title: Genome re-sequencing of semi-wild soybean reveals a complex Soja population structure and deep introgression.
abstract: Semi-wild soybean is a unique type of soybean that retains both wild and domesticated characteristics, which provides an important intermediate type for understanding the evolution of the subgenus Soja population in the Glycine genus. In this study, a semi-wild soybean line (Maliaodou) and a wild line (Lanxi 1) collected from the lower Yangtze regions were deeply sequenced while nine other semi-wild lines were sequenced to a 3-fold genome coverage. Sequence analysis revealed that (1) no independent phylogenetic branch covering all 10 semi-wild lines was observed in the Soja phylogenetic tree; (2) besides two distinct subpopulations of wild and cultivated soybean in the Soja population structure, all semi-wild lines were mixed with some wild lines into a subpopulation rather than an independent one or an intermediate transition type of soybean domestication; (3) high heterozygous rates (0.19-0.49) were observed in several semi-wild lines; and (4) over 100 putative selective regions were identified by selective sweep analysis, including those related to the development of seed size. Our results suggested a hybridization origin for the semi-wild soybean, which makes a complex Soja population structure.
authors.affiliation: Department of Agronomy & James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Qiu
authors.affiliation: Department of Agronomy & James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Department of Agronomy & James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, China.
authors.forename: Sanling
authors.initials: S
authors.lastname: Wu
authors.affiliation: Department of Agronomy & James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, China.
authors.forename: Ying-Ying
authors.initials: YY
authors.lastname: Wang
authors.affiliation: Department of Agronomy & James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, China.
authors.forename: Chu-Yu
authors.initials: CY
authors.lastname: Ye
authors.affiliation: Department of Agronomy & James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, China.
authors.forename: Xuefei
authors.initials: X
authors.lastname: Bai
authors.affiliation: Department of Agronomy & James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, China.
authors.forename: Zefeng
authors.initials: Z
authors.lastname: Li
authors.affiliation: Department of Agronomy & James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, China.
authors.forename: Chenghai
authors.initials: C
authors.lastname: Yan
authors.affiliation: Department of Agronomy & James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, China.
authors.forename: Weidi
authors.initials: W
authors.lastname: Wang
authors.affiliation: Department of Agronomy & James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, China.
authors.forename: Ziqiang
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Institute of Nuclear Agricultural Science, Zhejiang University, Hangzhou, China.
authors.forename: Qingyao
authors.initials: Q
authors.lastname: Shu
authors.affiliation: Department of Pharmaceutical Sciences, North Carolina Central University, Durham, North Carolina, United States of America.
authors.forename: Jiahua
authors.initials: J
authors.lastname: Xie
authors.affiliation: Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Korea.
authors.forename: Suk-Ha
authors.initials: SH
authors.lastname: Lee
authors.affiliation: Department of Agronomy & James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, China.
authors.forename: Longjiang
authors.initials: L
authors.lastname: Fan
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D018744:DNA, Plant / Q000235:genetics*; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013025:Glycine max / Q000033:anatomy & histology / Q000145:classification* / Q000235:genetics*
chemical_list: D018744:DNA, Plant