title: Impacts of nucleotide fixation during soybean domestication and improvement.
abstract: 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.
authors: Shancen
authors: S
authors: Zhao
authors: Fengya
authors: F
authors: Zheng
authors: Weiming
authors: W
authors: He
authors: Haiyang
authors: H
authors: Wu
authors: Shengkai
authors: S
authors: Pan
authors: Hon-Ming
authors: HM
authors: Lam
mesh_terms: D018556:Crops, Agricultural / Q000235:genetics*; D017343:Genes, Plant; D054884:Host-Pathogen Interactions / Q000235:genetics; D058977:Molecular Sequence Annotation; D009711:Nucleotides / Q000235:genetics*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D013025:Glycine max / Q000235:genetics*
chemical_list: D009711:Nucleotides