Glycine max Variation

In this work, we perform a detailed examination of the imputation of missing genotypes in a catalog of SNP markers obtained via a genotyping by sequencing (GBS) approach among a collection of 301 soybean lines. In addition, we extend the work by using imputation to integrate two highly complementary SNP datasets (from GBS and a SNP array). In all cases, we measured the accuracy of genotype imputation through the resequencing of a subset of the lines and show that the resulting datasets are highly accurate. In a final segment of the work, we show that performing genome-wide association scans with superior marker coverage (resulting from marker imputation) leads to improved QTL detection.

本研究对301份大豆品系中通过测序基因分型（GBS）方法获得的SNP标记目录中缺失基因型的插补（imputation）进行了详细分析。此外，我们通过插补整合了两个高度互补的SNP数据集（分别来自GBS和SNP芯片（SNP array）），以此拓展了研究内容。在所有情况下，我们通过对部分品系进行重测序来评估基因型插补的准确性，并证明所得数据集具有极高的准确性。在研究的最后部分，我们发现使用标记插补获得的更优标记覆盖度进行全基因组关联扫描（genome-wide association scans），可提升数量性状位点检测（QTL detection）的效果。