Jiangxi Super -rice Research and Development Center, Jiangxi Provincial Key Laboratory of Rice Germplasm Innovation and Breeding, National Engineering Research Center for Rice, Jiangxi Academy of Agricultural Sciences, Nanchang, China.
School of Life Sciences, Institute of Life Sciences and Green Development, Hebei Basic Science Center for Biotic Interaction, Hebei University, Baoding, China.
Nat Commun. 2024 Nov 18;15(1):9994. doi: 10.1038/s41467-024-54427-3.
Wild species of crops serve as a valuable germplasm resource for breeding of modern cultivars. Rice (Oryza sativa L.) is a vital global staple food. However, research on genome evolution and diversity of wild rice species remains limited. Here, we present nearly complete genomes of 13 representative wild rice species. By integrating with four previously published genomes for pangenome analysis, a total of 101,723 gene families are identified across the genus, including 9834 (9.67%) core gene families. Additionally, 63,881 gene families absent in cultivated rice species but present in wild rice species are discovered. Extensive structural rearrangements, sub-genomes exchanges, widespread allelic variations, and regulatory sequence variations are observed in wild rice species. Interestingly, expanded but less diverse disease resistance genes in the genomes of cultivated rice, likely due to the loss of some resistance genes and the fixing and amplification of genes encoding resistance genes to specific diseases during domestication and artificial selection. This study not only reveals natural variations valuable for gene-level studies and breeding selection but also enhances our understanding on rice evolution and domestication.
野生作物种是现代栽培品种选育的宝贵种质资源。水稻（Oryza sativa L.）是全球重要的主食。然而，野生稻种的基因组进化和多样性研究仍然有限。本研究提供了 13 种代表性野生稻种的近乎完整基因组。通过与之前发表的 4 个基因组进行泛基因组分析，共鉴定到 101723 个基因家族，其中包括 9834 个（9.67%）核心基因家族。此外，还发现了 63881 个在栽培稻种中不存在但在野生稻种中存在的基因家族。在野生稻种中观察到广泛的结构重排、亚基因组交换、等位基因的广泛变异和调控序列变异。有趣的是，栽培稻种基因组中扩展但多样性较低的抗病基因可能是由于在驯化和人工选择过程中一些抗病基因的丢失以及编码特定疾病抗性基因的基因的固定和扩增。这项研究不仅揭示了对基因水平研究和育种选择有价值的自然变异，也增进了我们对水稻进化和驯化的理解。
