A bumper crop of SNPs in soybean through high-density genotyping-by-sequencing (HD-GBS).

Abstract

Genome-wide association studies (GWAS) have revolutionized the investigation of complex traits over the past decade and have unveiled numerous useful genotype-phenotype associations. To be comprehensive, GWAS can require identifying and genotyping hundreds of thousands to millions of genome-wide genetic markers in large panels of accessions (Gupta et al., 2019). Similarly, many advances in crop genomics are closely tied to technological developments in next-generation sequencing (NGS). In general, NGS-based genotyping methods are classified in three categories, namely whole-genome re-sequencing (WGRS), SNP arrays, and reduced-representation sequencing (RRS; e.g. genotyping-by-sequencing (GBS)). While SNP arrays (e.g. SoySNP50K) and GBS are popular genotyping methods in many crop species, they often provide an insufficient number of markers for fine mapping and high-resolution GWAS studies (Patil et al. 2016), especially when highly diverse sets of accessions need to be characterized. In contrast, WRGS can generate high-density genome-wide genotyping data but, when performed on a large scale (thousands of samples), it can prove quite costly.