Putative variants, genetic diversity and population structure among Soybean cultivars bred at different ages in Huang-Huai-Hai region

Abstract

Abstract Soybean cultivars bred in the Huang-Huai-Hai region (HR) are rich in pedigree information. To date, few reports have exposed the genetic variants, population structure and genetic diversity of cultivars in this region by making use of genome-wide resequencing data. To depict genetic variation, population structure and composition characteristics of genetic diversity, a sample of soybean population composed all by cultivars was constructed. We re-sequenced 181 soybean cultivar genomes with an average depth of 10.38×. In total, 11,185,589 single nucleotide polymorphisms (SNPs) and 2,520,208 insertion-deletions (InDels) were identified on all 20 chromosomes. A considerable number of putative variants existed in important genome regions that may have an incalculable influence on genes, which participated in momentous biological processes. All 181 varieties were divided into five subpopulations according to their breeding years, SA (1963–1980), SB (1983–1988), SC (1991–2000), SD (2001–2011), SE (2012–2017). PCA and population structure figured out that there was no obvious grouping trend. The LD semi-decay distances of sub-population D and E were 182 kb, and 227 kb, respectively. Sub-population A (SA) had the highest value of nucleotide polymorphism (π). With the passage of time, the nucleotide polymorphism of SB and SC decreased gradually, however that of SD and SE, opposite to SB and SC, gave a rapid up-climbing trend, which meant a sharp increase in genetic diversity during the latest 20 years, hinting that breeders may have different breeding goals in different breeding periods in HR. Analysis of the PIC statistics exhibited very similar results with π. The current study is to analyze the genetic variants and characterize the structure and genetic diversity of soybean cultivars bred in different decades in HR, and to provide a theoretical reference for other identical studies.