Soybean genome variation revealed by high-depth resequencing of multiple cultivated and wild soybean genomes

Soybean is an important global crop for seed protein and oil content that has undergone substantial phenotypic and physiological changes during domestication. Here, we resequenced the genomes of 10 cultivated accessions and six accessions of their wild progenitors (Glycine soja) to >15 × mean depth. We investigated genome-wide variation patterns in soybean and obtained 5 million high-quality single nucleotide polymorphisms (SNPs) after excluding sites with missing data in any accession. Nuclear genome phylogeny strongly supported a single origin for cultivated soybean, although chloroplast genome phylogeny unexpectedly provided evidence of paleoallodipolidization.