Utilizing the full potential of rice collections mainly depends on an in‐depth exploration and understanding of the vast diversity in its germplasm. The AfricaRice genebank holds the largest collection of rice germplasm originating from the African continent. In the present study, we comprehensively characterized a collection of 9013 accessions, including Oryza barthii A. Chev., Oryza glaberrima Steud., Oryza longistaminata A. Chev. & Roehr., Oryza sativa L. ssp. indica, and Oryza sativa L. ssp. japonica, for genetic diversity and population structure using genotyping‐by‐sequencing through DArTseq analysis. We identified 27,718 high‐quality single nucleotide polymorphism markers after the genotypic data were filtered. Based on the analyses, the collection has extensive genetic diversity, and the average genetic distance of the entire set was 0.267 (range 0.001–0.469), with 45.1% of pairs of accessions being highly distant and 40.1% moderately distant from each other. Neighbor‐joining tree, principal component, and Bayesian population structure analyses clustered the 9013 accessions into six groups, based roughly on their taxonomic and biological status. The first, second, and third groups consisted of accessions belonging to O. glaberrima, O. barthii, and O. longistaminata, respectively. The fourth, fifth, and sixth groups were improved‐indica, japonica, and traditional‐indica accessions, respectively. The highest value of genetic variance proportion (PhiPT) was found in the species group followed by groups based on cluster analysis and on Bayesian population structure at K = 6. These results allow us to better understand the genetic diversity present in 9013 rice accessions maintained in the AfricaRice genebank and offer a valuable tool for pre breeding, breeding, and further genetic applications.

中文翻译：

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使用 DArTseq 在 AfricaRice 基因库中维护的水稻种质的遗传变异和种群结构


充分利用水稻藏品的潜力主要取决于对其种质资源的巨大多样性的深入探索和理解。AfricaRice 基因库拥有来自非洲大陆的最大水稻种质资源库。在本研究中，我们全面表征了 9013 份种质，包括 Oryza barthii A. Chev.、Oryza glaberrima Steud.、Oryza longistaminata A. Chev。& Roehr.，Oryza sativa L. ssp. indica和Oryza sativa L. ssp. japonica，通过DArTseq分析进行基因分型和种群结构。过滤基因型数据后，我们鉴定了 27,718 个高质量的单核苷酸多态性标记。根据分析，该种质具有广泛的遗传多样性，整个集合的平均遗传距离为 0.267 （范围 0.001–0.469），其中 45.1% 的种质对彼此高度遥远，40.1% 的种质对彼此之间中等距离。邻接树、主成分和贝叶斯种群结构分析大致根据它们的分类和生物学状态，将 9013 份种质分为六组。第一、第二和第三组分别由属于 O. glaberrima、O. barthii 和 O. longistaminata 的种质组成。第 4 、 第 5 和 第 6 组分别为改良 - 籼稻、 粳稻 和 传统 - 籼稻种质。遗传方差比例 （PhiPT） 值最高，在物种组中发现，其次是基于聚类分析和贝叶斯种群结构的组，K = 6。 这些结果使我们能够更好地了解 AfricaRice 基因库中保存的 9013 个水稻种质中存在的遗传多样性，并为预育种、育种和进一步的遗传应用提供了有价值的工具。