Difference between GWAS/MAS and GS

The difference between MAS and genomic selection is that MAS only utilizes the SNPs that are significant in a GWAS, whereas genomic selection uses a genome-wide panel of dense markers so that all QTL are expected to be  in LD with at least one marker. 

There are two advantages of genomic selection over MAS.

Firstly, potentially all the genetic variance for a trait can be tracked by the marker panel because the marker effect does not need to exceed the significance threshold to be used to predict breeding value.

Secondly, the marker effects are not biased upward by multiple testing — in contrast to using marker effects from GWAS. Because a large number of markers are tested against a significance threshold in a GWAS, it is likely to be the markers with favourable error terms that exceed the significance threshold.