title: Landscape of genomic diversity and trait discovery in soybean.
abstract: Cultivated soybean [Glycine max (L.) Merr.] is a primary source of vegetable oil and protein. We report a landscape analysis of genome-wide genetic variation and an association study of major domestication and agronomic traits in soybean. A total of 106 soybean genomes representing wild, landraces, and elite lines were re-sequenced at an average of 17x depth with a 97.5% coverage. Over 10 million high-quality SNPs were discovered, and 35.34% of these have not been previously reported. Additionally, 159 putative domestication sweeps were identified, which includes 54.34 Mbp (4.9%) and 4,414 genes; 146 regions were involved in artificial selection during domestication. A genome-wide association study of major traits including oil and protein content, salinity, and domestication traits resulted in the discovery of novel alleles. Genomic information from this study provides a valuable resource for understanding soybean genome structure and evolution, and can also facilitate trait dissection leading to sequencing-based molecular breeding.
authors.affiliation: Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia 65211, USA.
authors.forename: Babu
authors.initials: B
authors.lastname: Valliyodan
authors.affiliation: Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia 65211, USA.
authors.lastname: Dan Qiu
authors.affiliation: Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia 65211, USA.
authors.forename: Gunvant
authors.initials: G
authors.lastname: Patil
authors.affiliation: Beijing Genomics Institute-Shenzhen, Shenzhen, 518083, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Zeng
authors.affiliation: Beijing Genomics Institute-Shenzhen, Shenzhen, 518083, China.
authors.forename: Jiaying
authors.initials: J
authors.lastname: Huang
authors.affiliation: Beijing Genomics Institute-Shenzhen, Shenzhen, 518083, China.
authors.forename: Lu
authors.initials: L
authors.lastname: Dai
authors.affiliation: Beijing Genomics Institute-Shenzhen, Shenzhen, 518083, China.
authors.forename: Chengxuan
authors.initials: C
authors.lastname: Chen
authors.affiliation: Beijing Genomics Institute-Shenzhen, Shenzhen, 518083, China.
authors.forename: Yanjun
authors.initials: Y
authors.lastname: Li
authors.affiliation: Department of Molecular Microbiology and Immunology and Medical Research Office, School of Medicine, University of Missouri, Columbia, 65212.|Department of Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, 65211, USA.
authors.forename: Trupti
authors.initials: T
authors.lastname: Joshi
authors.affiliation: Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia 65211, USA.
authors.forename: Li
authors.initials: L
authors.lastname: Song
authors.affiliation: Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia 65211, USA.
authors.forename: Tri D
authors.initials: TD
authors.lastname: Vuong
authors.affiliation: Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia 65211, USA.
authors.forename: Theresa A
authors.initials: TA
authors.lastname: Musket
authors.affiliation: Department of Molecular Microbiology and Immunology and Medical Research Office, School of Medicine, University of Missouri, Columbia, 65212.
authors.forename: Dong
authors.initials: D
authors.lastname: Xu
authors.affiliation: Division of Plant Sciences and NCSB, University of Missouri-Fisher Delta Research Center, Portageville, MO, 63873, USA.
authors.forename: J Grover
authors.initials: JG
authors.lastname: Shannon
authors.affiliation: Beijing Genomics Institute-Shenzhen, Shenzhen, 518083, China.
authors.forename: Cheng
authors.initials: C
authors.lastname: Shifeng
authors.affiliation: Beijing Genomics Institute-Shenzhen, Shenzhen, 518083, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Liu
authors.affiliation: Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia 65211, USA.
authors.forename: Henry T
authors.initials: HT
authors.lastname: Nguyen
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping; D014644:Genetic Variation; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D059014:High-Throughput Nucleotide Sequencing; D000069600:Plant Breeding; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable; D017422:Sequence Analysis, DNA; D013024:Soybean Oil / Q000096:biosynthesis / Q000235:genetics*; D013025:Glycine max / Q000235:genetics*
chemical_list: D013024:Soybean Oil