Resequencing of 672 Native Rice Accessions to Explore Genetic Diversity and Trait Associations in Vietnam.
Resequencing of 672 Native Rice Accessions to Explore Genetic Diversity and Trait Associations in Vietnam.
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DOI：
10.1186/s12284-021-00481-0
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发表时间：
2021-06-10
期刊：
影响因子：
--
通讯作者：
De Vega JJ
中科院分区：
文献类型：
--
作者：
Higgins J;Santos B;Khanh TD;Trung KH;Duong TD;Doai NTP;Khoa NT;Ha DTT;Diep NT;Dung KT;Phi CN;Thuy TT;Tuan NT;Tran HD;Trung NT;Giang HT;Nhung TK;Tran CD;Lang SV;Nghia T;Van Giang N;Xuan TD;Hall A;Dyer S;Ham LH;Caccamo M;De Vega JJ
由于地理位置，纬度范围和各种生态系统，越南拥有丰富多样的水稻地方品种。在地势低洼的湄公河和红河三角洲的最高稻米生产区正遭受气候变化，特别是降雨和温度变化的日益严重的威胁之际，这种遗传多样性是一种非常宝贵的资源。我们分析了672个越南水稻基因组，其中616个是新测序的，涵盖了在越南各地不同生态系统中种植的水稻品种。我们描述了四个粳稻和五个籼稻在越南可能适应原产地的亚群。我们将这些越南水稻基因组的群体结构和遗传多样性与亚洲栽培水稻的3000个基因组进行了比较。命名的Indica-5（I5）亚群在越南扩大，并包含低地Indica加入，这与任何其他亚群的加入有很低的共同祖先，以前被忽视的混合物。我们对19个性状的表型测量进行了评分，并确定了453个独特的基因型-表型显著关联，包括21个QTL（数量性状位点）。最强的协会观察到的粒度性状，而较弱的协会观察到的一系列特征，包括穗长，抽穗期和叶宽。我们展示了越南水稻多样性与更广泛的亚洲水稻多样性之间的关系，通过使用多种方法来清楚地了解越南境内的新多样性，主要是围绕Indica-5亚群。我们的研究结果突出了传统的越南水稻品种之间的基因组组成和性状关联的差异，这可能是适应多种环境条件和区域偏好在一个非常多样化的国家的产品。我们的研究结果突出了性状及其相关的基因组区域，这些区域是培育新一代低投入可持续和气候适应性水稻的新基因座和等位基因的潜在来源。在线版本包含补充材料，可通过10.1186/s12284-021-00481-0获得。
Vietnam possesses a vast diversity of rice landraces due to its geographical situation, latitudinal range, and a variety of ecosystems. This genetic diversity constitutes a highly valuable resource at a time when the highest rice production areas in the low-lying Mekong and Red River Deltas are enduring increasing threats from climate changes, particularly in rainfall and temperature patterns. We analysed 672 Vietnamese rice genomes, 616 newly sequenced, that encompass the range of rice varieties grown in the diverse ecosystems found throughout Vietnam. We described four Japonica and five Indica subpopulations within Vietnam likely adapted to the region of origin. We compared the population structure and genetic diversity of these Vietnamese rice genomes to the 3000 genomes of Asian cultivated rice. The named Indica-5 (I5) subpopulation was expanded in Vietnam and contained lowland Indica accessions, which had very low shared ancestry with accessions from any other subpopulation and were previously overlooked as admixtures. We scored phenotypic measurements for nineteen traits and identified 453 unique genotype-phenotype significant associations comprising twenty-one QTLs (quantitative trait loci). The strongest associations were observed for grain size traits, while weaker associations were observed for a range of characteristics, including panicle length, heading date and leaf width. We showed how the rice diversity within Vietnam relates to the wider Asian rice diversity by using a number of approaches to provide a clear picture of the novel diversity present within Vietnam, mainly around the Indica-5 subpopulation. Our results highlight differences in genome composition and trait associations among traditional Vietnamese rice accessions, which are likely the product of adaption to multiple environmental conditions and regional preferences in a very diverse country. Our results highlighted traits and their associated genomic regions that are a potential source of novel loci and alleles to breed a new generation of low input sustainable and climate resilient rice. The online version contains supplementary material available at 10.1186/s12284-021-00481-0.
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影响因子：
5.3
作者：
Phung NT;Mai CD;Mournet P;Frouin J;Droc G;Ta NK;Jouannic S;Lê LT;Do VN;Gantet P;Courtois B
通讯作者：
Courtois B
影响因子：
1.2
作者：
Cingolani, Pablo;Platts, Adrian;Ruden, Douglas M.
通讯作者：
Ruden, Douglas M.
影响因子：
5.3
作者：
Ta KN;Khong NG;Ha TL;Nguyen DT;Mai DC;Hoang TG;Phung TPN;Bourrie I;Courtois B;Tran TTH;Dinh BY;LA TN;DO NV;Lebrun M;Gantet P;Jouannic S
通讯作者：
Jouannic S
影响因子：
3
作者：
Alexander DH;Lange K
通讯作者：
Lange K
影响因子：
14.9
作者：
Mansueto L;Fuentes RR;Borja FN;Detras J;Abriol-Santos JM;Chebotarov D;Sanciangco M;Palis K;Copetti D;Poliakov A;Dubchak I;Solovyev V;Wing RA;Hamilton RS;Mauleon R;McNally KL;Alexandrov N
通讯作者：
Alexandrov N