Impacts of nucleotide fixation during soybean domestication and improvement

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• 作者：Shancen Zhao (1) (2)
  Fengya Zheng (1)
  Weiming He (2)
  Haiyang Wu (2)
  Shengkai Pan (1)
  Hon-Ming Lam (1)
  
  1. Centre for Soybean Research ; Partner State Key Laboratory of Agrobiotechnology ; The Chinese University of Hong Kong ; Shatin ; New Territories ; Hong Kong
  2. BGI-Shenzhen ; Main Building ; Beishan Industrial Zone ; Yantian District ; Shenzhen ; 518083 ; China
  
• 关键词：Soybean domestication ; Genetic improvement ; Artificial selection ; Nucleotide fixation ; Plant ; pathogen interaction
• 刊名：BMC Plant Biology
• 出版年：2015
• 出版时间：December 2015
• 年：2015
• 卷：15
• 期：1
• 全文大小：1,068 KB
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• 刊物主题：Plant Sciences; Agriculture; Tree Biology;
• 出版者：BioMed Central
• ISSN：1471-2229

文摘

Background Plant domestication involves complex morphological and physiological modification of wild species to meet human needs. Artificial selection during soybean domestication and improvement results in substantial phenotypic divergence between wild and cultivated soybeans. Strong selective pressure on beneficial phenotypes could cause nucleotide fixations in the founder population of soybean cultivars in quite a short time. Results Analysis of available sequencing accessions estimates that ~5.3 million single nucleotide variations reach saturation in cultivars, and then ~9.8 million in soybean germplasm. Selective sweeps defined by loss of genetic diversity reveal 2,255 and 1,051 genes were involved in domestication and subsequent improvement, respectively. Both processes introduced ~0.1 million nucleotide fixations, which contributed to the divergence of wild and cultivated soybeans. Meta-analysis of reported quantitative trait loci (QTL) and selective signals with nucleotide fixation identifies a series of putative candidate genes responsible for 13 agronomically important traits. Nucleotide fixation mediated by artificial selection affected diverse molecular functions and biological reactions that associated with soybean morphological and physiological changes. Of them, plant-pathogen interactions are of particular relevance as selective nucleotide fixations happened in disease resistance genes, cyclic nucleotide-gated ion channels and terpene synthases. Conclusions Our analysis provides insights into the impacts of nucleotide fixation during soybean domestication and improvement, which would facilitate future QTL mapping and molecular breeding practice.