Genome evolution and diversity of wild and cultivated rice species

Weixiong Long (), Qiang He, Yitao Wang, Yu Wang, Jie Wang, Zhengqing Yuan, Meijia Wang, Wei Chen, Lihua Luo, Laiyang Luo, Weibiao Xu, Yonghui Li, Wei Li, Longan Yan, Yaohui Cai (), Huilong Du () and Hongwei Xie ()
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Weixiong Long: Jiangxi Academy of Agricultural Sciences
Qiang He: Hebei University
Yitao Wang: Hebei University
Yu Wang: Hebei University
Jie Wang: Jiangxi Academy of Agricultural Sciences
Zhengqing Yuan: Wuhan University
Meijia Wang: Hebei University
Wei Chen: Jiangxi Academy of Agricultural Sciences
Lihua Luo: Jiangxi Academy of Agricultural Sciences
Laiyang Luo: Jiangxi Academy of Agricultural Sciences
Weibiao Xu: Jiangxi Academy of Agricultural Sciences
Yonghui Li: Jiangxi Academy of Agricultural Sciences
Wei Li: Hebei University
Longan Yan: Jiangxi Academy of Agricultural Sciences
Yaohui Cai: Jiangxi Academy of Agricultural Sciences
Huilong Du: Hebei University
Hongwei Xie: Jiangxi Academy of Agricultural Sciences

Nature Communications, 2024, vol. 15, issue 1, 1-16

Abstract: Abstract 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.

Date: 2024
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DOI: 10.1038/s41467-024-54427-3

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