Crop Research Institute/National Engineering Laboratory for Wheat and Maize, Shandong Academy of Agricultural Sciences (SAAS), Jinan, 250100, PR China; Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843-2474, USA.
Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843-2474, USA; Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.
Plant Sci. 2021 Jul;308:110910. doi: 10.1016/j.plantsci.2021.110910. Epub 2021 Apr 14.
Molecular tools and knowledge of crop germplasm are vital for their effective utilization. In this study, we developed 40,866 high-quality and well distributed SNPs for a rice mini-core collection (RMC) developed by the United States Department of Agriculture (USDA). The high-quality SNPs clustered the USDA-RMC into five subpopulations (Ind, indica; Aus, aus; Afr, African rice; TeJ, temperate japonica; TrJ, tropical japonica) and one admixture (Adm). This classification was further confirmed by phylogenetic and principal component analyses. The rice ARO (aromatic) subpopulation of previous studies was re-assigned with Adm and the WD (wild-type) subpopulation was re-defined to the Afr subpopulation because most of its accessions are African cultivated rice. The Aus and Ind subpopulations had a substantially wider genetic variation than the TrJ and TeJ subpopulations. The genetic diversities were much larger between the Ind or Aus subpopulation and the TrJ or TeJ subpopulation than between the Afr subpopulation and the Ind, Aus, TrJ or TeJ subpopulation. Comparative agronomic trait analysis between the subpopulations also supported the genetic structure and variation of the RMC, and suggested the existence of extensive variation in the genes controlling agronomic traits among them. Furthermore, analysis of ancestral membership of the RMC accessions revealed that reproductive barrier or wide incompatibility existed between the Indica and Japonica groups, while gene flow occurred between them. These results provide high-quality SNPs and knowledge of genetic structure and diversity of the USDA-RMC necessary for enhanced rice research and breeding.
分子工具和作物种质资源知识对于其有效利用至关重要。本研究为美国农业部（USDA）开发的水稻迷你核心种质（RMC）开发了 40866 个高质量、分布均匀的 SNP。高质量 SNP 将 USDA-RMC 聚类为五个亚群（Ind，籼稻；Aus，粳稻；Afr，非洲稻；TeJ，温带粳稻；TrJ，热带粳稻）和一个混合群（Adm）。这一分类进一步通过系统发育和主成分分析得到了证实。先前研究中的水稻 ARO（芳香）亚群被重新分配到 Adm，WD（野生型）亚群被重新定义为 Afr 亚群，因为其大多数品种都是非洲栽培稻。Aus 和 Ind 亚群的遗传变异明显大于 TrJ 和 TeJ 亚群。Ind 或 Aus 亚群与 TrJ 或 TeJ 亚群之间的遗传多样性比 Afr 亚群与 Ind、Aus、TrJ 或 TeJ 亚群之间的遗传多样性大得多。亚群间的比较农艺性状分析也支持了 RMC 的遗传结构和变异，并表明控制农艺性状的基因在它们之间存在广泛的变异。此外，对 RMC 品种祖先隶属关系的分析表明，籼稻和粳稻群体之间存在生殖障碍或广泛的不亲和性，而它们之间存在基因流。这些结果为增强水稻研究和育种提供了高质量的 SNP 以及 USDA-RMC 的遗传结构和多样性知识。
