Genetic diversity and association mapping in the Colombian Central Collection of Solanum tuberosum L. Andigenum group using SNPs markers.
Genetic diversity and association mapping in the Colombian Central Collection of Solanum tuberosum L. Andigenum group using SNPs markers.
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DOI：
10.1371/journal.pone.0173039
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发表时间：
2017
期刊：
影响因子：
3.7
通讯作者：
Yockteng R
中科院分区：
文献类型：
--
作者：
Berdugo-Cely J;Valbuena RI;Sánchez-Betancourt E;Barrero LS;Yockteng R
马铃薯（Solanum tuberosum L.）是世界上第四重要的农作物食品，哥伦比亚拥有世界上最重要的马铃薯种质保藏中心之一（哥伦比亚中央保藏中心-CCC）。人们对其作为分子育种计划遗传多样性来源的潜力知之甚少。在本研究中，我们使用 5968 个 SNP 分析了来自 CCC 的 809 个 Andigenum 组种质，以确定：1）Andigenum 种质的遗传多样性和种群结构，以及 2）该收集品在绘制整个马铃薯基因组质量性状方面的有用性。基于主成分、聚类分析和贝叶斯推理的遗传结构分析表明，CCC 可以根据其倍性水平细分为两个主要组：Phureja（二倍体）和 Andigena（四倍体）。与 Phureja 种群相比，Andigena 种群的遗传多样性更高，但遗传亚结构更少（分别为 3 个和 5 个亚种群）。使用 4666 个 SNP 对定性形态学数据进行关联作图分析，结果显示 23 个标记与 9 个形态性状显着相关。本研究表明，CCC 是一个在遗传和表型上高度多样化的种质资源库，可用于实施关联作图，以识别与感兴趣的性状相关的基因，并协助未来的马铃薯遗传育种计划。
The potato (Solanum tuberosum L.) is the fourth most important crop food in the world and Colombia has one of the most important collections of potato germplasm in the world (the Colombian Central Collection-CCC). Little is known about its potential as a source of genetic diversity for molecular breeding programs. In this study, we analyzed 809 Andigenum group accessions from the CCC using 5968 SNPs to determine: 1) the genetic diversity and population structure of the Andigenum germplasm and 2) the usefulness of this collection to map qualitative traits across the potato genome. The genetic structure analysis based on principal components, cluster analyses, and Bayesian inference revealed that the CCC can be subdivided into two main groups associated with their ploidy level: Phureja (diploid) and Andigena (tetraploid). The Andigena population was more genetically diverse but less genetically substructured than the Phureja population (three vs. five subpopulations, respectively). The association mapping analysis of qualitative morphological data using 4666 SNPs showed 23 markers significantly associated with nine morphological traits. The present study showed that the CCC is a highly diverse germplasm collection genetically and phenotypically, useful to implement association mapping in order to identify genes related to traits of interest and to assist future potato genetic breeding programs.