Evidence of selection, adaptation and untapped diversity in Vietnamese rice landraces-猫眼课题宝

DOI：

10.1101/2020.07.07.191981

发表时间：

2020-07

期刊：

bioRxiv

影响因子：

通讯作者：

中科院分区：

其他

文献类型：

作者：

J. Higgins;B. Santos;T. Khanh;K. H. Trung;T. D. Duong;Nguyen Thi Phuong Doai;N. T. Khoa;D. Ha;N. T. Diep;K. T. Dung;Cong Nguyen Phi;T. Thủy;N. T. Tuan;H. Tran;N. Trung;H. T. Giang;Ta Thi Kim Nhung;C. Tran;S. Lang;L. T. Nghia;N. Giảng;T. Xuan;Anthony Hall;S. Dyer;L. Hàm;M. Cáccamo;J. D. Vega

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3,000个亚洲栽培水稻基因组进行了比较。命名的Indica-5（I5）亚群在越南扩大，并包含低地Indica加入，这与来自任何其他亚群的加入具有非常低的共同祖先，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。我们确定了在越南这些亚群的育种过程中选择的籼稻和粳稻亚型的基因组区域，并详细讨论了I5中的52个选定区域，这些区域构成了尚未开发的栽培稻多样性资源。我们的研究结果突出了性状及其相关的基因组区域，这些区域是通过精细的表型分析和数据整合确定的。这些是培育新一代可持续和有弹性的水稻的新基因座和等位基因的潜在来源。

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 3,000 genomes of Asian cultivated rice. The named Indica-5 (I5) subpopulation was expanded in Vietnam and contained lowland Indica accessions, which had with 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 identified genomic regions selected in both Indica and Japonica subtypes during the breeding of these subpopulations within Vietnam and discuss in detail fifty-two selected regions in I5, which constitute an untapped resource of cultivated rice diversity. Our results highlight traits and their associated genomic regions, which were identified by fine phenotyping and data integration. These are a potential source of novel loci and alleles to breed a new generation of sustainable and resilient rice.

Evidence of selection, adaptation and untapped diversity in Vietnamese rice landraces

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