Comparative population genomics reveals the domestication history of the peach, Prunus persica, and human influences on perennial fruit crops.
Comparative population genomics reveals the domestication history of the peach, Prunus persica, and human influences on perennial fruit crops.
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比较种群基因组学揭示了桃子，李子perica和人类对多年生水果作物的影响的驯化史。
DOI：
10.1186/s13059-014-0415-1
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发表时间：
2014-07-31
期刊：
影响因子：
12.3
通讯作者：
Wang J
中科院分区：
文献类型：
--
作者：
Cao K;Zheng Z;Wang L;Liu X;Zhu G;Fang W;Cheng S;Zeng P;Chen C;Wang X;Xie M;Zhong X;Wang X;Zhao P;Bian C;Zhu Y;Zhang J;Ma G;Chen C;Li Y;Hao F;Li Y;Huang G;Li Y;Li H;Guo J;Xu X;Wang J
最近，许多研究利用下一代测序已经调查了植物进化和驯化的一年生作物。桃（Prunus persica）是一种典型的多年生果树，集观赏和食用于一体。与其他水果作物不同，栽培桃包括大量的表型，但很少有多态性。在这项研究中，我们探讨了桃驯化的遗传基础和人类对其进化的影响。我们对10个野生桃品种和74个栽培桃品种进行了大规模的重测序，其中包括9个观赏品种、23个育种品种和42个地方品种。我们鉴定了460万个SNPs，其中大量可以解释栽培桃的表型变异。种群分析表明，一个单一的驯化事件，P. persica从野生桃的物种形成。观赏和食用桃都属于P. persica，沿着与另一个地理上分离的亚组，Prunus ferganensis。在食用选择和观赏选择中分别鉴定出147个和262个基因。其中一些基因与重要的生物学特征有关。我们在不同的植物中进行了群体杂合性分析，表明自由重组效应可能会影响驯化历史。人类在桃的驯化过程中进行人工选择，促进其无性繁殖，导致SNP杂合子比率急剧下降。我们的分析增强了我们对多年生水果作物驯化历史的了解，我们生成的数据集可能对未来的比较种群基因组学研究有用。本文的在线版本（doi：10.1186/s13059-014-0415-1）包含补充材料，可供授权用户使用。
Recently, many studies utilizing next generation sequencing have investigated plant evolution and domestication in annual crops. Peach, Prunus persica, is a typical perennial fruit crop that has ornamental and edible varieties. Unlike other fruit crops, cultivated peach includes a large number of phenotypes but few polymorphisms. In this study, we explore the genetic basis of domestication in peach and the influence of humans on its evolution. We perform large-scale resequencing of 10 wild and 74 cultivated peach varieties, including 9 ornamental, 23 breeding, and 42 landrace lines. We identify 4.6 million SNPs, a large number of which could explain the phenotypic variation in cultivated peach. Population analysis shows a single domestication event, the speciation of P. persica from wild peach. Ornamental and edible peach both belong to P. persica, along with another geographically separated subgroup, Prunus ferganensis. We identify 147 and 262 genes under edible and ornamental selection, respectively. Some of these genes are associated with important biological features. We perform a population heterozygosity analysis in different plants that indicates that free recombination effects could affect domestication history. By applying artificial selection during the domestication of the peach and facilitating its asexual propagation, humans have caused a sharp decline of the heterozygote ratio of SNPs. Our analyses enhance our knowledge of the domestication history of perennial fruit crops, and the dataset we generated could be useful for future research on comparative population genomics. The online version of this article (doi:10.1186/s13059-014-0415-1) contains supplementary material, which is available to authorized users.
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影响因子：
4.5
作者：
Cornille A;Gladieux P;Smulders MJ;Roldán-Ruiz I;Laurens F;Le Cam B;Nersesyan A;Clavel J;Olonova M;Feugey L;Gabrielyan I;Zhang XG;Tenaillon MI;Giraud T
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