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

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 JinXiu qing Zhang, Zhang xiong Liu, Li juan Zhang, Jie Chen, Ke jing Wang, Rasmus Nielsen, Rui qiang Li, Peng yin Chen, Wen bin Li, Jochen C. Reif, Michael Purugganan, Jian Wang, Meng chen Zhang, Jun Wang, Li juan Qiu

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Article number579
JournalBMC Genomics
Volume14
Issue number1
DOIs
StatePublished - Aug 28 2013

Keywords

  • Artificial selection
  • Evolution
  • Genetic diversity
  • Population genomics
  • Soybean

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

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  • Cite this

    Li, Y. H., Zhao, S. C., Ma, J. X., Li, D., Yan, L., Li, J., Qi, X. T., Guo, X. S., Zhang, L., He, W. M., Chang, R. Z., Liang, Q. S., Guo, Y., Ye, C., Wang, X. B., Tao, Y., Guan, R. X., Wang, J. Y., Liu, Y. L., ... Qiu, L. J. (2013). Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing. BMC Genomics, 14(1), [579]. https://doi.org/10.1186/1471-2164-14-579