Background

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.

Results

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.

Conclusions

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.

中文翻译：

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对 672 个本地水稻种质进行重测序以探索越南的遗传多样性和性状关联

背景

由于其地理位置、纬度范围和各种生态系统，越南拥有种类繁多的水稻地方品种。在湄公河和红河三角洲低洼地区水稻产量最高的地区正面临气候变化（尤其是降雨和温度模式）带来的日益严重的威胁之际，这种遗传多样性构成了一种非常宝贵的资源。

结果

我们分析了 672 个越南水稻基因组，其中 616 个是新测序的，包括在越南各地发现的不同生态系统中种植的水稻品种范围。我们描述了越南可能适应原产地的四个粳稻和五个籼稻亚群。我们将这些越南水稻基因组的种群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。命名的籼 5 (I5) 亚群在越南扩展并包含低地籼种质，这些种质与来自任何其他亚种群的种质具有非常低的共享血统，并且以前作为混合物被忽视。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-表型显着关联，包括 21 个 QTL（数量性状基因座）。

结论

我们展示了越南的水稻多样性如何与更广泛的亚洲水稻多样性相关联，方法是使用多种方法清晰地了解越南境内存在的新多样性，主要围绕 Indica-5 亚群。我们的研究结果突出了传统越南水稻品种之间基因组组成和性状关联的差异，这可能是在一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性状及其相关基因组区域，这些区域是培育新一代低投入可持续和气候适应型水稻的新位点和等位基因的潜在来源。