seqkit根据基因id_AgriSeq 靶向测序法基因分型技术

有助于加速动植物育种项目的创新解决方案

分子育种技术可大幅减少农业动植物品种改良所需的成本和时间。基因组技术的进步使得我们可以针对比以往更大的群体进行更高通量的基因分型，从而加速推进这类育种项目。Applied Biosystems AgriSeq 靶向测序法基因分型 (GBS) 解决方案是我们最新的创新技术，可以帮助您更经济地进行高通量的动植物基因分型。

每天可检测多达 260 万个基因分型位点，每个位点仅需几美分的成本

AgriSeq 靶向 GBS 解决方案利用高效的超多重 PCR 反应，在单次反应中可靶向并一致的扩增数百乃至数千个位点。之后，可对扩增子文库进行条码标记和混合，以便在 Ion Torrent 新一代测序 (NGS) 系统上同时进行数百份样品的测序分析。AgriSeq 靶向 GBS 技术对于每个位点的基因分型成本仅为几美分甚至更低，因此每天能从高质量的 NGS 数据中获得多达 260 万个基因型结果。无论您是希望实现更准确的标记辅助育种选择，还是要改善您的家畜亲缘分析和性状监测，我们的解决方案都可以帮助您推进您的动植物育种项目。

可扩展的基因分型技术

AgriSeq 基因分型技术采用 Ion Torrent NGS 平台运行，经验证每份样品可同时检测 100-5,000 个位点。采用 Ion 540 芯片，AgriSeq 基因分型技术可实现每张芯片产出高达 800,000 个基因型结果，平均读取深度为 100x，从而实现最大的基因型检出率。不同的panel，以及不同的物种，均可在同一次实验中运行。

可重现的结果

对于各种样品均可实现高的位点检出率和更高的重现性，有助于确保精确的选择。AgriSeq 靶向 GBS 技术的位点检出率可超过 96%，同时保证 >99% 的运行间和运行内的重现性。AgriSeq 靶向 GBS 的数据能够与正交基因分型技术(如 基因芯片技术)保持高一致性 (>99%)。

快速、简单的工作流程

包括文库构建、自动模板制备、测序和数据分析在内的操作流程可在约 2 天内完成，且手动操作时间 <4 小时，从而使每位实验人员每天可处理多达 4 块 96 孔板或 384 孔板。Ion Chef 系统可自动进行模板制备和芯片上样——仅需 15 分钟手动操作时间——然后进行过夜运行。

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AgriSeq companion animal and livestock genotyping solutions

Key features of AgriSeq ready-to-use panels include:

Reproducible genotyping of ISAG-recommended markers for all species with high call rates

Simple, high-throughput workflow

Customizable approach to combine with compatible parentage, traits or disorders, or additional markers of interest

The AgriSeq Canine Traits and Disorders Panel contains 154 markers targeting clinically important genetic traits and disorders in canines. The panel includes 97 SNPs and complex markers such as 6 MNPs, 13 insertions, and 38 deletions. Most of these markers are common to all breeds, while some are breed specific for certain traits and conditions. The performance of the panel was verified using orthogonal testing, robustness testing, and field testing with diverse DNA samples from canine oral swabs. The panel enables multiplexed simultaneous genotyping of 154 markers to deliver reliable genotyping results for 136 genetic disorders and 18 traits using the AgriSeq targeted GBS workflow. The CanFam 3.1 reference genome is used for the analysis.

Contains 379 SNPs and 2 deletion markers designed to deliver reliable genotyping results for parentage The AgriSeq Canine SNP Parentage and Identification Panel contains 379 SNPs and 2 deletion markers designed to deliver reliable genotyping results for parentage determination and identity verification of canines by targeted GBS. The panel enables multiplexed simultaneous genotyping using the AgriSeq targeted GBS workflow. The performance of the panel was verified using orthogonal testing, robustness testing, and field testing with diverse DNA samples from canine oral swabs. The panel was also qualified using the 2019 ISAG/ICAR 2nd SNP Typing Canine Comparison samples. The CanFam 3.1 reference genome is used for the analysis.

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Figure 1. Performance of AgriSeq canine panels. Call rates were calculated for both panels after testing >180 diverse DNA field samples from canine oral swabs with the AgriSeq workflow. The mean call rate for the AgriSeq Canine Traits and Disorders Panel was 99.1% (A), and for the AgriSeq Canine SNP Parentage and Identification Panel was 99.2% (B), demonstrating the high performance obtained from customer samples.

The AgriSeq Feline Parentage and Identification Plus Traits and Disorders (PITD) Panel is a combined panel for determining parentage and identification (111 SNP markers) plus targeting 64 clinically important traits and disorders (43 SNP, 1 MNP, 4 insertion, and 16 deletion markers) in felines by targeted GBS. The performance of the panel was verified using orthogonal testing, robustness testing, and field testing with diverse DNA samples from feline oral swabs (Figure 4). The 111 SNP parentage and ID markers were also qualified using the 2019 ISAG/ICAR 2nd SNP Typing Feline Comparison samples. The comprehensive AgriSeq Feline PITD Panel is designed to deliver reliable genotyping results for parentage determination, including identity verification and prediction of 42 genetic disorders and 22 traits that are clinically important. When desired, additional custom markers referencing the Felis_catus_8.0 can be added if compatible.

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Figure 2. Performance of AgriSeq Feline panel. A total of 258 feline oral swab DNA samples were tested either in duplicate or in quadruplicate with the AgriSeq workflow using the AgriSeq Feline PITD kit. The call rate, the number of markers generating a genotype call for each sample, was calculated for all samples with at least 100x mean read depth, the minimum recommended. The mean call rate was 99.3% and all samples had call rates >92.5%, demonstrating the high performance obtained from field samples.

The Applied Biosystems Bovine ISAG SNP Parentage Panel (2013) contains primers targeting the 200 ISAG-recommended SNPs available for simple multiplexed analysis using the AgriSeq targeted GBS workflow. The ISAG has standardized a set of 100 core SNPs and 100 additional SNPs with sufficient minor allele frequency (MAF) and genomic spacing for accurate bovine parentage determination across a wide range of breeds (Figure 5). You can download SNP information from the ISAG website [3]. Qualified using the 2015 ISAG/ICAR 3rd SNP Typing Bovine Comparison samples, our comprehensive Bovine ISAG Parentage Panel is designed to deliver reliable genotyping results for animal parentage testing. The Bos taurus reference genome is needed for analysis of the Bovine ISAG SNP Parentage Panel and can be obtained by contacting our technical support specialists.

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Figure 3. Performance of AgriSeq Bovine panel.Evaluation of 96 diverse bovine gDNA samples from the United States Department of Agriculture (USDA), representing 19 different breeds with the Bovine ISAG SNP Parentage Panel (2013), with 4 replicates each. All 384 individually barcoded libraries were pooled onto a single Ion 540™ Chip and sequenced on the Ion S5™ XL System. All but one of the samples tested gave a mean sample call rate of >95%. The mean call rate across all samples was 98.5%.

定制化的panel设计、验证和中间试验项目

农业基因组学工作的挑战性来自于很多原因，包括序列的复杂性、高遗传多样性和有限的可用序列。我们通过panel设计、湿实验室验证和数据分析提供端到端的项目管理服务，从而确保能为您的项目提供所需的高性能panel。这些低成本的概念验证中间试验项目是确认 AgriSeq 靶向 GBS技术适合于您的研究的好方法。

IonCode 条形码接头

IonCode 条形码接头是包含 768 种独特的条形码接头的一系列产品，它们可与 Ion Torrent 半导体测序系统配套实现最佳的性能。结合 AgriSeq高通量筛选建库试剂盒使用时，用户可混合多达 768 个扩增子文库进行多重测序分析，从而帮助您提高实验室效率并降低每份样品的测序成本。

Ordering information

A43406,A43407,A43408,A35297,A31975

A34143,A34144

A31173,A36546,A36524, A36525,A36526,A36527,A43540,A42849,A43541,A43562,A42962,A43542,A43559,A43730,A43729

A43558,A43557,A43543,A44671