Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing

Research output: Contribution to journalJournal articleResearchpeer-review

  • Ying-hui Li
  • Shan-cen Zhao
  • Jian-xin Ma
  • Dong Li
  • Long Yan
  • Jun Li
  • Xiao-tian Qi
  • Xiao-sen Guo
  • Le Zhang
  • Wei-ming He
  • Ru-zhen Chang
  • Qin-si Liang
  • Yong Guo
  • Chen Ye
  • Xiao-bo Wang
  • Yong Tao
  • Rong-xia Guan
  • Jun-yi Wang
  • Yu-lin Liu
  • Long-guo Jin
  • Xiu-qing Zhang
  • Zhang-xiong Liu
  • Li-juan Zhang
  • Jie Chen
  • Ke-jing Wang
  • Rui-qiang Li
  • Peng-yin Chen
  • Wen-bin Li
  • Jochen C. Reif
  • Michael Purugganan
  • Jian Wang
  • Meng-chen Zhang
  • Jun Wang
  • Li-juan Qiu
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.
Original languageEnglish
Article number579
JournalBMC Genomics
Number of pages12
Publication statusPublished - 2013

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