title: Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection.
abstract: We report a large-scale analysis of the patterns of genome-wide genetic variation in soybeans. We re-sequenced a total of 17 wild and 14 cultivated soybean genomes to an average of approximately ×5 depth and >90% coverage using the Illumina Genome Analyzer II platform. We compared the patterns of genetic variation between wild and cultivated soybeans and identified higher allelic diversity in wild soybeans. We identified a high level of linkage disequilibrium in the soybean genome, suggesting that marker-assisted breeding of soybean will be less challenging than map-based cloning. We report linkage disequilibrium block location and distribution, and we identified a set of 205,614 tag SNPs that may be useful for QTL mapping and association studies. The data here provide a valuable resource for the analysis of wild soybeans and to facilitate future breeding and quantitative trait analysis.
authors.affiliation: State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong. honming@cuhk.edu.hk
authors.forename: Hon-Ming
authors.initials: HM
authors.lastname: Lam
authors.forename: Xun
authors.initials: X
authors.lastname: Xu
authors.forename: Xin
authors.initials: X
authors.lastname: Liu
authors.forename: Wenbin
authors.initials: W
authors.lastname: Chen
authors.forename: Guohua
authors.initials: G
authors.lastname: Yang
authors.forename: Fuk-Ling
authors.initials: FL
authors.lastname: Wong
authors.forename: Man-Wah
authors.initials: MW
authors.lastname: Li
authors.forename: Weiming
authors.initials: W
authors.lastname: He
authors.forename: Nan
authors.initials: N
authors.lastname: Qin
authors.forename: Bo
authors.initials: B
authors.lastname: Wang
authors.forename: Jun
authors.initials: J
authors.lastname: Li
authors.forename: Min
authors.initials: M
authors.lastname: Jian
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.forename: Guihua
authors.initials: G
authors.lastname: Shao
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Samuel Sai-Ming
authors.initials: SS
authors.lastname: Sun
authors.forename: Gengyun
authors.initials: G
authors.lastname: Zhang
mesh_terms: D000383:Agriculture; D032461:Chromosomes, Plant / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics*; D007178:Inbreeding; D015810:Linkage Disequilibrium / Q000235:genetics; D009154:Mutation / Q000235:genetics; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D013025:Glycine max / Q000235:genetics*