Genome-wide view of genetic diversity reveals paths of selection and cultivar differentiation in peach domestication.
Genome-wide view of genetic diversity reveals paths of selection and cultivar differentiation in peach domestication.
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DOI：
10.1093/dnares/dsw014
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发表时间：
2016-06
期刊：
影响因子：
--
通讯作者：
Tao R
中科院分区：
文献类型：
--
作者：
Akagi T;Hanada T;Yaegaki H;Gradziel TM;Tao R
驯化和品种分化是建立栽培作物的必要过程。这些过程本质上涉及种群结构的重大变化，包括人工选择关键基因的变化。在这项研究中，加入桃（Prunus persica）和它的野生近缘植物全基因组分析，以确定遗传结构的变化和基因选择与他们的分化。全基因组信息的单核苷酸多态性位点的分析揭示了不同的变化，在遗传结构和划定之间的驯化桃及其野生亲属和桃地方品种和现代水果（F）和现代观赏（O-A）品种。连锁不平衡扩展/衰减和强大的人口瓶颈或近亲繁殖的显着变化的迹象进行了鉴定。站点频谱和扩展单倍型纯合性为基础的全基因组遗传多样性的评估支持选择性扫描区分驯化桃从其野生亲属和每个F/O-A集群的地方品种集群。具有强选择性扫描的区域隐藏有希望的候选基因进行选择。进一步的基于序列的评价进一步定义了候选物并揭示了它们的特征。所有结果表明，通过分析目前已建立的人群的全基因组遗传多样性，确定与每个分化相关的关键基因的机会。这种方法避免了遗传群体的特殊发展，这对长寿的树木作物来说特别困难。
Domestication and cultivar differentiation are requisite processes for establishing cultivated crops. These processes inherently involve substantial changes in population structure, including those from artificial selection of key genes. In this study, accessions of peach (Prunus persica) and its wild relatives were analysed genome-wide to identify changes in genetic structures and gene selections associated with their differentiation. Analysis of genome-wide informative single-nucleotide polymorphism loci revealed distinct changes in genetic structures and delineations among domesticated peach and its wild relatives and among peach landraces and modern fruit (F) and modern ornamental (O-A) cultivars. Indications of distinct changes in linkage disequilibrium extension/decay and of strong population bottlenecks or inbreeding were identified. Site frequency spectrum- and extended haplotype homozygosity-based evaluation of genome-wide genetic diversities supported selective sweeps distinguishing the domesticated peach from its wild relatives and each F/O-A cluster from the landrace clusters. The regions with strong selective sweeps harboured promising candidates for genes subjected to selection. Further sequence-based evaluation further defined the candidates and revealed their characteristics. All results suggest opportunities for identifying critical genes associated with each differentiation by analysing genome-wide genetic diversity in currently established populations. This approach obviates the special development of genetic populations, which is particularly difficult for long-lived tree crops.