Higgins Janet, Santos Bruno, Khanh Tran Dang, Trung Khuat Huu, Duong Tran Duy, Doai Nguyen Thi Phuong, Khoa Nguyen Truong, Ha Dang Thi Thanh, Diep Nguyen Thuy, Dung Kieu Thi, Phi Cong Nguyen, Thuy Tran Thi, Tuan Nguyen Thanh, Tran Hoang Dung, Trung Nguyen Thanh, Giang Hoang Thi, Nhung Ta Kim, Tran Cuong Duy, Lang Son Vi, Nghia La Tuan, Van Giang Nguyen, Xuan Tran Dang, Hall Anthony, Dyer Sarah, Ham Le Huy, Caccamo Mario, De Vega Jose J
Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK.
NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK.
Rice (N Y). 2021 Jun 10;14(1):52. doi: 10.1186/s12284-021-00481-0.
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.
由于其地理位置、纬度范围以及多样的生态系统，越南拥有种类繁多的水稻地方品种。在地势低洼的湄公河和红河三角洲的水稻主产区正遭受气候变化，尤其是降雨和温度模式变化带来的日益严重威胁之际，这种遗传多样性构成了一项极具价值的资源。
我们分析了672个越南水稻基因组，其中616个是新测序的，涵盖了越南各地不同生态系统中种植的各类水稻品种。我们描述了越南境内可能适应其原产地的四个粳稻亚群和五个籼稻亚群。我们将这些越南水稻基因组的群体结构和遗传多样性与3000份亚洲栽培稻基因组进行了比较。命名为籼稻 - 5（I5）的亚群在越南有所扩展，包含低地籼稻种质，这些种质与其他任何亚群的种质共享祖先的比例极低，之前被视为混杂品种而被忽视。我们对19个性状进行了表型测量，并确定了453个独特的基因型 - 表型显著关联，包括21个数量性状基因座（QTL）。在粒型性状上观察到最强的关联，而在一系列特征上观察到较弱的关联，包括穗长、抽穗期和叶宽。
我们通过多种方法展示了越南境内的水稻多样性与更广泛的亚洲水稻多样性之间的关系，从而清晰地呈现了越南境内存在的新型多样性，主要围绕籼稻 - 5亚群。我们的研究结果突出了传统越南水稻种质在基因组组成和性状关联方面的差异，这可能是在这个非常多样化的国家适应多种环境条件和区域偏好的产物。我们的研究结果突出了一些性状及其相关的基因组区域，这些是培育新一代低投入可持续且适应气候变化的水稻的新基因座和等位基因的潜在来源。
