Population Dynamics Among six Major Groups of the Oryza rufipogon Species Complex, Wild Relative of Cultivated Asian Rice.
Population Dynamics Among six Major Groups of the Oryza rufipogon Species Complex, Wild Relative of Cultivated Asian Rice.
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DOI：
10.1186/s12284-016-0119-0
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发表时间：
2016-12
期刊：
影响因子：
--
通讯作者：
McCouch SR
中科院分区：
文献类型：
--
作者：
Kim H;Jung J;Singh N;Greenberg A;Doyle JJ;Tyagi W;Chung JW;Kimball J;Hamilton RS;McCouch SR
了解亚洲栽培稻（O. sativa）野生祖先Oryza rufipogon物种复合体（ORSC）的种群结构，对植物育种和水稻驯化的认识具有重要意义。利用基因分型测序（113,739个snp）和Sanger测序（25个多态性位点）对286份不同的ORSC材料进行核变异和叶绿体变异评估。共鉴定出6个野生亚群，其中25%为混合亚群。其中3个野生类群在遗传和地理上与籼稻、稻和粳稻亚群亲缘关系较近，并携带籼稻基因渐近；另外三个野生类群在遗传上存在差异，具有独特的叶绿体单倍型，并且位于物种范围的极端地理位置。遗传亚群与传统物种名称O. rufipogon（多年生）和O. nivara（一年生）呈显著相关（r 2 = 0.562），并根据形态和生活史进行区分。为进一步的遗传研究，建立了95份纯种（自交系）野生多样性小组。结果表明，栽培稻亚群与一个一年生野生亲缘关系最为密切，粳稻与一个多年生野生亲缘关系最为密切，而籼稻则与一个一年生和多年生野生祖先的混合种群关系最为密切。在水稻种植区，ORSC与O. sativa之间的基因流动很普遍，威胁着ORSC野生种群的身份和多样性。这3个地理上孤立的ORSC居群具有栽培水稻中罕见的变异，为研究古代水稻亚居群的遗传组成提供了一个独特的窗口。本文的在线版本（doi:10.1186/s12284-016-0119-0）包含补充材料，可供授权用户使用。
Understanding population structure of the wild progenitor of Asian cultivated rice (O. sativa), the Oryza rufipogon species complex (ORSC), is of interest to plant breeders and contributes to our understanding of rice domestication. A collection of 286 diverse ORSC accessions was evaluated for nuclear variation using genotyping-by-sequencing (113,739 SNPs) and for chloroplast variation using Sanger sequencing (25 polymorphic sites). Six wild subpopulations were identified, with 25 % of accessions classified as admixed. Three of the wild groups were genetically and geographically closely related to the O. sativa subpopulations, indica, aus and japonica, and carried O. sativa introgressions; the other three wild groups were genetically divergent, had unique chloroplast haplotypes, and were located at the geographical extremes of the species range. The genetic subpopulations were significantly correlated (r 2 = 0.562) with traditional species designations, O. rufipogon (perennial) and O. nivara (annual), differentiated based on morphology and life history. A wild diversity panel of 95 purified (inbred) accessions was developed for future genetic studies. Our results suggest that the cultivated aus subpopulation is most closely related to an annual wild relative, japonica to a perennial wild relative, and indica to an admixed population of diverse annual and perennial wild ancestors. Gene flow between ORSC and O. sativa is common in regions where rice is cultivated, threatening the identity and diversity of wild ORSC populations. The three geographically isolated ORSC populations harbor variation rarely seen in cultivated rice and provide a unique window into the genetic composition of ancient rice subpopulations. The online version of this article (doi:10.1186/s12284-016-0119-0) contains supplementary material, which is available to authorized users.
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影响因子：
18
作者：
Civáň P;Craig H;Cox CJ;Brown TA
通讯作者：
Brown TA
DOI：
10.1186/s12284-014-0007-4
发表时间：
2014
期刊：
Rice (New York, N.Y.)
影响因子：
--
作者：
Kim H;Jeong EG;Ahn SN;Doyle J;Singh N;Greenberg AJ;Won YJ;McCouch SR
通讯作者：
McCouch SR
影响因子：
4.9
作者：
Clement, M;Posada, D;Crandall, KA
通讯作者：
Crandall, KA
影响因子：
5.1
作者：
Khush, GS
通讯作者：
Khush, GS
影响因子：
0.8
作者：
Eizenga, Georgia C.;Ali, Md Liakat;McCouch, Susan R.
通讯作者：
McCouch, Susan R.