Zhao Shancen, Zheng Fengya, He Weiming, Wu Haiyang, Pan Shengkai, Lam Hon-Ming
BMC Plant Biol. 2015 Mar 8;15:81. doi: 10.1186/s12870-015-0463-z.
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.
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.
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.
植物驯化涉及对野生物种进行复杂的形态和生理改造以满足人类需求。大豆驯化和改良过程中的人工选择导致野生大豆和栽培大豆之间出现显著的表型差异。对有益表型的强烈选择压力可能会在相当短的时间内导致大豆品种创始群体中的核苷酸固定。
对现有测序种质的分析估计，栽培品种中约有530万个单核苷酸变异达到饱和，然后大豆种质中约有980万个。由遗传多样性丧失定义的选择性清除分别揭示了2255个和1051个基因参与了驯化和随后的改良。这两个过程都引入了约10万个核苷酸固定，这导致了野生大豆和栽培大豆的分化。对已报道的数量性状位点（QTL）和具有核苷酸固定的选择信号进行荟萃分析，确定了一系列负责13个重要农艺性状的假定候选基因。人工选择介导的核苷酸固定影响了与大豆形态和生理变化相关的多种分子功能和生物反应。其中，植物与病原体的相互作用尤为重要，因为在抗病基因、环核苷酸门控离子通道和萜烯合酶中发生了选择性核苷酸固定。
我们的分析提供了对大豆驯化和改良过程中核苷酸固定影响的见解，这将有助于未来的QTL定位和分子育种实践。
