title: Population structure and domestication revealed by high-depth resequencing of Korean cultivated and wild soybean genomes.
abstract: Despite the importance of soybean as a major crop, genome-wide variation and evolution of cultivated soybeans are largely unknown. Here, we catalogued genome variation in an annual soybean population by high-depth resequencing of 10 cultivated and 6 wild accessions and obtained 3.87 million high-quality single-nucleotide polymorphisms (SNPs) after excluding the sites with missing data in any accession. Nuclear genome phylogeny supported a single origin for the cultivated soybeans. We identified 10-fold longer linkage disequilibrium (LD) in the wild soybean relative to wild maize and rice. Despite the small population size, the long LD and large SNP data allowed us to identify 206 candidate domestication regions with significantly lower diversity in the cultivated, but not in the wild, soybeans. Some of the genes in these candidate regions were associated with soybean homologues of canonical domestication genes. However, several examples, which are likely specific to soybean or eudicot crop plants, were also observed. Consequently, the variation data identified in this study should be valuable for breeding and for identifying agronomically important genes in soybeans. However, the long LD of wild soybeans may hinder pinpointing causal gene(s) in the candidate regions.
authors.affiliation: 1Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea.
authors.forename: Won-Hyong
authors.initials: WH
authors.lastname: Chung
authors.forename: Namhee
authors.initials: N
authors.lastname: Jeong
authors.forename: Jiwoong
authors.initials: J
authors.lastname: Kim
authors.forename: Woo Kyu
authors.initials: WK
authors.lastname: Lee
authors.forename: Yun-Gyeong
authors.initials: YG
authors.lastname: Lee
authors.forename: Sang-Heon
authors.initials: SH
authors.lastname: Lee
authors.forename: Woongchang
authors.initials: W
authors.lastname: Yoon
authors.forename: Jin-Hyun
authors.initials: JH
authors.lastname: Kim
authors.forename: Ik-Young
authors.initials: IY
authors.lastname: Choi
authors.forename: Hong-Kyu
authors.initials: HK
authors.lastname: Choi
authors.forename: Jung-Kyung
authors.initials: JK
authors.lastname: Moon
authors.forename: Namshin
authors.initials: N
authors.lastname: Kim
authors.forename: Soon-Chun
authors.initials: SC
authors.lastname: Jeong
mesh_terms: D001483:Base Sequence; D001947:Breeding; D002874:Chromosome Mapping; D019143:Evolution, Molecular; D018745:Genome, Plant; D008969:Molecular Sequence Data; D056910:Republic of Korea; D017422:Sequence Analysis, DNA; D013025:Glycine max / Q000235:genetics*
keywords: domestication; resequencing; soybean; variation