title: Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing.
abstract: BACKGROUND
  Artificial selection played an important role in the origin of modern Glycine max cultivars from the wild soybean Glycine soja. To elucidate the consequences of artificial selection accompanying the domestication and modern improvement of soybean, 25 new and 30 published whole-genome re-sequencing accessions, which represent wild, domesticated landrace, and Chinese elite soybean populations were analyzed.
  
  
  RESULTS
  A total of 5,102,244 single nucleotide polymorphisms (SNPs) and 707,969 insertion/deletions were identified. Among the SNPs detected, 25.5% were not described previously. We found that artificial selection during domestication led to more pronounced reduction in the genetic diversity of soybean than the switch from landraces to elite cultivars. Only a small proportion (2.99%) of the whole genomic regions appear to be affected by artificial selection for preferred agricultural traits. The selection regions were not distributed randomly or uniformly throughout the genome. Instead, clusters of selection hotspots in certain genomic regions were observed. Moreover, a set of candidate genes (4.38% of the total annotated genes) significantly affected by selection underlying soybean domestication and genetic improvement were identified.
  
  
  CONCLUSIONS
  Given the uniqueness of the soybean germplasm sequenced, this study drew a clear picture of human-mediated evolution of the soybean genomes. The genomic resources and information provided by this study would also facilitate the discovery of genes/loci underlying agronomically important traits.
authors.affiliation: Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) / Key Lab of Germplasm Utilization (MOA), Chinese Academy of Agricultural Sciences, 100081 Beijing, China. wangj@genomics.org.cn.
authors.forename: Ying-hui
authors.initials: YH
authors.lastname: Li
authors.forename: Shan-cen
authors.initials: SC
authors.lastname: Zhao
authors.forename: Jian-xin
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authors.lastname: Ma
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authors.forename: Long
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authors.lastname: Yan
authors.forename: Jun
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authors.forename: Xiao-tian
authors.initials: XT
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authors.forename: Xiao-sen
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authors.forename: Wei-ming
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authors.lastname: He
authors.forename: Ru-zhen
authors.initials: RZ
authors.lastname: Chang
authors.forename: Qin-si
authors.initials: QS
authors.lastname: Liang
authors.forename: Yong
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authors.lastname: Guo
authors.forename: Chen
authors.initials: C
authors.lastname: Ye
authors.forename: Xiao-bo
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authors.lastname: Wang
authors.forename: Yong
authors.initials: Y
authors.lastname: Tao
authors.forename: Rong-xia
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authors.lastname: Guan
authors.forename: Jun-yi
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authors.lastname: Wang
authors.forename: Yu-lin
authors.initials: YL
authors.lastname: Liu
authors.forename: Long-guo
authors.initials: LG
authors.lastname: Jin
authors.forename: Xiu-qing
authors.initials: XQ
authors.lastname: Zhang
authors.forename: Zhang-xiong
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authors.lastname: Liu
authors.forename: Li-juan
authors.initials: LJ
authors.lastname: Zhang
authors.forename: Jie
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authors.lastname: Chen
authors.forename: Ke-jing
authors.initials: KJ
authors.lastname: Wang
authors.forename: Rasmus
authors.initials: R
authors.lastname: Nielsen
authors.forename: Rui-qiang
authors.initials: RQ
authors.lastname: Li
authors.forename: Peng-yin
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authors.lastname: Chen
authors.forename: Wen-bin
authors.initials: WB
authors.lastname: Li
authors.forename: Jochen C
authors.initials: JC
authors.lastname: Reif
authors.forename: Michael
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authors.lastname: Purugganan
authors.forename: Jian
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authors.lastname: Wang
authors.forename: Meng-chen
authors.initials: MC
authors.lastname: Zhang
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Li-juan
authors.initials: LJ
authors.lastname: Qiu
mesh_terms: D001499:Bayes Theorem; D001947:Breeding; D019143:Evolution, Molecular; D005828:Genetics, Population; D018745:Genome, Plant; D006239:Haplotypes; D006801:Humans; D054643:INDEL Mutation; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D013025:Glycine max / Q000235:genetics*