确地说出，描述〔事实真相〕

• ~ loci/gene/qtl /location /region /area /mutation /
• This advantage eliminates the need to initially pinpoint the key factor that determines a specific characteristic.
• However, the fact that NIRS can readily pinpoint individuals within a population targeted for an improvement programme could be an especially useful tool for tree breeders.
• Additionally, the availability of genomic data has made it possible to pinpoint loci with large effects contributing to inbreeding depression in wild populations, although this will continue to be a challenging task in many study systems due to low statistical power.
• Identifying candidate deleterious alleles could increase the power of mapping analyses Identifying non-synonymous mutations with predicted deleterious effects could advance our ability to pinpoint mutations causing inbreeding depression.
• Genomic data could potentially be combined with analysis of founder-specific pedigree inbreeding to pinpoint chromosomal regions and haplotypes harboring deleterious recessive alleles with large effects.
• In particular, we pinpoint the limitation of the results obtained by inappropriate linkage analysis models, making the conclusions more precise and appealing for biological interpretations.
• An understandingof the changein geneticand environmental varianceswith advancingstandagemay facilitate the developmentof a model that couldbe used to predictthe resultsof early selectionand pinpoint the optimum age for selection.
• By combining heterozygous mutations, we **pinpoint**ed an optimal balance of flowering signals, resulting in a new partially determinate architecture that translated to maximum yields.

pertain relate 有关的

• On the basis of an ultrahigh-density SNP bin map con- structed with population sequencing,we calculated single-locus and epistatic genetic effects in the whole genome and identified compo- nents pertaining to heterosis of the hybrid.
• Spatially and temporally replicated studies of selection in aquatic environments are also uncommon (Table 1), so our results pertain mainly to ter-restrial systems.
• The second data set pertains to international maize (Zea mays L.) trials in which two dis- ease traits of maize lines evaluated in five environments were measured.
• All information pertaining to the conserved ortholog set (COS) markers is available online, including gene annotation, contig membership, and positional coordinates against the Arabi- dopsis tiling path
• The variance of relative ranks pertains to an indicator of stability performance over all trials, with a higher variance value suggesting lower stability.

promise许诺；有指望，有前途

• Molecular technologies are bridging the gap between genotyping and genome typing,which promises to help unlock the secrets of adaptive evolution and to refine inferences about population history.
• In addition, the promise of NIRS technique for food quality evaluation is demonstrated, and some prob- lems which need to be solved or investigated further are also discussed.
• Thus, improving cold hardiness by within-family selection appears to hold much promise.
• These directions promise to sustain research aimed at addressing emerging challenges in forestry and produce applied output**s to **preserve, enhance and responsibly use world forests.
• Estimates showed that selection concentrated on a few easily measurable traits such as wood density and core length holds promise to obtain superior genetic gains for mechanical properties, but negative impacts would be expected on fibre anatomy traits related to pulp quality.

proli.fer.ation - a sudden increase in the amount or number of something激增

• The strategy incorporates a high-dimensional group of differential equations that characterizes the proliferation, differentiation, and reprogramming of cancer SC in a dynamic cellular and molecular system.
• Expansion of gene families reported to be involved in fruit development may explain formation of the pome, a Pyreae-specific false fruit that develops by proliferation of the basal part of the sepals, the receptacle.
• In fact, despite the proliferation of QTL mapping works in recent years, a number of constraints have determined severe limitations on an efficient utilization of QTL mapping informa- tion in plant breeding through MAS.

paved the way

• The first successes in sequencing rice and, subsequent-ly, the first large and complex crop genomes have paved the way for sequencing other important crops.
• Impressive progress in next-generation se- quencing (NGS) technologies has paved the way for the detection and exploitation of genetic variation in a given DNA or RNA molecule
• the formal introduction of the closed test principle by Marcus et al. (1976) paved the way for stepwise rejective multiple tests

pre.serve

• to save something or someone from being harmed or destroyed维护，保护，保存〔使免受破坏〕

• to make something continue without changing保持，维持

  • Similarly, a gene resource population is defined either in the form of natural stands or clonal archives, but its main purpose is preserving the existing genetic legacy, i.e., gene conservation, rather than being considered for a given improvement pro- gramme

• gene resoure population - be defined in the form of - natural stands - clonal archives - genetic legacy

  • This approach, embedded within a mixture likelihood framework, leads to enhanced accuracy, precision, and flexibility of functional mapping while preserving its biological relevance.
• embeded with - leads to - enhanced accuracy, precision and flexibility

• biological relevance 生物相关性

  • Our study demonstrates that a clear breeding strategy that preserves genetic diversity results in more long-term genetic gain.
• result in

play a pivotal role in

• The response of subsoil OC to warming and labile carbon addition can be different from that of topsoil (Fierer et al., 2003a; Wild et al., 2014) and will be pivotal in predicting the change of SOC storage under climate warming.
  
  • the response of - can be different from that of - be pivotal in
• No genes from the four families above were down-regulated, indicating that these gene families may play a pivotal role in the early stage of infection
  
  • down regulated - in the early stage of infection
• Cuticular waxes, along with cutin (the structurally important class of compounds in the cuticle) are embedded in the matrix of the cuticle and play a pivotal role in cell-to-cell interactions (Buschhaus
  
  • along with - cell-to-cell interaction
• Gene regulatory networks play a pivotal role in every process of drug response, including cell differentiation, cell cycle, metabolism, and signal transduction
  
  • gene regulatory networks - process of drug response - cell differentiation - metabolism - signal transduction
• Caused by epigenetic modifications such as DNA methylation established during gametogenesis and maintained throughout somatic development in the offspring, genetic imprinting has been shown to play a pivotal role in regulating the formation, development, function, and evolution of complex traits and diseases .
  
  • epigenetic modifications - methylation
• The ability of SNPs to be mapped to the same position as fragment-based markers previously developed within the same candidate genes, as well as the pivotal role that SNPs currently play in the dissection of complex phenotypic traits, illustrate the usefulness of high-throughput SNP genotyping technologies to the continued development of pine genomics.
  
  • the ability of - the dissection of complex phenotypic traits - usefulness
• Genetic interactions or epistasis have been thought to play a pivotal role in shaping the formation, development and evolution of life.
  
  • genetic interaction - epistasis - have been thought to - shaping the formation - development and evolution
• Such a phenomenon, also called the parent-of-origin effect, has been recognized to play a pivotal role in embryological development and pathogenesis in many species.
  
  • embryological development - pathogenesis

permit- to allow something to happen, especially by an official decision, rule, or law。permit和allow能通用但前者不能和adv连用；前者更正式，后者一般对人

• The pedigree reconstruction permitted the identification of selfed individuals, thus allowing evaluating the impact of selfing on marker-based genetic parameter estimation.
• The availability of the pedigree in the studied population permitted parsing 剖分 the selfs from both the HS and FS families and allowed the creation of two additional relationship classes
  
  • the availablility of
• This procedure permits computationally demanding genetic evaluations of complex pedigrees.
  
  • computationally demanding - genetic evaluation
• This feature permits rapid inference for both the polygenic model and the genomic relationship model.

persist 坚持/继续/存在

• persist
  
  • variation/accuracy /heritance /maternal effects /spatial heterogeneity /qtl linked phase /polymorphism ~
• Clearly, long microsatellite alleles do not persist indefinitely.
• Nonetheless, high levels of genetic variation persist within populations.
• In contrast with pedigree analyses, which involve detecting co-inheritance (i.e., linkage) between QTL and genetic markers over a few gen- erations, association studies involve detecting co-inheritance that has persisted over many generations
  
  • pedigree analyses
• Because these marker–QTL linkages are tight, recombination does not cause them to decay rapidly, and accuracies from BayesB persist longer than those from ridge regression

propose 建议 理论 In everyday English, people usually say that someone puts forward plans, ideas etc, rather than proposes them. 在日常英语中,表示某人提出计划、想法等,人们一般说 put forward ,而不说 propose

• propose
  
  • ~ a joint modeling framework
  • ~ a algorithm /model /approach /method /test /design /procedure /methodology/definition /technique /system /way /extension /scheme /strategy
  • ~ distribution/value /density
  • ~ joint analysis
  • propose to 或直接跟从句
• We propose that the ideal predictor is the expectation of the phenotype conditional on the SNP genotypes. That
• we propose a joint modeling framework for functional mapping of specific quantitative trait loci (QTLs) which controls developmental processes and the timing of development and their causal correlation over time.
  
  • developmental processes - causal correlation
• A Bayesian algorithm for functional mapping has been proposed recently by
  
  • bayesian algorithm
• A linear random effects model and EM estimation approach are proposed by
  
  • EM estimation approach
• Here I propose a general definition of the heritable variation that determines the potential of a population to respond to selection.
  
  • a general definition - heritable variation - the potential of a population to respond to selection
• Here we propose an extension to genomic selection, optimal haploid value (OHV) selection, which predicts the best doubled haploid that can be produced from a segregating plant.
• We argue that the classical definition of unbiasedness is not useful in this context and propose to use a different definition of unbiasedness that is a property of the estimator we advocate.

put forward v. 提出；拿出；放出；推举出

• ~ ideas/approach /plans /argument

• Ever since R. A. Fisher put forward his ideas in the 1920s, statisticians have recognized such randomized multifactorial perturbation as the ideal experimental design for uncovering causation.

  • ever since - statisticians - recognized - ideal experimental design - uncovering causation

• The decomposion approach was put forward and excecuted successfully in WinBUGS by Vines et al. (1996)

  • decomposion approach - excecuted

• Another argument put forward for the use of long-term regional means is that only “repeatable” or static interaction can be exploited for variety recommendations.

put forth 提出

• ~model/research /hypothesis/ proposal
• Similar theoretical models for de- velopmental genetic studies were also put forth using random regression theory
• these results do not rule out the possibility put forth by Isik
• As a part of the considerable effort to re-introduce the American chestnut to its native range, a significant amount of research has been put forth to produce and propagate American chestnut trees with blight resistance.
• Weinberg (2000) put forth a popular model that breaks down cancer development and proliferation into six essential cellular capabilities, each of which requires genetic alterations.
• Models presented in Section III have been put forth as complements to definitions.
• One prominent hypothesis recently put forth involves the combined action of loop-extrusion ‘motors’ (probably cohesins)
• we will comment on some of the computational difficulties in working with these huge data sets and put forth some proposals for simple functionality for statistical software that would greatly improve the ease with which the masses of traffic data can be analysed.
• Supporters of the overdominance hypothesis put forth two main objections to the dominance hypothesis.

Q

R

recourse依赖

• In conclusion, when the sole objective is to establish the PF hypothesis, it is usually possible to find a suitable randomised design that also allows analysis without taking recourse to complex spatial modelling.
• Factorial experiments, where crosses are made among genotypes from two different heterotic pools, can be analysed similarly as diallels, without taking recourse to the coefficient of conancestry.
• We believe that often the use of the coefficient of coancestry can be motivated and justified heuristically without taking recourse to strong assumptions about the population genetic structure.
• These interactions can be social, as with higher organisms, or physical, due to competition for limited **recourse**s, such as space, light, or nutrients, as with plants and lower organisms.
• The major criticism of model-based approaches is that estimates of treatment effects and their standard errors rely solely on the chosen model, whereas the randomization-based analysis is validated by recourse to randomization theory.
• In such cases, although density dependence is still operating, there may be no recourse except direct field testing under different spacings.
• However, the only recourse we often have is to sample and maintain sufficiently large populations so that even those alleles that occur at low frequency would have high probability of being saved.
• However, because application of ML estimation typically requires recourse to asymptotic properties, some results based on the classical, first-order asymptotic theory are presented, to enhance understanding of this method of estimation.
• Animal model evaluations combine information from an animal and all relatives, but the algebra required to derive solutions can be explained easily without recourse to matrix algebra (VanRaden and Wiggans, 1991).

refer

• Genome wide selection refers to marker-based selection without first identifying a subset of markers with significant effects.

reside vi. 住，居住；属于

• In the v1.01 assembly, two of the pine lp3 genes (AAB07493, AAB96829) were found to reside on the same scaffold
• The effect was more pronounced for rare SNPs, which in general are harder to tag using a small number of surrogate SNPs and are better predicted by the extended haplotypes upon which the SNP mutation resides.
• However, because of the broader scope, their results reside on stronger assumptions and important factors affecting prediction accuracy are not accounted for.
• The more austral slash pine may have resided in only one of these refugia: south Florida - Caribbean
• Analyses typically show many linkages between the abundances of transcripts and the regions in the genomes where the structural genes for those transcripts reside.

re.fine improve; make sth. purer提升 精炼

• refine
  
  • ~ precision /method /approach /technique /relationship /gene
• The relationships could either be among relatives in families or among unrelated individuals in a general population with cryptic relatedness; both could be refined or derived with whole genome data.
  
  • cryptic (mysterious or not easily understood) relatedness
• Correlational selection can alter, destroy, refine or generate genetic correlations between suites of co-adapted traits
  
  • 改变破坏提高
• The ability to understand the genetic basis of biological phenomena requires the development and refinement of statistical approaches that identify associations between genetic markers and phenotypes.
  
  • Some further refinement is needed. 需要进一步的改进。
• Derivatives of the residual log-likelihood with respect to the four correlation-model parameters are derived, and the REML algorithm coded in Splus for testing and refinement as a precursor先驱 to its implementation into the software ASReml, with additional generality of linear mixed models. Suggestions are given regarding initial values for the estimation. A residual likelihood ratio test for anisotropy[物] 各向异性 is also developed and investigated.
• The most important technological breakthrough was the introduction of microsatellite markers to molecular ecology, an advance that was accompanied by a proliferation and refinement of statistical techniques for the analysis of parentage data.
  
  • the most important - technological breakthrough - the introduction of … in - accompanied by - proli.fer.ation –a sudden increase in the amount or number of something激增 - statistical technique
• Since then, the categorical allocation分配 approach has been updated and refined, resulting in a very useful technique for parentage assignment
• In the case of family structure or cryptic relatedness, dividing association statistics by λGC will generally produce the approximate null distribution, although a refinement to the method may be needed when there is uncertainty in the estimate of λGC
• When the environment in which the experiment is performed has two recognized gradients, such as soil moisture and soil composition, the Latin square design represents a more refined form of blocking that allows removing the influence of both gradients from the out-come of the experiment in assessing treatment effect
• Contigs with <10 clones had their clone order refined using our automa- ted contig ordering application,CORAL 完善克隆的顺序
• Positional precision is refined by the incorporation of bootstrap analysis (yellow bar) and SNP density analysis (brown). 改善
  
  • The unique properties of GRPs allow this multiscalar biological data to be harnessed for rapid refinement and identification of key polymorphic genes.

re.tain- to keep something or continue to have something保留，保有；继续拥有

• Based on the assessment of the SNP markers and several agromorphologic traits, accessions that retain gene diversity of the whole collection were selected to develop several soybean sets of different sizes using an heuristic approach

  • agromorphologic traits - accessions - an heuristic approach

• Therefore, it is still unclear why mutations frequently occur around the target locus and larger genomic region with three mutations has been retained by the artificial selection.

  • it is still unclear - genomic region - artificial selection

• Few genes would be expected to retain high sequence similarity for this time if they did not have essential functions.

  • would be - essential functions

• These three species were chosen because they have retained structurally similar genomes and clear patterns of paralogy among syntenic gene copies

• Unlike other angio.sperms, the Amborella genome lacks evidence for recent transposon insertions while retaining ancient and divergent transposons.

  • angiosperm - lacks evidence - transposons

represent- to speak officially for someone; to form or be something

• Seed orchards represent the link between tree breeding and silvicultural activities.

  • seed orchatd - silvicutural activities

• The actual genetic superiority of these selected trees is evaluated based on the performance of their offspring in progeny tests [14], which represent an essential component of all programmes and serve, among other purposes, to exclude low-ranking parents from both breeding and production populations.

• However, the vast majority of seed orchards are clonal and on average consist of 30–50 different parents, each of which is represented by one or more vegetatively propagated units/copies, termed ramets.

• Although the genetic quality of an indi- vidual is mostly related to the survival rate of its offspring (in other words, an individual is of higher genetic quality when it possesses a genotype that increases its fitness relative to that of an individual with a different genotype [44]), in forest tree breeding, this concept would not suffice as it only represents one of many aspects that need to be considered.

• Genotyping of the same markers in other populations can be achieved with further sequencing runs, accurately representing the new populations and avoiding bias towards the sequence of the markers in the originally surveyed population.

• The vast majority of these clones are entirely redundant, suggesting that they potentially represent a duplicated sequence within the genome or cloning bias resulting in the over-represen- tation of a small genomic region.

reconcile 调和 使和解 使和好

• Thus, the mechanisms proposed to explain the generation of complex gene families in pine must reconcile the dispersed nature 分散的性质 of these gene families with the apparent paradox that the order of genes along pine chromosomes may be well conserved.

  • the dispersed nature - the apparent para.dox - the order of genes along pine chromosomes

• Because every contamination event is outcrossing, both the observed high selfing (0.174 ± 0.025) and contamination (0.184 ± 0.027) estimates must be reconciled.

  • con.tamin.ation event

• The theoretical basis for the resemblance between relatives due to genetic factors was developed by R.A. Fisher in a now famous and classic paper that reconciled Mendelian and biometrical genetics 生统遗传学.

  • theoretical basis - the re.sembl.ance 长得像 - genetic factor - in a now famous and classic paper - bio.metrical genetics

• In this situation Bayesian and frequentist inference can be reconciled.

  • in this situation - bayesian and frequentist inference

• Given that many epiloci were mapped to the vicinity 附近 of a gene, these genes may be directly affected by these epiloci, but this becomes increasingly difficult to reconcile with increasing genomic distances.

  • the vicinity of a gene - directly affected - increasingly difficult - increasing genomic distances

recognized as 被认为是 某人被认作 被公认为 认识到

• Its role in shaping organism’s development has been unanimously 全体一致地 recognized.

• Genes that control circadian rhythms in organisms have been recognized, but have been difficult to detect because circadian behavior comprises periodically dynamic traits and is sensitive to environmental changes

• Models for the analysis of longitudinal data must recognize the relationship between serial observations on the same unit.

• The results indicate that Peruvian should be recognized as a heterotic group.

• It is widely recognized that the mixed linear model is an important tool for parameter estimation in the analysis of complex pedigrees, which includes both pedigree and genomic information, and where mutually dependent genetic factors are often assumed to follow multivariate normal distributions of high dimension.

• Genes have been widely recognized to be involved in human body growth, but their detailed controlling mechanisms are poorly understood.

  • detailed controlling mechanisms - poorly understood

• It has been recognized that these sex-dependent differences are controlled by an array of specific genetic factors, mediated through various environmental stimuli.

  • sex-dependent differences - specific genetic factors - environmental stimuli - an array of

rule out 排除 eliminate exclude

• This method uses the principle of exclusion to rule out sibling groups that have incompatible sibling genotypes.
• This is similar to the way exclusion is used to rule out genotypically incompatible parents in parentage assignment programs.
• However, although the majority of the paternities were resolved, we cannot completely rule out that there may be gene flow from outside the study stand.
• Thus, presence of quantitative treatment factors in a design does not rule out the need for multiple comparisons.
• Consequently, failure to detect a QTL near the location of a candidate gene in a particular cross does not necessarily rule out involvement of the gene in trait variation at the population level (Ishimaru et al. 2001).
• In the same manner, the failure to detect common QTLs for genetically correlated traits does not rule out the existence of shared regulatory genes but may only indicate that any such loci lack meaningful polymorphisms in the study families.
• Similar to other studies comparing association- mapping approaches based on empirical data (e.g.,Yuet al. 2006; Zhao et al. 2007), however, we cannot rule out the possibility that some markers might be linked to functional polymorphisms of the trait under consideration.

S

straightforward to直接 容易 爽快

• Furthermore, di.sting.uishing between demo.graphy and selection as causes of genetic di.verg.ence is not straightforward
• It is often straightforward to incorporate an HMM model into a MCMC framework48 (see also REF. 47), and so it is likely that Bayesian analyses for sequence data will become more wide- spread in future, built on the maximum-likelihood framework.
• It would be straightforward to similarly consider models cen- tred on dominance or recessivity, but this does not yet seem to have been implemented.
• Genomic relationship ker- nels that are “orthogonal” to each other could enhance prediction ability but such kernels are not straightforward to construct
• Integrating gene effects across scales of biological organization in such situations is not straightforward

summarize- make a short statement giving only the main information简短陈述主要信息；SUM UP

• Principal component analysis was used to summarize the variation observed among provenances into two principal components, which accounted for 79% of the total variation for all traits.
  
  • which指代two principal components
• we summarize current progress in empirical studies on the application of genomic selection for prediction of hybrid perfor- mance.
• The increasing success of the implementation of genomic selection to predict hybrid performance in plant breed- ing motivated us to summarize the recent theoretical and experi- mental progress in this area.
• Biplots summarized the GxE interaction successfully and confirmed the positive correlation between all environments for volume and survival.
• This paper does not attempt to review all methods but defers to Kempton (1984), who summarized the models succinctly by stating that ‘methods for describing patterns in VrE are the method of principal components, and of regression onto an independent environmental variable or onto the marginal means of the VrE table’
• we review the methods available for estimating quantitative genetic and selection parameters and discuss their merits and shortcomings, to provide a tool that summarizes the potential uses of molecular data to obtain such parameters in wild populations.
• The objectives of this article are to review essential aspects of GS and summarize the important take-home messages from recent theoretical, simulation and empirical studies.
• Here we summarize current trends and future prospects for utilizing NGS-based technolo- gies to develop crops with im- proved trait performance and in- crease the efficiency of modern plant breeding
• According to the shape of the exploratory semivariograms, several candidate spatial models were fitted to the collected yield data, as **summarized in Tables **3, 4 and 5.
• Table 2 summarizes the results from the TBS-based model and untransformed model.
• Based on the identification and quantification of competi-
  tion and environmental heterogeneity (summarized in Table 3) and theDIC values (Table 4), we retained only DBH at age 35 to conduct all the analyses in relation to the study of the impact of simultaneously adjusting for competition genetic effects and environmental heterogeneity on the variance components and selection decisions.

sub.jectd to - experience/control by /affect by

• subject to
  
  • ~ analysis /effort /regulation /
• Genes located in SNP deserts were subjected to functional annotation and GO enrichment analysis using GOEAST
• we note that of the SNPs that reached a P < 10^7 in ref. 11 and that have been subjected to replication efforts, all have been confirmed

sub.stitute- instead of

• DNA fingerprinting and pedigree reconstruction can substitute for artificial matings, by allowing parentage delineation of naturally produced offspring
• An alternative approach is to substitute a genomic relation-ship matrix (Van Raden 2007) for the classical pedigree-based one

suc.cinct - clearly expressed in a few words；CONCISE

• The randomization diagram in Fig. 1 succinctly summarizes the design and the appro-priate randomization.

suf.fice- to be enough

• Because heterosis is an environmentally modified quantitative phenotype, genomic analyses alone will not suffice.

  • environmentally modified - genomic analyses alone

• Because only a small proportion will have obvious functional consequences for the resultant protein, lesser evidence of association may suffice to implicate variants of this sort.

  • have obvious functional consequences - lesser evidence - suffice to - implicate

• In cases where a spatial component was needed, the one-dimensional version often suffice.

  • in case 在某种情况下

• Such lines become fully homozygous after many generations, so that it suffices to show only one haplotype.

• Blood and blood subtypes, for instance, are relevant for autoimmune diseases or blood-based cancers, and any tissue will suffice if the epigenetic variant is present soma-wide.

supersede substitute for; displace

• They have been **supersede**d by more sophisticated methods, often in the context of livestock data (Lynch & Walsh 1998; Sorensen & Gianola 2002), which have been further developed as computing power has increased.
• Although this technique is an important tool in breeding programs, it has been **supersede**d by microsatellite or simple sequence repeat (SSR) markers and is now rarely used.
• However, that function has now been **supersede**d by kin.blup and A.mat, the latter being a utility for estimating the additive relationship matrix (A) from markers.
• Although historically these systems have had wide ranging applications, their use is becoming increasingly restricted to particular scientific fields in which they are specifically warranted, while they are being **supersede**d by other methods in the areas in which they fail.

T

topple 推翻

• Quantitative genetic variation whether our statistical models of genetic variation in traits are so unrealistic that the edifice may topple .
• He did not offer further comment, but in an interview with The New York Times last week, he said the draft law that targeted aid groups was rooted in a pervasive belief inside Egypt’s ruling class that foreign money had played a role in fomenting the uprising that topple d President Hosni Mubarak in 2011.
• Two Muslim activists, Linda Sarsour and Tarek El-Messidi, asked Muslims to donate $20,000 in a crowdfunding effort to repair hundreds of Jewish headstones that were topple d near St. Louis last week.
• Though the activists do not have cost estimates yet, Mr. ElMessidi said on Monday that the money raised would most likely be enough to repair the graves near St. Louis and in Philadelphia, where about 100 headstones were topple d on Sunday.
• Windstorms will generally topple trees in the emergent or upper continuous canopy.

transcend 超过

• Toward a unified genetic map of higher plants, **transcend**ing the monocot-dicot divergence.
• Because DOM dynamics **transcend**s continents, oceans, and landscapes, its overall influence on the cycling and fate of nutrients, organic pesticides, and metal(loid)s in the hydrosphere and biosphere should be probed using multidisciplinary approach.
• In the long run, the identification of virtually all of the genes in the genome, an understanding of their function, and how those genes are regulated, should enable future advances in marker assisted selection strategies that could transcend and complement current breeding practices.

than

• In the presence of large effect QTL, BayesB did a better job of QTL detection and its genomic predictions were more accurate and persistent than those from GBLUP.

  • persistent continuing to exist or happen 持续 持久
  • those 指的是 its genomic predictions

• this means that the observed difference in phenotypes is larger than expected based on marker solutions

  • expected 后省略 difference in phenotypes

• BayesC is expected to result in smaller estimates of variance than BayesB

• attributed less than 1 % genetic variance

• which would account for less than 1 % of phenotypic variance

  • 少于1%

• The estimated effects of the 4_78 QTL were always smaller than obtained with training on all 7 generations, and were never larger for BayesC than for BayesB.

  • effects 小于或大于 smaller/larger

• On average, training in any one generation had accuracy of 0.43 for BayesB and 0.39 for BayesC, compared to less than 0.27 for the models that fitted all SNPs with an equal variance ratio.

  • compared to less than
  • for models 这里是for 不是in

• MOE and MOR of small clear specimens of mature wood were better predicted by density and velocity than by either variable alone

• they were substantially lower than the values for the same model for MOE

  • substantially
  • values lower than
  • 还是for the models

• The single-variable regression models indicated that velocity was a slightly better predictor than was velocity of MOE or MOR

• Among-tree correlations (Table 2c) were generally higher **than **were among-specimen correlations

• only one of the three- variable models was significantly better than its two-variable counterpart

  • counterpart

• The regression models for the tree averages explained
  more variation than did the corresponding models using the specimens

  这里than后喜欢用一个倒装

• the b value for density (0.58–0.61) was much higher than that for

  • 很经典的是than后跟that/those for

• Notice that correlations with neighbors in proximal positions are stronger (4/6) than with neighbors located diagonally (1/3).

  correlation可以用higher/stronger

• The average accuracy of prediction of breeding values, calculated from model 3 (the one with the smallest DIC), was higher for parents (0.61) and progeny (0.54) than corresponding values (0.40 and 0.32) calculated from model 1.

  • 从模型*而来 用from
  • correspongding value

trivial 琐碎的；无价值的；不重要的；平常的

• This is not a trivial problem这不是一个微不足道的问题, but based on the observed number of BSE cases and some assumptions about the disease, we can estimate the number of infected animals slaughtered prior to showing symptoms. New
• In practice, achieving a further distinction between the latter two categories of epialleles** is not trivial **and will require a combination of molecular and transmission genetic analysis.

thrive

• Siberian larch grows on variable sites as pure or mixed stands, but it thrives the best on well-drained排水良好的 sandy or rocky soils.
• In this re- gion, loblolly pine (Pinus taeda L.) thrives on various sites from east Texas to southern Missouri to north Florida to south New Jersey and is one of the fastest growing pine spe- cies, accounting for more than 84% of planted seedlings in the United States
• Siberian larch has even thrived better than domestic species
• It is a light-demanding, fast-growing pioneer species, which thrives in fertile soils of adequate moisture and rapidly colonizes open forest patches after a forest fire or clear-cutting
• Conifers dominate a variety of biomes by virtue of their capacity to survive and thrive in the face of extreme abiotic stresses.

tractable易于驾驭的 易于解决的

• This framework can be generalized to an arbitrary number of time points, where growth is measured, and becomes computationally more tractable, when the assumption of variance stationarityis made. In
• This simple filter excludes a huge proportion of the space of possible networks, making the problem tractable
• Because our continuous axes are constructed to be orthogonal, results are insensitive to the number of axes inferred, as we verify empirically. In addition, our approach is computationally tractable on a genome-wide scale.
• Low frequency variants of intermediate effect might also contribute to explaining missing heritability that should be tractable through large meta-analyses and/or imputation of genome- wide association data.
• Bayesian posterior probabilities, making the calculations tractable for complicated genetic models that have resisted analysis using maximum likelihood or other classical methods.

U

usher引导，招待；迎接；开辟

• The recent proliferation of hypervariable molecular markers has ushered in a surge of techniques for the analysis of parentage in natural and experimental populations.

ubiquit.ous无所不在omnipresent

• The role of imprinting in shaping development has been ubiquitously observed in plants, animals, and humans.
• Features such as hypervariability and ubiquitous occurrence explain their usefulness, but these features also pose several questions.
• As a ubiquitous phenomenon, studies of variation in phenotypic plasticity among genotypes, expressed as GEI, have been a long-standing focus of develop- mental and evolutionary biology
• Endogenous non-coding small RNAs consisting of 20–24 nucleotides are ubiquitous in eukaryotic genomes, where they play important regulatory roles, [69] and they provide an excellent source for molecular marker development.
• Conifers are the largest and most ubiquitous group of gymnosperms. They are woody perennials that shape many northern hemisphere ecosystems and support large industries through the provision of wood, fiber, and energy.
• In the light of our findings on the omnipresence of structured QEI in the current data, we would not subscribe to the view that an increase in population size is more important than an increase in the number of test environments.
• With the increasing omnipresence of marker technology in plant breeding, the classical problem of how to handle genotype environment interaction (GEI) is gradually being absorbed into more basic questions towards the existence and description of differential gene expression, where the term gene' is replaced byquantitative trait locus’ (QTL).
• Available proteomics studies emphasized the omnipresent background expression of stress-related proteins during SE development and maturation.
• The recognition that a third source of mutations, i.e., those due to R, are omnipresent helps explain the pathogenesis of these malignancies.

unequivocal

• Our results from the base model unequivocally demonstrate that the residual variance has absorbed the (co)variances arising from genetic and/or non-genetic competitive effects, and this absorption occurred irrespective of whether competition was primarily between or within families.
• Since its first discovery in the middle 1980s [2,3], such imprinted inheritance of a gene that obviously violates traditional Mendelian inheritance has been unequivocally demonstrated in an incredible range of species spanning from plants to animals to humans
• Also, it is important to note that, in most of
  these previous studies, the true causative genetic variant was not unequivocally identified, and most methQTLs did not demonstrate a strict one-to-one relationship between the cis-genotype and the epigenotype;* rather*, a specified genotype generates an increased probability of methylation.

unveil- show remove

• The indica diversity panel selected in the study to unveil the genomic regions relevant for salinity tolerance was found diverse to the extent that SNP-trait associations were stronger under salinity compared with control treatment.

• In this article, we have derived a high-dimensional statistical model for unveiling the genetic machinery for drug response by integrating two different but biologically related processes—pharmacokinetics (PK) and pharmacodynamics (PD)—into a genetic mapping framework.

  • genetic machinery - drug response - biologically related processes - genetic mapping framework

• Because of low domestication, large open-pollinated native populations, and high levels of both genetic and phenotypic variation, they are ideal organisms to unveil the molecular basis of population adaptive divergence in nature.

  • low domestication - native population - high levels of variation - ideal organism - molecular basis - adaptive divergence 适应趋异

• The estimation of allele frequencies in natural populations would provide the spatial framework to unveil the action of natural selection in the wild and to correlate environmental and allelic variation.

  • spatial framework - natural selection - correlate environmental and allelic variation

• Under many circumstances, quantitative genetic models have been largely insufficient to unveil the precise genetic architecture of a complex trait because they cannot estimate the number of genes involved and the chromosomal locations and genetic effects of these genes.

  • under many circum.stances在很多情况下 - quantitative genetic model - largely in.suf.fic.ient - precise - chromosomal locations

V

W

whilst ==while

• If molecular data are used to reconstruct different types of pairwise relationships, these can be integrated to form a complex pedigree potentially spanning a number of generations. Whilst this approach could theoretically incorporate the sibship-reconstruction methods outlined in the previous section, it is more typically used with parentage analysis, such that a multigenerational pedigree is con- structed from a combination of maternal and paternal identity information.

warrant 保证/值得/to promise that something is true/to need or deserve

• warrant
  
  • ~ better understanding /the statistical properties /usefulness /application
  • assumptions ~ test
  • further improvements are ~ed
• Elite populations with Ne ranging from 20 to 100 are frequently used in advanced tree breeding programs (White et al. 2007) providing substantially higher LD that would warrant the application of GS.
• Our results imply that a higher fraction of SOC of the Haibei alpine grassland subsoil is prone to positive priming induced by substrate input increases, which warrants better understanding in warming-induced vegetation changes on the Qinghai-Tibetan Plateau.
• Results from simulation studies and real data analysis warrant the statistical properties of the model and its usefulness in practice.
• Simulation studies are used to investigate power and error rates of this approach and to highlight situations in which violations of multivariate normality assumptions warrant the permutation test.
• As the FLM represents an appealing alternative to the infinitesimal model for genetic parameter estimation and for inclusion of polygenic background variation in QTL mapping analyses, further improvements are warranted and might be achieved via improvement of the sampler or treatment of the number of loci as an unknown.
  
  • an appealing alternative
• An area that especially warrants more detailed study is the extent and molecular basis of evolutionary genetic correlations between plant growth measures, such as height and internode elongation, and ecophysiological traits 生理生态的 such as efficiency of photosynthesis and resource use, carbon and nutrient allocation, and production of defense chemicals.

X

Y

Z

根据，依据

in the light of

• in light of these weaknesses it was natural that an alternative would be sought, and so maximum likelihood estimation duly came to be considered.
• The potential benefits of prenatal genetic testing for TCS must be assessed in light of social considerations regarding the acceptability or lack thereof of abortion and societal attitudes towards disability.
• The purpose of this paper is to show that in the light of fundamental difficulties in the computation of paternity probabilities these guidelines are ill-advised.
• However, in light of all the evidence, it seems more likely that selection acted on the FY*O mutation itself.
• Possible concerns over the practicalities of using large numbers of clones in seed orchards may disappear in the light of the lack of any clear advantage in increasing effective numbers of orchards clones above about 15.
• in light of the consideration of the coordinated expression of traits owing to genes and development, our model, which can be viewed as `high-dimensional’, should be able to produce results that are closer to biological realism than those without such a solid developmental basis of phenotypic traits.
• Complementary to our previous functional mapping [19-21], we name this new mapping framework \systems mapping\ in light of its systems dissection and modeling of phenotypic formation.
• The new model, named systems mapping in light of its systems feature of phenotypic description, was used to map QTLs for biomass partitioning in a mapping population of soybeans composed of 184 recombinant inbred lines (RIL) derived from two cultivars, Kefeng No. 1 and Nannong 1138-2.
• Currently, GWAS have been increasingly used in genetic research in light of their power to comprehend the genetic control of complex traits or diseases.
• We describe and assess a dynamic model for clustering gene expression profiles into distinct groups in light of their biological relevance and function.
• Further, in light of a possible move from open-pollinated orchards to control-pollinated orchards (Sweet 1995), paternity analysis using genetic markers remains important in evaluating the fidelity of control crosses, especially when carried out without bagging (Sweet et al.
• A deep understanding of the attributes of Canadian wood fibre is doubly important in light of the analyses being conducted in the Biopathways Project, which examines, among other things, the role of wood fibre in optimizing the forest value chain.
• Identify the desirable attributes in light of the market preferences of end products at present and in the future.

显著的，明显的

overtly

• Another is to more overtly make use of possible differences among genomic regions in contribution of variation in the trait, but if it is assumed that the variance in the trait associated with each SNP is sampled from the same normal distribution, the methods are equivalent (Goddard 2009; Hayes et al. in press) and can be used by extension of BLUP methodology, `genome-wide BLUP (GWBLUP)’.

notable

significant

marked

remarkable

prominently

pronounced -obvious

• pronounced
  
  • /effects /trend/differences ~
  • ~ differentiation/heterosis /right tail/performance /stability/ variation /influence /impact /reduction
• The population structure was weak, but FST indicated more pronounced differentiation in the SGS populations.
• and the effect of the Karnofsky score is only pronounced in the group with prior ther- apy.
• The period of winter chilling exerts a pronounced in- fluence on the range of life-history plasticity and the variation of bet-hedge strategy when the life-history trait expressed (i.e., seed emergence).
• This trend was especially pronounced in the SGS populations where it could also result from non-random mating of unrelated individuals and additional selection for traits associated with overdominance and heterosis effects.
• These effects may be particularly pronounced in the subsoil that is relatively depleted of energy-rich OC and are hence worthy of comparison with the topsoil in terms of predicting SOC responses to warming.
• The effect of in- breeding depression was more pronounced at higher levels of inbreeding.

长期；长时间 long-term ; over extended periods of time

• In addition, preadult mortality is often higher in individuals with extended periods of immature development, owing to a greater risk of predation (Benrey and Denno 1997).
• Somatic embryo development occurs follow- ing transfer of embryogenic callus to development medium and cultures can be maintained for extended periods of time by transfer of the proliferating proembryonic masses to fresh medium at 4–6- week intervals.
• The maintenance of bal- anced polymorphisms over an extended period of time through frequency-dependent selection will in turn facilitate indirect selection on modifier (epistatic) alleles to act over sufficiently long periods of time, rather than being limited to act during the spread of alleles prior to fix- ation.
• These technical variations are difficult to standardize and keep constant over extended time periods.

应用，采用

adopt

• Some of the reluctance to adopt GS may be due to the additional modeling challenges of crop improvement scenarios.

• a regression approach adopted from the spatial econometric literature

  • econometric literature 计量经济学文献

• Parentage assignments carried out under a maximum likelihood framework revealed a significantly higher success rate of MCP in 2006 (84 %) following technical improvements adopted to minimize pollen contamination and maximize male reproductive success, although significant variability in the correct maternity and full parentage was seen among individual families.

  • parentage assignments - carried out

• Given this unforeseen source of parentage error, we adopted a criterion by which the most likely single parent (higher LOD score) that the marker analysis revealed was considered to be the maternal parent of the offspring, overriding the maternal clone identity used up to that point from which the seeds had been harvested.

  • unforeseen - criterion by which - the mose likely

• The Cooperative Forest Genetics Research Program has adopted an advanced-generation breeding strategy designed to maximize genetic gain in the short term and provide for continued improvement in the long term, while maintaining a broad genetic base for gene conservation.

  • advanced-generation breeding strategy - in the short time - a broad genetic basis - gene conservation

• Despite major advances in the statistical analysis of multi-environment trial data, such methodology has not been adopted within national variety testing programs.

  • multi-environment trial data - methodology - national variety testing programs

• If this approach is adopted the averaging will include pairs of trials that are poorly (sometimes negatively) correlated so that substantial cross-over variety by environment interaction would be ignored.

  • sub.stant.ial - cross-over variety

apply

• Additionally, the cost of genotyping will significantly in- fluence how the technique is applied.
• The fit of the spatial mixed models applied to yield data was signif- icantly better than that of the classical approach, resulting in a positive impact on selection decisions and increasing the accuracy of genetic gain prediction.
• Jacquard’s suggested transformation was applied to the GD values to in- crease the separations of the matings:
• These strategies have however rarely been applied in plant genome mapping.
• In the absence of detectable length polymorphisms, two other approaches were applied depending on the fragment sizes.
• This method has been previously applied to AFLP markers by Young et al.
• Paternity analyses have also been applied in natural-stand progeny arrays

实施

carry out 开展,实施一项活动

• carry out
  
  • ~ test trail /experiment /analysis /study /research /simulation /
• A short-term retrospective test trial was carried out using 90 open-pollinated families representing 30 prove- nances of black spruce (Picea mariana (Mill.) BSP) from Quebec
• ANOVA were carried out using PROC MIXED (SAS Institute Inc. 1997) with the restricted maximum likelihood method to estimate the variance com-ponents.
• Research carried out in land classification over the last 30 years made it possible to divide the southern Quebec pro- ductive forest territory into about 2000 homogeneous land districts (Robitaille and Saucier 1998).
• We carried out extensive simulation studies to examine the robustness and statistical performance of our method.
• Capillary electrophoresis was carried out at an oven temperature of 60 ?C in POP-7 polymer using dye set G5.
• QTL detection experiments were carried out for juvenile wood density (JWD) and stem diameter at breast height (DBH) using selective genotyping.
• Simulations carried out by Carson et al. (2003b) suggested that selectively genotyping a small proportion of individuals in many circumstances would maintain most of the power of large population sizes and result in successful QTL detection.
• Sampling of validation and training data sets was carried out across and within families, which allows comparing across-and within-family information.
• Parentage assignments carried out under a maximum likelihood framework revealed a signifi- cantly higher success rate of MCP in 2006 (84 %) following technical improvements adopted to minimize pollen contam- ination and maximize male reproductive success, although significant variability in the correct maternity and full parent- age was seen among individual families.
• Pollen applications were done every other day, and a total of three pollen applications were carried out on each isolated female cone to ensure maximumsuccess.
• Microsatellite PCR amplification and genotyping in an ABI 3100XL were carried out in three multiplex systems following the same procedures described earlier for Eucalyptus (Faria et al. 2011)
• A Bayesian analysis of genetic parameters for quantitative traits was carried out in 37 E. globulus open-pollinated families under cold conditions in southern Chile.

perform

• The Bayesian approach was performed using Gibbs sampling algorithm.

conduct

• The experimentwas conducted in the Andean foothills within Bío-Bío Province, Municipality of Mulchen, southern Chile (37° 56′ S Latitude; 72° 2′ W Longitude; and altitude of 320 m).
• To understand the process of dog diversification better, we conducted an extensive genome-wide survey of more than 48,000 single nucleotide poly- morphisms in dogs and their wild progenitor, the grey wolf.
• Following this scheme, four cycles of recurrent FS selection were conducted between 1994 and 2002.

稍微

slightly

somewhat- more than a little but not very

• somewhat
  
  • ~ larger/lower /smaller /less /higher /closer /expensive /
• For most trait types, individual effect PVE estimates were small (<5%, Table 1) but water use efficiency traits exhibited somewhat larger median PVE both in QTL studies and in association studies (8.4 and 5.0%, respectively).
• These estimates were somewhat lower than the corresponding estimates for QTL mapping crosses and were considerably lower compared to local heritabilities thus indicating an issue of missing heritability.
• However, for DBH, the estimated correlations in the present study were somewhat lower than those reported by Cappa and Cantet (2008) for Pinus taeda (−0.79) at age 13 and tree spacing of 3.5m × 3.5 m and by Costa e Silva et al. (2013) for Eucalyptus globulus (−0.92, average across 2 and 4 years and planting spacing of 5.0 m × 2.125 m).
• In our study, the FL was about 2.4 mm at rings 8–11, which is somewhat higher than previously reported by Lundqvist et al. (2002): 1 mm close to pith, 1.8–2.2 at ring 10, 2–2.5 at ring 15, and 2.5–3.5 at rings above 25.
• This ap- proach is feasible if the paternal analysis cost per indi- vidual is somewhat expensive, perhaps in the order of $30–$50/individual for some tree-improvement pro- grams.
• The classical approach to analysis of first-generation open-
  pollinated progeny trials of tree species with mixed-mating systems is to assume that all trees have uniform within-family relatedness, i.e. they are either half-sib or somewhat closer than half-sib, because of inbreeding including selfing and the presence of some full-sibs.
• we suggest that the mathematical mechanics of the lin- ear model used caused their estimate of heritability to be somewhat overstated夸大夸张过高.

因此

hence

therefore

thereby

thus

consequently

as a consequence

accordingly

as a result of

包含 组成 构成 成分

encompass 涵盖

• DNA transposons encompass only 5.6% of the genome.
• The large plot size is necessary to encompass substantial populations of most tree species in the community.
• The nonheritable component (E) encompasses part of the dominance and epistasis deviations. Furthermore, the additive genetic component (A) may encompass a part of the dominance and maternal effects due to the full-sib (FS) design.
• Although most genomic selection has focused on rather narrow breeding efforts within one breeding programme137, the long-term goal should be to produce models that encompass the worldwide diversity of a species, incorporating information on phenotype and performance in numerous environments.
• To fully explore the scope of variation within the chemical traits and their genetic control, large numbers of individuals, families and provenances are re- quired which encompass the range of E. globulus.
• Seedling seed orchards usually encompass a broader genetic base because of the larger number of individuals involved in mating (the male component of the open-pollinated progenies is often unknown); on the other hand, they are expected to provide lower genetic gain because their pedigrees are not fully known [28].
• The genomic selection (GS) concept encompasses a broad range of methods.

consist of = comprise = compose of

• The corn breeding pedigree consisted of either 15 or 60 families, each having 60 doubled haploids
• The collection consisted of c. 1000 stocks, mostly natural accessions and individual mutant lines generated by a handful of Arabidopsis researchers
• The seed orchard population consisted of 59 clones (1-19 ramets/clone) with outcrossing rates of 98-99% and pollen contamination levels of 31-41%

comprise

• CAP comprised 674 founder or major recurrent muta- tions from 162 genes representing 125 severe, early-onset diseases.
• At each time-point, samples from 7 to 11 distinct trees per popula- tion were collected and analyzed by GC-MS, so that the study comprised, in total, foliar samples of 110 distinct individuals.
• The elite panel comprised 1367 lines, con- stituted part of the proprietary breeding program of Flori- mond-Desprez, and was genotyped with 836 SNPs.

compose

• All tissues are composed of multiple cell types (for example, blood contains >50 distinct cell types).
• The repetitive fraction of mammalian genomes is mainly composed of two classes of retroelements termed short (SINEs) and long interspersed repetitive elements (LINEs) that contain poly(A) tails
• The two trials composed of 196 progeny were designed as a 14 × 14 simple lattice and performed in the experimental station of the Federal University of Vic ¸osa at Coimbra, Minas Gerais state, Brazil, in the 1999/2000 and 2001/2002 growing seasons. Each plot corresponded to a 5 m row with 25 plants (ideal stand).
• The mapping population is composed of 177 recombinant inbred lines (RILs), derived from a Mesoamerican cultivar (Jamapa) and an Andean cultivar (Calima).

constitute 构成 组成 任命

• In conifers, the rapid decay of linkage disequilibrium (LD) can constitute a severe barrier to application of GS.
• These molecular markers constitute reliable tools to recover paternal identity in polycross trials.

• so this might constitute a conservative estimate for selection coefficients at positive outliers detected

  • a conservation estimate - at positive outliers detected

• We try below to summarize available knowledge on these genes, acknowledging 承认 the fact that genomic stud- ies of drought stress in plants reveal large numbers of potential candidates that ultimately constitute complex regulatory networks

  • we try below to - drought stress - complex regulatory networks - ultimately

• Many tree species would constitute good models for this purpose due to their large-sized natural populations with little confounding substructure and domestication history, outcrossing mating systems leading to high gene flow, sufficient nucleotide diversity, and long history of ecological and quantitative ge- netics research

  • little confounding substructure - domestication history - leading to - sufficient nucleotide diversity

• It was found that the orchard constitutes a population with a mating system that is far from panmixis.

  • panmixis 随机交配 随机交配群体

• Population structure analysis indentified two subpopulations of 77 and 41 accessions, respectively, while a third group was constituted by 19 accessions whose classifications were not defined (i.e. hybrids).

  • population structure analysis - be constitute by - classifications were defined 定义分类

• These results, together with the earlier biochemical evidence, suggest that there may be factors that impose limits on the compositional and structural variation of a genome, and that the set of dinucleotide odds ratio values constitute a genomic signature.

  • biochemical evidence - impose limits on - the compositional and structural variation 成分和结构的变化 - genomic signature

make up = constitute

• A total of 152 markers eventually made up the 25 framework maps (Ta- ble 2, Fig. 1), and the remaining 78 markers were attached to each map as accessory markers.
• Figure 2 demonstrates the fortunate position the dairy industries are in if the reference population is made up of progeny-tested bulls

incorporate- to include something as part of a group, system, plan etc把〔某事物〕并入；包含

• In contrast to simpler techniques typically used to estimate herita- bilities in studies of wild populations to date, such as parent–offspring regression or sib analyses, these models incorporate multigenerational information from complex pedigrees and allow estimation of a range of causal components of variance.
• This framework, called systems mapping, incorporates a system of differential equations that quantifies how alterations of different components lead to the global change of trait development and function through genes, and provides a quantitative and testable platform for assessing the interplay between gene action and development.
  
  • system mapping - differential equation - lead to - global change - a quantitative and testable platform - assessing - interplay == interaction

• In this article, we put forward a conceptual framework
  to incorporate the design principles of trait formation and development into a statistical framework for QTL mapping.

  • put forward - a conceptual framework - the design principles - trait formation and development

• Bayesian statistics allow scientists to easily incorporate prior knowledge into their data analysis.

  • bayesian statistica - prior knowledege - easily

• Our model was derived within the maximum-likelihood-based mixture model framework, incorporated by biologically meaningful growth equations and environment-dependent genetic effects of QTL, and implemented with the EM algorithm.

• Work to provide efficient computation of the adjustments and to incorporate these ideas for BLUPs is in progress.

• Recently available mixed model methodology permits the covariance structure to be incorporated into the statistical model.

• we used the best linear unbiased predictor (BLUP) approach with an individual-tree model that incorporated pedigree infor- mation

阐明 说明 阐发

elucidate （这个词在文中只用1次）

• elucidate
  
  • ~ a comprehensive|global picture /the potential /the whole landscape /the nature of /relationship /correlation /genetic architecture /mechanism /role
  • To elucidate the potential of GS for conifer breeding, we simulated 60-year breeding programs in Cryptomeria japonica with and without GS.

• The revised model provides a framework that reconciles the genetic architecture of development at different stages and elucidates a comprehensive picture of the genetic control mechanisms of growth that change gradually from a simple to a more complex level.

  • provide a framewok - a comprehensive picture - change gradually - from a simple to a more complex level

• Thus, identified QTLs from this approach cannot be used to elucidate the whole landscape of ontogenetic growth and development.

  • the whole landscape - ontogenetic growth and development

• The model can not only help geneticists to precisely identify an entire set of genes underlying complex traits but also allow them to elucidate a global picture of how genes control developmental and dynamic processes of trait formation.

  • not only, but also - help someone to - precisely identify - an entire set of - allow someone to - a globle picture - dynamic processes - trait formation

• This set of COS markers, identified computationally and experimentally, may further studies on comparative genomes and phylogenetics and elucidate the nature of genes conserved throughout plant evolution.

• Currently, we have mapped > 550 COS markers in tomato and expect to map up to 1000 to elucidate the syntenic relationships between these two genomes; the results from this study will be the topic of a future publication.

• Drosophila melanogaster provides an attractive system for elucidating the unifying principles of the genetic architectures that drive behaviours, as genetically identical individuals can be reared rapidly in controlled environments and extensive publicly accessible genetic resources are available.

  • unifying principles - drive behaviours - genetically identical - extensive publicly accessible genetic resources

• The model provides a powerful tool for elucidating the genetic basis of complex binary diseases.

  • a powerful tool - genetic basis - complex binary disease

• The new model is equipped with a capacity to characterize the genetic effects of QTLs on seasonal alternation季节动态 at different ages and then to better elucidate the genetic architecture of development.

  • equipped with a capacity - seasonal alternation - qtl on

• These two hypotheses of genetic control have been elucidated in the literature.

• Despite their success in identifying genes that affect complex disease or traits, current genome-wide association studies (GWASs) based on a single SNP analysis are too simple to elucidate a comprehensive picture of the genetic architecture of phenotypes.

• Here we describe how functional mapping and studies of plant ontology 本体论 can be integrated so as to elucidate the expression mechanisms of QTLs that control plant growth, morphology, development, and adaptation to changing environments.

• A detailed picture of the genetic architecture of quantitative traits can be elucidated with a well-saturated genetic map of molecular markers.

• Further simulations elucidating the potential of GSB based on the IBD probabilities might be fruitful 卓有成效的.

• To identify these biomarkers, we need a major shift from traditional genomic analyses alone, moving the focus towards systems approaches to elucidating genetic variation in biochemical pathways of drug response.

  • a major shift from - moving the focus towards - systems approaches - biochemical pathways - drug response

• The developed model provides a quantitative and testable framework for assessing the interplay between genes and the developmental PCD process, and will have great implications for elucidating the genetic architecture of the PCD process.

  • testable framework - interplay between - have great implications for

• Recent efforts in integrating gene expression analysis and genetic mapping, termed expression quantitative trait loci (eQTL) mapping or genetical genomics analysis, offer new prospect 前途 in elucidating the genetic architecture of gene expression.

• The biological processes involved were not elucidated in the cited studies, but thinnings increase wind speeds, precipitation and solar radiation in stands, which might hypothetically accelerate natural pruning 自然整枝 rates (Heikinheimo, 1953).

  • precipitation - solar radiation - natural pruning rates

• However, a definitive model to elucidate the relationship between disrupted clocks 生物钟 and HCC remains elusive.

  • a definitive model - remains elusive

• At the same time, few resources exist for elucidating the mechanisms by which this fungus is able to infect pine species.

  • exist for

• Further research to elucidate correlations may require larger sample sets to obtain estimates with smaller error.

  • larger sample sets

• Generally, a given crop needs both natural and breeding populations to elucidate different features.

  • natural and breeding populations

• In addition, the estimation of QTL main and interaction effects is very likely biased (Beavis 1994), which makes it challenging to reliably elucidate the role of epistasis through genome-wide QTL mapping studies.

  • main and interaction effects - be very likely biased - make it challenging - the role of -qtl mapping studies

• This article reports the first study of its kind to attempt to elucidate the genetic architecture of the heterochrony 异时性 of leaf area and dry weight growth trajectories and, more importantly, to characterize environment-dependent changes of the effects of hQTLs on developmental timing.

  • this article reports the first study of its kind to - attepmt to - leaf area - growth trajectory - environment- dependent changes - developmental timing

• Hence, an understanding of the dynamics and the inheritance of DNA methylation in plants represents an important prerequisite 前提 for elucidating epigenetic para.digms 表观遗传模式 in plant genetics, breeding, development and evolution.

  • an understanding - the dynamics and the inheritance - DNA mehtylation - prerequisite - epigenetic paradigm

• In an attempt to elucidate the molecular mechanisms of Melampsora rust resistance in Populus trichocarpa , we have mapped two resistance loci, MXC3 and MER , and intensively characterized the flanking genomic sequence for the MXC3 locus and the level of linkage disequilibrium (LD) in natural populations.

  • in an attempt to - molecular mechanism - rust resistance- intensively characterized - the flanking genomic sequence

• The 1000 Genomes Project has already elucidated the properties and distribution of common and rare variation, provided insights into the processes that shape genetic diversity, and advanced understanding of disease biology.

  • the properties and distribution - common and rare variation - provide insight into - shape genetic diversity - advanced understanding

• Through the game analysis above, one can better dissect the genetic architecture of phenotype formation. Using classic quantitative genetic theory (Table 1), a specific landscape of genetic control can be elucidated.

  • dissect the genetic architecture - phenotype formation - a specific landscape of genetic control

• Multiple regression analysis was used to explore relationships between parameter values and test environments, to elucidate regional differences, and to identify environmental patterns of importance for planning of breeding programs.

  • regression analysis was used to explore - regional differences - environmental patterns of important - planning of breeding programs

• In order to elucidate the influence of age and height, their values were fixed at 10 (Fig. 1a) and 20 years (Fig. 1b) for certain mean height values.

  • mean height values

• Because much of the observed heterosis among inbred lines may be due to the recovery of inbreeding depression, the genetics of heterosis may be best elucidated by studying the genetics of inbreeding depression.

  • 杂种优势是近交衰退恢复的原因杂优遗传最好通过研究近交衰退遗传来解释 - due to - recovery of

关于

• regarding = in respect of; concerning
• in respect of (/ with respect to) = as regards; with reference to:
• in terms of = with regard to This is used to refer to a particular aspect or subject related the thing talked about
• as for = with regard to:

with regard to

• The contrasting behavior of apical and cam- bial meristems, with regard to their responses to spacing, can also be explained by differ- ences in their sink strength and growth phenology.
• Changes in aggression between pigs selected for IGEg were not influenced by G6E interactions with regard to the level of environmental enrichment.
• This indicates that the association between crown length and heartwood is significant with regard to environmental factors, no matter to what extent they are independently modified by genes.
• Furthermore, there is increasing evidence that spatial soil ecology can yield new insights with regard to understanding the factors that maintain and regulate soil biodiversity, as well as to how the spatial distributions of soil organisms influence both plant growth and plant community structure.
• The Italian and Chinese FY data show patterns of variation that are very unusual, particularly with regard to frequency spectrum and linkage disequilibrium, but do not fit the predictions of any simple model of selection.

in terms of 按照 在…方面

• The methods were compared in terms of inference of the number of QTL and accuracy of genomic estimated breeding values (GEBVs), using simulated scenarios and real data from North American Holstein bulls.
  
  • 从这几方面进行比较
• This new strategy represents a significant advantage in terms of time-savings (i.e. more than eight months), greenhouse space and work during the generation of mutant plant populations.
• Early selection at age 6 would account for 69 % of the genetic gain from direct selection at age 28 in terms of wood density.
  
  • 按照密度选择的话
• The demand is in terms of computer time rather than in terms of programming complexity.
  
  • 需求是按照计算时间而非程序的复杂性
• Overall, genomic SSRs tend to perform better in terms of heterozygosity and number of alleles.
• The cross-validation investi- gated the performances of the partitioned and standard RR-BLUP mod- els in terms of their predictive ability measured by the R-squared value, and the accuracy and precision of the GEBV measured by the mean square error (MSE) from the linear regression models.

with respect to 关于，如果，至于，相对于

• Connections between BL and other marker-based regression models are discussed, and the sensitivity of BL with respect to the choice of prior distributions assigned to key parameters is evaluated using simulation.
• Possible uses of a genetic linkage map with respect to population ecology and genetics are discussed.
• The results are discussed with respect to the maintenance of heritable variation and the bias introduced in the calculation of the full-sib heritability estimate by high levels of dominance variance.
• Third, the long-term success of the identified heterotic pattern is assessed by estimating the useful- ness, selection limit, and representativeness of the heterotic pattern with respect to a defined base population.
• In many situations, estimates of linear combinations are invariant with respect to covariance structure, yet standard errors of the estimates may still depend on the covariance structure.
• These markers have already been used to measure pollen contamination and selfing rates, directly quantify the proportion of seeds fathered by each seed orchard parent, and test for deviations from random mating with respect to distance between orchard trees
• The influence of two parameters was studied: the relative importance of breeding value for seed value and the size of the penalty for reducing the value of the seed crop with respect to lost gene diversity.
• Heterosis results in the phenotypic superiority of a hybrid over its parents with respect to traits such as growth rate, reproductive success and yield.
• Lastly, we point to some recent results showing that new models are needed to improve predictions particularly with respect to the use of distantly related indi- viduals in the training population.
• Our survey leads to some important insights with respect to the utility of the different approaches.
• The individual progeny tests differ with respect to age, composition and ability to screen the breeding values of the parent trees.

研究的局限

remain elusive

• The evolution of body shape is thought to be tightly coupled to changes in regulatory sequences, but specific molecular events associated with major mor- phological transitions in vertebrates have remained elusive.
• Much progress is being made in addressing these problems, but many questions remain.
• The evolution of body shape is thought to be tightly coupled to changes in regulatory sequences, but specific molecular events associated with major mor- phological transitions in vertebrates have remained elusive.
• The identities of genes underlying these traits, however, have remained elusive and thus so have the patterns of adaptive molecular diversity in forest tree genomes.
• The genes underlying cold hardiness, however, have remained elusive, despite numerous efforts to map quantitative trait loci (QTL)
• The identification of the genes that underlie these adaptive traits, however, has remained largely elusive, yet尽管 emerging association genetic studies (cf. Gonza´lez- Martı´nez et al. 2008) have begun to identify handfuls of such loci.
• A growing body of evidence shows that the extent to which phenotypic changes are driven by the environment, known as phenotypic plasticity, is also under genetic control, but an overall picture of genetic variation for phenotypic plasticity remains elusive.
• Obesity is globally prevalent and highly heritable, but its underlying genetic factors remain largely elusive.
• Heterosis, also known as hybrid vigour, is widespread in plants and animals, but the molecular bases for this phenomenon remain elusive
• Bringing bioinformatics to geneticists is a crucial first step towards integrating the kindred fields and characterizing the frustratingly elusive genes that influence complex phenotypes.

limit

• Although well-documented software often exists for the fixed analog of the additive genetic model, and in some cases also a simple mixed model, the applicability of such software in animal breeding is often limited.
  
  • analog
  • in some cases
  • the applicability

has not been -ed yet

• However, convergence and mixing of the Gibbs chains depend on data structure, and reliabil- ity of GS results for multiple categorical traits in a setting typically encountered in the horse has not been investigated yet.

rare

• It is commonly believed that homozygous lethal or sublethal alleles are responsible for producing empty seeds upon sel”ng (Orr-Ewing 1957; Sarvas 1962; Hag- man and Mikkola 1963; Mergen et al. 1965), but direct evidence is rare (Fowler 1964, 1965; Hedrick and Muona 1990)

still non-resolved

• While the genetic basis of heterosis has been investigated for many decades, it is still non-resolved.

not in place

• Consequently, criteria for maximizing high short-term selection gains without promptly diminishing genetic variance are required in the search for heterotic patterns, but such approaches are not yet in place.

few

• Although there have been numerous QTL mapping studies for a wide range of traits in diverse crop species, relatively few markers have actually been implemented in plant breeding programs (Young, 1999).
• Very few published reports compare the estimated heritabilities from different types of markers.

scarce

• Unfortunately, direct comparisons of both markers using the available repertoire of analytical approaches are still scarce, so, at present, it is not clear which marker is most useful for the inference of demographic processes.
• Singlets are inevitably classified as source-specific transcripts and are likely to be relatively scarce.
• The AMDH population was the least polymorphic with the lowest number of markers and an overall lower marker density: many regions were not polymorphic at all or had a very scarce number of markers.
• Additionally, scarce genomic resources in terms of recombinant populations and genome information have been generated for L. albus.
• Although the epigenetic mechanisms that establish genetic imprinting have been a focus of many genetic studies, our knowledge about the number of imprinting genes and their chromosomal locations and interactions with other genes is still scarce, limiting precise inference of the genetic architecture of complex diseases.

inadequate

• The current methods for defining prokaryotic species are inadequate and incapable of keeping pace with the levels of diversity that are being uncovered in nature.
• Until recently, analysis techniques available in computer software only offered the user limited and inadequate choices.
• Those methods perform well in data sets in which population structure is the only kind of structure present but are inadequate in data sets that also contain family structure or cryptic relatedness.
• Previous work focused on lower-order interactions between a pair of genes, but it is obviously inadequate to explain a complex network of genetic interactions and pathways.

little is known; unknown

• Although the ecological consequences of climate change are increasingly well documented, the effects of climate on the key evolutionary process driving adaptation— natural selection—are largely unknown.
• Requirements for successful implementation of multivariate animal threshold models including phenotypic and genotypic information are unknown.
• Those studies, however, were all based on single-trial spatial analyses. Until recently, little has been known about the effectiveness of the use of spatial analysis for METs.
• Although heterosis in maize (Zea mays L.) has been studied since the early 1900s, very little is known about how heterosis affects the physiological components of grain yield.
• While genes of several differentiation-related keratins have been cloned and studied, relatively little is known about the molecular basis underlying their tissue-specific and differentiation-dependent expression.
• However, they have generally been evaluated against a narrow genetic background, and little is known about their correlations with mandatory selection criteria such as growth and straightness.
• Within- and between-tree variation in resin canal occurrence has been poorly documented and little is known about factors controlling canal frequency or the relationship between canal distribution and the formation of timber blemishes.
• However, little is known about the mechanisms that control HCN channel trafficking to subcellular compartments or that regulate their surface expression.
• Despite such importance, however, it is no surprise that little is known about the genetic detail involved in shape variation, because no approach is currently available for mapping quantitative trait loci (QTLs) that control shape.
• Flavour is an important food trait, yet little is known about the genetic architecture and mode of inheritance of apple flavour compounds.
• In animals,DNAmethylation is related to gene silencing during ontogenic development. Little is known about DNA methylation in plants, although occasional changes in the DNA methylation state of specific gene promoters have been reported in angiosperms during some developmental processes.
• Although many imprinted genes have been identified and play a key role in development, little is known about the contribution of imprinting to quantitative variation in trait expression.
• Both environmental and genetic factors are known to affect the quantity of oleoresin flow in loblolly pine, Pinus taeda L., but little is known about the genetic contribution to phenotypic variation in this trait.
• Despite its importance in the maintenance of genetic diversity via genotype-by-environment interactions, little is known about the detailed genetic architecture of this phenomenon, thus limiting our ability to predict the pattern and process of microevolutionary responses to changing environments.
• However, the above findings were demonstrated through interspecies comparisons with other Larix species and their hybrids, and little is known about variation within the hybrid species.
• Ye et al. (2010) mentioned that forest geneticists and tree breeders know that genetic effects on tree growth are strong, yet little is known regarding the effects of competition among genetically selected materials on stand productivity; the effects of competition are dependent upon both the genetic composition (i.e., inter- genotypic competition) and the proximity of neighbors (i.e., density competition).

No study

• No study has been reported about the quantitative genetic variation of survival and growth traits under cold conditions in germplasm that has been naturalized in southern Chile.

lack

• Although considerable attention has been focused on identifying the regulatory control mechanisms of phase change, a detailed understanding of the genetic architecture of this phenomenon is still lacking.
• RNA-seq, based on deep-sequencing techniques, has been widely employed to precisely measure levels of transcripts and their isoforms expressed under different conditions. However, robust statistical tools used to analyze these complex datasets are lacking.

poor understood

• The influence of abiotic stresses on the use of GD as a predictor of hybrid performance is poorly understood.
• Genes have been widely recognized to be involved in human body growth, but their detailed controlling mechanisms are poorly understood.
• While the successional dynamics and large-scale structure of Douglas-fir forest in the Pacific Northwest region is well studied, the fine-scale spatial characteristics at the stand level are still poorly understood.
• The genomic architecture of adaptive traits remains poorly understood in non-model plants.
• However, genetic mechanisms of this high adaptability at both individual and popula- tion levels are still not fully understood.
• Despite this high cost, the extent to which harvesting productivity is affected by tree genetics is not well understood.
• Although such allometric relationships may be under genetic determination, their precise genetic mechanisms have not been clearly understood due to a lack of a statistical analytical method.
• the genetic mechanisms of heterosis are only partly understood, and a global view of heterosis from a representative number of hybrid combinations is lacking.
• An important analytical result involving contrasts is sometimes not completely understood.

不一致 未证实

this is in contrast to a study that reported

• This is in contrast to a simulation study that reported introduced pedigree errors as low as 2% decreased additive genetic variance to a level equivalent to the simultaneously increasing dominance variance (Ericsson 1999).

different from the results reported by

• This is different from the results reported by Dutkowski et al. (2006) where there was generally not much difference between height and diameter in model improvement.

un.sub.stantiated未经证实的

• Hence, let us take a pragmatic view: if something works in practice is that not sufficient even if the theoretical foundations are generally unsubstantiated?
• Unfortunately, much of what has been written of FeUds 53 felid natural history is also unsubstantiated.
• It may of course be true that the results are irrelevant but the paper contains only an unsubstantiated dismissal.

与前人研究一致（同意…观点）证实

borne out 证实

• Indeed predictions made by, for example, Robertson (1967) of contributions of increasingly many genes of increasing small effect have generally been borne out.
• The basic assumption is that many loci contribute to risk, as borne out by analysis at least for schizophrenia (Purcell et al.
• In general, these predictions were borne out in results of a variety of molecular genetic assays (Gilbert et aI., 1990; Wayne et aI., 1991b).
• The prediction that better dispersal reduces aggregation was partially borne out.

cor.robor.ate

• This study corroborates previous findings where the frequencies of both these SNPs were found to vary clinally with latitude.
• Therefore, the RAPD markers were shown to display dominant

subscribe to the view

• In the light of our findings on the omnipresence of structured QEI in the current data, we would not subscribe to the view that an increase in population size is more important than an increase in the number of test environments.

in line with

• This is generally in line with the observation of Dutkowski et al. (2006).
• Indirect evidence for this also comes from our realized gain trials where estimated gains at age 12 are in line with the observed gains based on progeny testing (Stoehr et al. 2010)
• However, results of selection over a few generations were short of expectations, although accuracies were generally in line with expectations (Muir et al., 2012).
• The number of QTL (NQTL=1, 3, 5, 10, 20, 30, 50, 100, 150, and 200), all with additive effects, in line with results from QTL and association mapping experiments that have typically found between a few and several tens of marker–trait associations controlling each trait.
• These results are not surprising and in line with findings in much larger and significantly more powerful genome-wide association studies in humans (Visscher 2008), domestic animals (Goddard and Hayes 2009), and crop plants (Buckler et al. 2009). These

congruent with

• The latter tests should generally be more congruent with the confidence intervals based on the same distances than the rank-based tests are. The
• The within-breed variation (89%) results based on SNPs were congruent with the microsatellite-based results (Li et al. 2007)
• The few explicit comparisons of the relative utility of microsatellites andAFLPs in plants (summarized in Ref. [17]) show that the two systems give **congruent **results when a sufficiently large number of microsatellite loci are analysed (e.g. 18 micro- satellite loci in the study of the fern Athyrium distentifo- lium).
• Linkage LOD thresholds were chosen as giving congruent results in the two parental linkage analyses.
• This observation is congruent with the positive genetic correlation between these two traits (Table 4).
• This is congruent with earlier genetic studies reporting that a similar set of genes control bud flush in both seed- ling- and sapling-aged trees (Li and Adams 1993).

compatible with 用的较少

• Apples are known to have been gathered in the Neolithic and Bronze Age in the Near East and Europe, and all archaeological findings indicate a fruit size compatible with those of the wild M. sylvestris41, a species bearing small astringent and acidulate fruits.
• Third, 7563 of the markers are SNP markers, which are compatible with high-throughput SNP-genotyping platforms for molecular breeding and genetics studies.
• However, the likelihood surface for estimating f was quite flat and, therefore, other parameter values are compatible with the data.

support

• The generally symmetric autocorrelations that we have found support the recommendation that blocks be as square as possible (Correll and Cellier 1987).

accord with

• These estimates start to approach the amount of mutational variation required to explain levels of segregating variation if s = 0.02, but not if s = 0.2, in accord with the inference from distributional properties of P element mutations affecting these traits.
• As reported by Kaya et al. (1999) in a study of Pinus taeda, the apparent presence of a small number of QTLs with strong effects **is not in total accordance with **the infinitesimal model (which assumes that quantitative traits are influenced by many genes with small and additive effects).
• The simpler case of equal error for each mean is not in accord with experience in many species.
• This is in accord with the general recom- mendation that patchy variation (low to moderate autocorrelations) needs smaller design features to cope with it. Unfortunately

be consistent with

• For fall cold-hardiness, co-location of QTLs was not observed for the different tissues assayed, which is consistent with previous reports of less synchronization of hardening in the fall.
• The results from the microsatellite analysis of ten rice inbred lines indicate that the number of alleles detect- able in rice by microsatellites is very high, which is consistent with results of previous reports (Panaud et al. 1996; Wu and Tanksley 1993; Zhang et al. 1995).
• Basic density (age 13)did not have significant variation at the family or locality level,although the trends in locality means (King Island low and theStrzelecki localities high) were consistent with previous studies that have reported significant differences [1, 10, 26]. This suggested that the small sample size and the use of only the outer part of the core reduced the power of the current studyand therefore significance would generally be underestimated.
• These phenotypic trends were consistent with previous reports of wood density in Scots pine (Persson et al. 1995; Hannrup and Ekberg 1998; Hannrup et al. 1998).
• These estimates are consistent with those from previous reports in loblolly pine and other conifers (Hodge and White, 1992) and are suggestive of strong genetic control.

as well as

• However, these results, as well as previous reports documenting effects of P element insertions (Mackay et aI., 1992a; Lyman et aI., 1996),

confirm

• We also confirmed the observation of Baird and Mead (1991) that where incomplete block models were better than randomized complete block models, the spatial analysis was even better.
• we did not find any evidence of population structure, which confirms previous reports showing absence of population genetic structure within the eastern Mississippi Valley range of P. taeda (see, for instance, Al-Rabab’ah and Williams 2002).
• This intriguing paper **not only confirms previous reports **that exposure of pregnant mice to methyl donor supplemented diets leads to altered epigenotypes of offspring carrying the Avy allele but further shows that the subsequent generation is also affected.
• Not surprisingly, our data confirmed the theoretical benefits of incomplete block designs already demonstrated by Fu (2003) in forest trees and many workers in agricultural vari- ety trials. More

in agreement with

• The results reported here are in agreement with all previous reports in that Larix decidua x kaempferi hybrids exhibited relatively fast growth.
• This is **in agreement with a previous study **that described that additive variance is expected to account for >50% (often about 100%) of the total genetic variance(Hill et al. 2008).

表重要

integral

• Mating designs are an integral factor of any tree breeding program.

pivotal

• Genetic interactions or epistasis have been thought to play a pivotal role in shaping the formation, development and evolution of life.

key

• Although many imprinted genes have been identified and play a key role in development, little is known about the contribution of imprinting to quantitative variation in trait expression.

crucial

• Knowledge of the genetic variation of key economic traits in Eucalyptus globulus under cold conditions is crucial to the genetic improvement of environmental tolerances and other economic traits.

important

• Heterotic groups and patterns are of fundamental importance in hybrid breeding of maize (Zea mays L.).
• It is important to determine whether the different phenotypes of these epithelia are the result of intrinsic divergence, extrinsic modulation, or a combination of both.
• Eucalyptus globulus Labill. ssp. globulus is one of the most important cultivated eucalypts in the world, mostly used as raw material for pulp and paper industry, and several breeding programs throughout the world are striving to improve key economic traits such as growth and wood density (Bundock et al. 2008).
• The results are important for developing tree improvement strategies to increase the profitability of future E. globulus plantations where cold is a significant constraint.

prominent

• However, because of the complexity encountered in multi-trait and multi-stage selection as well as the complexity in the genetics of economically important traits molecular markers still do not have a prominent role in breeding programs (Hallauer, 1999)
• Phase change plays a prominent role in determining the form of growth and development.

表证实

confirm

• The results of this study confirm the potential for selective breeding of this eucalypt in areas of southern Chile where cold is a significant constraint.

substantiate

• These results substantiate the complex nature of quantitative traits, and further challenge the expectations of applying the results of a few discrete associations directly to the simultaneous improvement of complex traits in forest trees.

表增加

augment;

• Use of vegetative propagation should be an efficient way to augment gains in growth rate with improvements in wood quality, form, and disease resistance.
• The studied seed crop was produced under ambient temperature环境温度 (i.e. no reproductive phenology manipulation) and pollination was augmented by pollen from within orchard’s pollen donors.

表明表现

display

show

present

demonstrate

indicate

reveal

exhibit

• It exhibits physiological plasticity and is successfully grown inmany parts of the world that are not subject to continental winter cold conditions (Moura et al. 2012).

manifest

• If loci with heterozygote advantage are common, artificial selection in agricultural species should, at least in part, select for strains that manifest substantial heterosis.
• Inbreeding depression may be manifested in many ways.
• Some of these QTLs may manifest their effects on endoreduplication via expression in the embryo.
• However, these genetic details did not manifest themselves in any noticeable pattern or correlation among GCA and SCA effects.
• Quantitative genetic mapping approaches have exploited this phenotypic manifestation to identify putatively imprinted loci affecting the expression of ‘complex’ traits. (同义词appearance)

表导致造成-强调结果

lead to

• While CM yielded estimates of ρAdAc that were equal to those of CSM (−0.85), ignoring the environmental heterogeneity** led to** overestimation of the environmental competition effects; i.e., CM yielded higher ^σ2 p than the estimate from CSM (1.21 vs. 0.98, respectively). 忽略环境异质性会导致高估环境竞争效应
• Knowing that differences in management practices in the same seed orchard led to the different estimates of contamination when assessed using loci drawn from the same marker set and using the same assignment method, it is more likely that differences in management contributed to the differing contamination estimates between the orchard’s 2005 and 2009 seed crops, though temporal variation in outside- and within-orchard paternal fecundity cannot be discounted as primary sources. 管理措施不同会导致不同的污染估计

cause

• A partitioning of these significantreciprocal effects suggests either maternal (e.g. cytoplasmic DNA effect) and non-maternal effects (e.g.interaction effect between nuclear and cytoplasmic DNA) or purely non-maternal interaction may be the causes of the reciprocal effects. 母本和非母本效应可能是正反交效应引起的

result in

• Additive genetic correlations between oleoresin yield and the growth traits were positive and moderately high, suggesting that directional selection to improve growth in loblolly pine will also result in increased production of oleoresin.

表程度

degree/extent to which

• This interacting phe- notype covariance is important because it measures the degree to which a particular trait covaries with the selective environment provided by conspecifics
• The social selection gradient identifies the degree to which a trait expressed in one individual affects the fitness of other individuals.
• This coefficient measures the degree to which the phenotypes of the two individuals interact to determine the fitness of the focal individual.
  
  • 该系数测量两个人的表型相互作用的程度，以确定焦点个体的适应度。
• The degree to which genetic variation is unique to individual disorders or shared across disorders is unclear.
  
  • 遗传变异对个体病症或跨疾病共有的程度尚不清楚。
• We cannot now determine the degree to which our results might have been influenced by between-site differences in the kinds of patients seen or in their assessments.
  
  • 我们现在不能确定我们的结果可能受到所见或患者评估类型间差异的影响程度。
• While genes with large effects have probably been important in trait evolution, the extent to which the same genes have contributed to parallel evolutionary changes in multiple lineages is unknown.
  
  • 虽然具有大效应的基因在性状进化中可能是重要的，但同一基因在多个谱系中平行进化变化的贡献程度是未知的。

magnitude

• However, the magnitude of effect of each individual association has been small, rarely exceeding 5% of the phenotypic variance.

表时间、年龄

age

• At age ten and a half, five traits (DBH, stem straightness, branch angle, branch size and cluster whorl number) were assessed at four sites. 在十岁半时

century

• This is the case in 21 sets of a 6 x 6 half-diallel mating scheme for radiata pine Australia-wide in the early 1980s.
• Last, we identify divergent lineages of dogs distinct from those breeds that radiated during the nineteenth century and that probably derive from ancient geograph- ically indigenous breeds.
• Similar to the rapid changes in other disciplines during the twentieth century, plant breeding has changed from selection based on the phenotype of individuals to selection based on the information derived at the deoxyribonucleic acid (DNA) level in molecular genetic laboratories and data from replicated field experiments.
• Moreover, the first modern sugar beet came from selections made in the middle of the eighteenth century from white fodder beets grown in German Silesia (modern day Poland), described as high-sugar content fodder beets (Fischer 1989).
• This feels natural, but as Shafer (1990) identified, ‘the rise of frequentism’ in probability came only** in the mid-19th century **from the writings of empiricist philosophers such as John Stuart Mill.
• The 20th century brought a strong dichotomy.
• in this connection Fisher noted the special role of Galton (1822-1911) in the birth of modern statistics towards the end of the 19th century.
• A classic example of an empirical model is **the 18th century **Bode’s geometric law of progression of the planetary distance dk from the Sun.

表原因

due to

due to = expected to, or caused by 不好结果的原因，能用because of 就不用这个词
- The genetic analysis of size change with increasing age, i.e., growth, has received considerable attention in quantitative developmental genetic studies, but the genetic architecture of ontogenetic changes in body shape and its associated allometry have been poorly understood partly due to the lack of analytical tools.
- We present a general Bayesian model for analyzing diallel data on dioecious diploid inbred strains that cleanly decomposes the observed patterns of variation into biologically intuitive components, simultaneously models and accommodates outliers, and provides shrinkage estimates of effects that automatically incorporate uncertainty due to imbalance, missing data, and small sample size.
- However, due to rapid developments in marker technology, statistical methodology for identifying quantitative trait loci (QTLs) and the jargon used by molecular biologists, the utility of DNA markers in plant breeding may not be clearly understood by non-molecular biologists.
- However, tension zones have a tendency to become trapped by, and therefore to coincide with, exogenous barriers due to ecological selection.
- Due to finite population size (Ne?100), the marker haplotypes were in linkage disequilibrium with the QTL located between the markers.

result from

• The biological and statistical advantages of functional mapping result from joint modeling of the mean-covariance structures for developmental trajectories of a complex trait measured at a series of time points.

result of

• It is important to determine whether the different phenotypes of these epithelia are the result of intrinsic divergence, extrinsic modulation, or a combination of both.

attribute

since

for

reason

研究目的

goal

• The major goal of this study was to investigate the relationship between heterosis and genetic distance determined with simple sequence repeat (SSR)markers.

aim

• The main aim of this study was to compare a number of recently proposed Bayesian and frequentist statistical methods for the estimation of genetic parameters and to apply the cross-validation (CV) approach in order to tune the variance components in simulated and field plant breeding datasets.
• The aim of the present research is to genetically analyze …
• Our aim is to draw attention to the various possibilities that are opening up using the new technologies, but we also highlight some of the pitfalls and drawbacks with these methods.
• Our aim was to estimate a mean value of the coancestry coefficient of the families present in a maritime pine Pinus pinaster Ait. (maritime or cluster pine) progeny trial originating from seed collected in a clonal seed orchard and to study how deviations from the standard assumption of theta = 0.125 affect heritability estimations.
• The aim of the present research is to genetically analyze …

objective

• The specific objectives of this study were to determine (i) if the genetic statistics obtained from Meth- ods 1 to 4, G&EII, and G&EIII would be the same, simi- lar, or different for a particular number of parental lines used in a diallel;
• The main objective of our study was to show how the recently proposed fast Bayesian inference method,INLA, can be used to estimate the genetic parametersin a plant breeding population with multiple randomfactors using animal models.
• The primary objective of our study was to develop a black spruce transcriptomic resource to facilitate on-going functional genomics projects related to growth and adaptation to climate change.
• The objective of this study was to quantify the physiological basis of heterosis for grain yield in maize by examining maize hybrids and their parental inbred lines** in terms of** grain yield and its component processes, dry matter accumulation (DMA) at maturity, and the partitioning of DMA to the grain (i.e., harvest index), as well as in terms of the physiological processes underlying those two components.
• The objectives of /our study/ this study/ this article were/was to (1) explore the prediction accuracy of **genomic selection for plant height and yield per plant in soybean [Glycine max (L.) Merr.], (2) **discuss the relationship between prediction accuracy and numbers of markers, and (3) evaluate the effect of marker preselection based on different methods on the prediction accuracy.
• The objectives of this study were to (i) explore the patterns of population structure in the pollen parent heterotic pool using different methods, (ii) investigate the genome-wide distribution of genetic diversity, and (iii) assess the extent and genome-wide distribution of linkage disequilibrium (LD) in elite sugar beet germplasm.
• The objectives of this study were to estimate heterosis and combining ability of 15 European winter B. rapa cultivars for biomass yield at end of flowering.
• The objective of this study was to investigate the age of transition from juvenile to mature wood and quantify genetic control in time of transition from juvenile to mature wood using 1866 radiata pine samples.
• The objective of this study was to determine the genetic location and effects of genomic regions controlling wood density at three stages, i.e., rings corresponding to ages 1-5 (WD1-5), rings corresponding to ages 6-10 (WD6-10), and outer wood density (WD14) in a full-sib pedigree (850.055x850.096) of Pinus radiata .
• The objective of this study was to develop a soybean core collection of the USDA Soybean Germplasm Collection by comparing the results of random, proportional, logarithmic, multivariate proportional and multivariate logarithmic sampling strategies.
• Our objectives were to assess the response due to genome wide selection compared with marker-assisted-recurrent selection (MARS) and to determine, the extent to which phenotyping can be minimized and genotyping maximized in genomewide selection.
• The objective of this study was to identify molecular markers linked to sex determina-tion loci in the dioecious plant Salix viminalis L.
• The primary objective of our study was to develop a black spruce transcriptomic resource to facilitate on-going functional genomics projects related to growth and adaptation to climate change.
• Our research objectives are to lean about genome organization and to identify markers associated with adaptive traits.
• The main objective of this study was to describe trends in genetic\nparameters for wood density and radial growth through cambial age in a\nradiata pine progeny test established in the south of Chile.
• The main objectives for establishing these trials were to: (1) characterize the genetic architecture among and within these provenances; and (2) determine the relative genetic worth of these provenances for possible inclusion in advanced-generation breeding programs in the Coastal Plain in the southeastern United States.
• Objectives of the present research was to determine the mean performance and correlations of parents, direct and reciprocal crosses in bread wheat varieties for different yield components under 6X6 diallel combinations.
• The objectives of this research were to survey the level of population structure and the extent of LD in oat germplasm and determine their implications for GWAS.
• The main objectives of this study were to (1) investigate genetic diversity within germplasm groups of elite European maize (Zea mays L.) inbred lines, (2) examine the population structure of elite European maize germplasm, and (3) determine the extent and genomic distribution of LD between pairs of simple sequence repeat (SSR) markers.
• The objectives of this study were to classify NDlines into heterotic groups and to evaluate the consistency between SSR grouping and test cross field data.
• The objective of this case study was to obtain some first-hand information about the functional consequences of a cosmetic tongue split operation for speech and tongue motility.
• The objective of this study was to integrate a large set of SSR markers from a variety of sources and published cDNA markers into a composite P. taeda genetic map constructed from two reference mapping pedigrees.
• The objectives of the present study were to (1) examine the optimum choice of the biometrical model to compare yield stability of hybrids versus lines, (2) investigate whether hybrids exhibit a more pronounced grain yield performance and yield stability, and (3) study optimal strategies to predict yield stability of hybrids.
• The objectives of this study were to (i) examine the association between parental genetic distance (GD) and specific combining ability (SCA), (ii) investigate the existence of genetically distant heterotic groups in elite germplasm, and (iii) draw conclusions for future hybrid breeding in winter triticale.
• The objective of this candidate gene case-control study was to characterize the distribution of polymorphisms in three candidate genes related to the immune function; interferon gamma (BoIFNG), toll-like receptor 4 (TLR4), and SLC11A1 genes and to test their role as potential risk factors for paratuberculosis infection in cattle.
• The specific objectives of this study were to ascertain in radiata pine…
• the present study was conducted with three main objectives: (i) to investigate the inheritance of various wood properties including wood density, stiffness, strength, internal checking, and external resin bleeding; (ii) to estimate genetic correlations between wood properties and between growth trait and wood properties; and (iii)to estimate the magnitude of G×E interaction for various wood properties.
• We focused on three main objectives, (1) to comparatively assess the prediction performance of pedigree-based and genomic best linear unbiased prediction within and across breeding cycles, (2) to gain insight into the main compo- nents driving prediction performance across subsequent breeding cycles, and (3) to develop recommendations for model training to obtain maximum across-cycle prediction accuracies.
• The objectives of the present research were to (1)
  evaluate the magnitude of yield heterosis among lines grouped by molecular markers and yield performance; (2) examine the consistency between marker based group and yield performance; (3) analyze combining ability effect for yield and yield components of the selected lines and its hybrids; and (4) explicate the utilization of positive loci (PLs) including effective- increasing loci (ILs) and effective-decreasing loci (DLs) for the prediction of heterosis for yield and yield components.
• Therefore, one of the objectives of this study was to search for evidence of recombination repression due to the heterogeneous genetic background of the hybrid.
• The objectives of most programs are to increase the economic value of specific traits of interest while conserving genes identi- fied as potentially advantageous under future environ- mental regimes, and maintaining a threshold level of genetic diversity in the offspring for future selection and environmental adaptation (Burdon & Shelbourne 1971).
• The objective of this study is to investigate the variation in heartwood content at different genetic levels, to determine its heritability and its relationships with other growth traits.
• Our objective was to understand the extent and type of genetic control of these traits in the F1, the importance of environmental effects on these traits, and the genetic relationships between wood properties and other commercial traits.
• The objectives of this study were to: understand the inheritance of flavour volatiles in a clonally replicated germplasm population; unravel correlation networks of volatiles; and to use genome-wide single nucleotide polymor- phism (SNP) markers to identify genomic regions that play a role in the expression of flavour volatiles.

to

我们的研究工作（非文章本身）是在过去完成的，所以使用过去式。

• Thus, the present study was initiated to examine the heritability, genetic correlations, and individual breeding values for stem straightness, growth traits, and survival in a breeding population of E. globulus established under cold conditions in southern Chile, using the Bayesian inference as methodology of prediction of genetic parameters.

连接、转折-副词-连词

contrast; also； Consequently； Therefore； however； thus；Moreover；

moreover

• Moreover, with respect to此外，关于林木 forest trees, delays before the assessment of individual performances are long (Neale and Will- iams 1991), and a strategy for predicting heterosis before making the crosses and thereby reducing the number of combinations to be tested would be particularly desirable.

contrast

• In contrast相比之下, long-term selection gain benefits from genetic variance, which is associated with a large effective population size of the heterotic pattern.

also 此外

• If there are reciprocal (or rather, favourable maternal) effects for crosses involving this particular clone, theseeffects cannot be readily used because the clone is bestused as a male. Also, in some large factorial or disconnected half-diallel experiments, there are always someprescribed crosses that cannot be made or are verydifficult to make owing to unavailability of matureramets, insufficient flowers, poor pollen viability orpoor mating success.

Consequently

• Consequently, criteria for maximizing high short-term selection gains without promptly diminishing genetic variance are required in the search for heterotic patterns, but such approaches are not yet in place.

Therefore

• Therefore, this cloneis preferred as a male in practical mating designs and incontrolled pollination for producing commercial seeds

as such 因此

• As such, they constrain, and are constrained by the choice of breeding strategy and the management of co-ancestry.

副词 adv

occasionally

• sometimes, but not regularly and not often；In everyday English, people often say once in a while rather than occasionally. 在日常英语中，人们常说once in a while，而不说occasionally
• Occasionally, the experimental design or the popu-lation structure is such that the macros cannot be used directly.
• The mean daily temperature during summer is consistently above 10 8C (occasionally up to 32-35 8C), and the longest day of the year (approximately 19 hours) is around midsummer in the southern Finland.
• A total of 177 trees from37 families (Tab. I) were sam- pled to cover the same range of eight subraces sampled by Apiolaza et al. [1], with one tree or occasionally two trees per plot sampled.
• The occasionally very high sum of PVE depicted for a few association mapping analyses in Fig. 4a (even biologically unreasonable) should in this context be interpreted cautiously, as they stem from起源于 the naive PVE sum- mation of a great number of detected loci that are often in LD with each other and possibly also inflated due to the Beavis effect

successively 陆续 先后 依次

• During Newton–Raphson iterations of the REML algorithm, step lengths of variance component estimate updates are successively reduced until all variance estimates are nonnegative.
• At the first step, single PCs were successively omitted, and for each omission, a measure of uniformity of map coverage by the remaining primer combinations was calculated.
• As it can be seen from the relationships among experimental and causal variance components, s2 a and s2 f contain portions of epistasis with successively decreasing contributions of interactions involving larger groups of loci.
• This will often involve an iterative process, in which the treatment structure is successively fine-tuned to address all relevant research questions.
• A very simple alternative way to generate an augmented p-rep design across locations is to generate a two-replicate resolvable incomplete block design, such as an a-design, for replicated entries at each location and then augment these successively in a one-by-one fashion with un- replicated entries.
• To decrease computation time while ensuring different SNPs to be tested within genes, association tests were also performed on a subset of SNPs defined as above with a less stringent cut-off value of 0.2 successively applied to the 160 G0 trees and the 28 unrelated G1 trees.
• We did this by assuming that the QTL having the largest true PVE would be most easy to detect and, given the distribution, subsequent QTL with smaller PVE would be successively detected, with increasing population size, until the desired amount of genetic variance was explained.

hereinafter 以下，在下文中

• Seven clones of eastern cottonwood (Table l), (hereinafter termed cottonwood) were chosen at random from the tree improvement programs of Crown Zellerbach
• Hereinafter, it is assumed that the distribution of x is continuous, and a continu- ous kernel function is employed throughout, as an approximation.
• Alternatively, this matrix can be derived from molecular marker information (hereinafter denoted as Am
• The trait was grain yield (GY). Hereinafter we refer to this data set as wheat-grain yield (W-GY).
• The ability of a model to predict yet-to-be observed phenotypes (hereinafter referred to as PA, for prediction accuracy) constitutes one of its most important properties from the perspective of its potential use for preventive and personalized medicine.
• For the ease of notation, hereinafter L2E means pL2E.

satisfactorily 令人满意地

• However, this model cannot satisfactorily explain how a dupli- cate gene can escape the load of deleterious mutations that would probably accumulate before enough beneficial mutations could confer a new function
• These effects often cannot be satisfactorily separated due to the limited size of datasets and our limited understanding of spatial processe
• If the two velocities differed more than 0.1 m/ms, additional series were taken to get a satisfactorily precision.
• Although parametric growth models has the advantage of relatively simple and parsimonious presentation and prediction, alternative semi-parametric or nonparametric methods may need to be considered when the parametric models do not fit the data satisfactorily
• In many situations, there may be no explicit growth curves that fit longitudinal data satisfactorily.
• Graphi- cal displays such as biplots can be particularly useful with large diallels for which it may be cumbersome笨重 to extract all information from tabulated summaries, but unfortunately the chances of finding a simple multiplicative model that satisfactorily represents the underlying interaction pattern tend to diminish with increasing size of the diallel.
• Certainly, spatial correlation may be extended across the whole field, but the assumptions underlying such models are less likely to hold satisfactorily than when restricted to within-block covariance.
• Besides competition by pollen from other sources, the suc- cess rate of SMP may be influenced by other factors including the prevailing environmental conditions at flowering and the number of occasions a graft must be pollinated in order to achieve a satisfactorily high success rate.
• In this test, the null hypothesis is that the restricted model satisfactorily models the response and the alternative hypothesis is that the full model is significantly better.

additionally 此外另外

• In addition, we simulated 5,000 pairs of correlated traits with environmental correlations. We fixed the heritability to 0.5 and allowed the genetic correla- tion to vary from −1 to 1. Additionally, we added a shared environmental term to the model, mimicking scenarios for both negative and positive environ- mental correlation.
• However, their proposal does not solve the problem satisfactorily in large-scale and “messy” data

adversely； not good or favourable不利的，有害的，反面的

• The different scenarios studied showed that plantation harvest productivity was affected by tree genetics to some degree but was mainly affected through positive covariation with stem diameter. Harvest produc- tivity is thus unlikely to have been adversely affected by past selection.
• Volume and stem form were poorly correlated both genetically and phenotypically. Volume was adversely correlated, both genetically and phenotypically, with branch size. Stem form and branch size showed strong positive correlations. Intensive selection for growth was found to lead to reduced gains in stem form and branch size and vice versa.

Intuitively

• Intuitively, correlated traits amount to a form of replication. 直觉上，相关性状相当于重复的一种形式
• We intuitively believe that the dramatic drop in the cost of DNA marker information we have experienced should have immediate benefits in accelerating the delivery of crop varieties with improved yield, quality and biotic and abiotic stress tolerance.
• They also intuitively understand that in actions such as thinning they are manipulating the canopy and its leaf area.

alike

• The stronger the correlation, the more the individual estimates within a tree are alike compared with estimates from other trees.
• In other words, measurements from two neighbouring growth rings were more alike than those separated by several growth seasons.
• The presence of spatial trend would suggest that neighboring plots tend to be more alike than those farther apart

apart

• The two out- ermost annual rings were generally taken apart分拆 for fibre length analyses (results to be presented elsewhere).
• For x(t), there exists a critical value at which the relationship falls apart.
• Japanese wild soybean populations that are more than 10 km apart are likely to genetically different
• The matrix should reflect the correlation decay among B-spline knots that are farther apart, either row- or
  column-wise.

beneficial

• For the sugar beet and barley tri- als the baseline model outperformed the spatial models in the majority of cases, while in some cases the addition of a spatial component proved beneficial.
• The extended meadow fescue map reported here provides the opportunity for beneficial cross-species transfer of genetic knowledge, particularly from the complete ge- nome sequence of rice
• The benefits in response from using optimum rather than classical weights were very small. However, they assumed an infinite population and so there was no accumulation of inbreeding.
• It influences the rate of loss of genetic variation, the efficiency of natural selection, and the accumulation of beneficial and deleterious mutations
• A significant improvement for this trait will be extremely beneficial for breeders, as a poor seed production represents one of the most limit- ing factors in several breeding schemes. However, when improving SY, attention must be paid on its correlations with forage yield and digestibility
• During the review process we benefited from valuable contributions made by the editor in charge of this article and by three anonymous reviewers.
• However, recent studies on the genetics of conifer seed size, dormancy and germination have demonstrated that genotypic differences rep- resent a major and important component of the total variation observed for these attributes (Chaisurisri et al. 1992, El-Kass- aby et al. 1992, 1993b), indicating that a knowledge of the genetic differences in seed traits would be beneficial in the maintenance of the genetic diversity of seed crops.

clonally

• Here, we evaluated the utility of genomic selection in a Pinus taeda population of c. 800 individuals clonally replicated and grown on four sites, and genotyped for 4825 single- nucleotide polymorphism (SNP) markers.
• The 926 individuals in CCLONES were clonally propagated, and eight ramets (i.e. clones) of each individual were planted on each of four sites in the southeastern USA
• Genetic variances and selection efficiencies for growth traits of white spruce (Picea glauca (Moench) Voss) were estimated from clonally replicated full-sib progeny tests established both in nursery and field environments in New Brunswick

necessarily一定的，必然的

• It was concluded that heterozygotes were not necessarily advantageous for trait performance even among genotypes derived from such a highly heterotic hybrid.
• The result is that local adaptation explains where genetic breaks are positioned, but not necessarily their existence, which can be best explained by endogenous内生的 incompatibilities.
• Furthermore, ecological and endogenous selections are not necessarily independent.
• Factors listed above are not necessarily independent from each other, but they are connected and affect the predictions accuracies together.
• We develop a robust model for mapping QTLs in a non-equilibrium natural population in which individuals are not necessarily randomly mating due to various evolutionary forces.
• This review is intended for tree breeders, forest managers, scientist and students who are not necessarily familiar with genomic or quan- titative genetics jargon.
• It was concluded that vigorous精力旺盛的 open-pollinated progeny were indicative of暗示 high breeding value, but that the converse could not necessarily be claim- ed.
• Because TEST STATISTICS (such as Fst) from real data will not always follow assumed idealized null distributions, and because statistical evidence is not necessarily biological evidence for selection, false positives are inevitable.

commonly普遍，通常，一般

• DBH is the most commonly measured growth trait and has been the focus of numerous genetic studies to date
• In- terval mapping commonly used in QTL identification (Lander and Botstein 1989) is to use two flanking markers, M1 and M2, at the same time to predict the segregation of the QTL bracketed by the two markers.
• The other WGS effort used the subspecies indica, which is commonly grown in China.
• Open-pollinated families of forest trees are commonly assumed to comprise half-sibs, which would result in the event of panmictic mating, each offspring being the result of an outcross to a differentmale parent.
• However, this assumption is hardly fulfilled and it is commonly observed that only a small portion of any orchard’s parents predominantly con- tribute to the orchard seed crop

normally；正常地；通常地，一般地

• It may also be that these trials simply included wider genetic diversity than is normally included in tree breeding populations.
• The Pfr form of phytochrome normally suppresses 抑制this elongation and its removal in far-red–rich light releases this suppression.
• Expression of these genes normally peaks at dawn and, although this is still true in the phyABDE mutants, the peak level was reduced in the mutants for each of the genes examined.
• Allopolyploids such as wheat or cotton have undergone sufficient divergence that the duplicated chromosomes normally do not pair, and the sequences of gene pairs are usually distinguishable
• The randomeffects wereassumed to be normally distributed with an expected value of zero and to be independent of each other.

unrealistically 不切实际

• Increasing σ to 0.4 (TABLE 2, column 2) increases P[|θ|>1], but it also implies that 32 SNPs per million have |θ|>0.4, which may be regarded as unrealistically high.
• Thus in these well-behaved cases Davies’ (1987) approximation (3.4) to his upper bound for the p-value when the nuisance parameter α is present only under the alternative hypothesis is exactly that for a χ23 variable, which provides an intuitively unrealistically large bound for a test involving not more than two parameters.
• The Kackar-Harville method can be used to account for these errors, but that method was found to yield unrealistically high standard errors for spatial models (Hu et al., 2006) and so was not used here.
• There are few statistical assumptions made with this method, but it is highly sensitive to genotyping error and can lead to unrealistically high observed contaminant levels, espe- cially when considering the frequency of mutation, null alleles, and genotyping error inherent in using micro- satellites
• As expected, the genetic relationships (half-sib, and full-sib; Figure 1) within the studied 15 half-sib families should have reduced the average covariance among relatives within the HS model, thus the resulting additive genetic variance is unrealistically inflated.
• Furthermore, he showed that the range of estimates of Ne required for the neutral theory to be true was unrealistically narrow for the diverse groups of higher organisms considered.

inevitably

• If violation of these principles leads to a strong bias between cases and controls, EIGENSTRAT is likely to detect the bias; however, a loss in power will inevitably result, because any putative disease association will resemble an unusually strong instance of the bias
• Such wood is characterized by wide annual rings, and will inevitably contain a significant volume of juvenile wood.
• Secondly, if pedigree reconstruction and selection were practiced over multiple series of tested half-sibs, coancestry would inevitably increase due to selection of genetically superior fathers common (e.g. in the PMX) to the test series.
• Thus, temporary reductions in stand foliage (Fig. 7) inevitably result in the loss of at least some potential stand growth, but increases in individual tree growth.
• Using the Fisher test spreads the research investment over the full range of risk models, but this inevitably means investing less in the detection of additive risks.
• When the genetic diversity was increased by allowing more trees to contribute to the next generation, it inevitably meant a decrease in genetic gain compared to equal contribution after double pair mating and a fixed breeding population size
• Unless relationships between wood density and growth or biomass and C concentration are strongly negative, selection on fast-growth will inevitably lead to an increase in C sequestration.

strictly

• Doerge and Craig (2000) assumed preferential pairings; that is, pairings occur strictly between the same chromosomes in the set.
• Further comparisons with grape—a species basal to rosids but belonging to the Vitaceae, a strictly different, although related, family—introduce the possibility of comparing interfamily mole- cular distances.
• That is, all individ- uals belonging to a single OP family were strictly assigned to either the training or validation population.
• Also, the results of the estimation depend strictly on the population you are working with.

rigorously

• This suggests that, while the SNP data cannot be used to draw rigorously quantitative conclusions about the rela- tive levels of variation in the CAP populations, popula- tion-specific bias is not extreme in the BOPA markers.

拉丁短语

sensu lato广义地

• Dividing the breeding population (sensu lato) into reproductively isolated sublines is a method to avoid detrimental effects of inbreeding (e.g., McKeand and Beineke 1980; van Buijtenen 1984; Zobel and Talbert 1984; White 1992).

ad hoc: formed, arranged, or done for a particular purpose only

• The key idea is to directly simulate the quantity of interest, e.g., response to selection, rather than trying to approximate it using some ad hoc measure of heritability.
• some pro- grams use ad hoc methods or make no attempt to correct for experiment-wide error, making the interpretation of results difficult.
• We also experi- mented with ad hoc smoothing schemes to encourage a and r to vary smoothly across the genome.
• Therefore, the model becomes ad hoc if the real distri- bution has a relatively heavy negative tail
• Therefore, we used the ad hoc criterion described by Evanno et al. (2005) to estimate the number of subpopulations, as it promises to reliably detect the true number of subpopulations also in complex genetic situations.
• It is not obvious how this problem can be solved satisfactorily, although some ad hoc approaches have been suggested in the literature.

ex situ & in situ迁地保护，原地保护

• This marked differentiation for quantitative traits despite high ap- parent gene flow results in a clinal variation, which suggests the use of altitude of seed source as an important principle for in situ or ex situ management of E. urophylla genetic resources.
• The Ethiopian collection is composed of highly genetically diverse germplasm, and the genetic information presented herein is valuable to ex situ and in situ conservation programs to promote the use of this germplasm for breeding programs.

in vitro & in vivo活体外和活体内

• Both in vitro and in vivo ubiquitination assays showed that HOS1 is required for ICE1 ubiquitination.
• .For this reason,PCR slippage probably cannot be used to gain insight into the mutational dynamics of microsatellites in vivo.

per se

• Genetic distance per se between parental genotypes, based on neutral molecular markers, however, does not reflect the potential of individual genotypes to produce heterosis in their progeny.
• Correlations between mid-parent and hybrid performance and between GCA and per se performance of parents/hybrids were tight for all traits except grain yield, which allows for pre-selection of parental lines.
• African and Chilean exhibited the best parental performances per se and yielded similarly to the lower three checks.
• In these cases, researchers have turned away from mar- ker development per se and toward large scale sequenc- ing as a means to develop comparative datasets across very large phylogenetic spans (e.g.
• The most likely explanation for the maintenance of this coat colour polymorphism is that selection is not acting on coat colour per se but instead on fitness-associated genes that are in strong linkage disequilibrium with the coat colour locus.

vice versa

• Intensive selection for growth was found to lead to reduced gains in stem form and branch size and vice versa.
• This strong negative rela- tionship indicates that selection for reduced MFA would lead to gains in MOE throughout the juvenile core or vice versa.
• Different scenarios were simulated to study the loss of accuracy of prediction, if epistatic effects were not simulated but modelled and vice versa.
• The solution to the first problem actu- ally compounds the second and vice versa.
• The regression was fit with MM′ as dependent and A as independent variable instead of vice versa because A is the expected value of G, not vice versa.
• Ab- sorption of light by the chromophore causes it to change conformation and this, in turn, causes a change in con- formation of the phytochrome protein from the Pr form to the Pfr form or vice versa

存活率

survival

• The overall 12-year-old tree survival rates were 86%, 92%, and
  79% for the 2000, 2001, and 2002 series, respectively (Table 1).
• These survival rates were within the range observed in the NBTIC’s first- and second-generation jack pine family tests (Weng et al. 2007, 2015), suggesting that the second-cycle genetic selection on height growth did not reduce tree adaptation measured by survival from the previous generation.
• Overall mean survival across the three sites was 94 % at age 12 and slightly lower at age 35 (81 %) (Table 1). The submontane moist maritime site demonstrated the highest survival rates at both assessment ages.

比例

percentage

• annual percentage of mortality of the selected line decreased from 68% in the initial generation to 8.8% in the sixth generation, which was similar to that of the nonselected control (C) in single-bird cages (9.1%).
• The average percentage ratio of SCA variance to GCA variance was 36%, across all series and the 3 growth traits, with a range of 19% to 65%.
• As compared to the wild-type the presence of the mutant alleles reduced the degree of bronchodilator response by 20% in the original population and by a similar percentage in the confirmatory population.

变幅

range

• The mean correlation coefficients are ranging from −0.19 to −0.36