Copy number variation of the restorer Rf4 underlies human selection of three-line hybrid rice breeding

Zhe Zhao, Zhi Ding, Jingjing Huang, Hengjun Meng, Zixu Zhang, Xin Gou, Huiwu Tang, Xianrong Xie, Jingyao Ping, Fangming Xiao, Yao-Guang Liu, Yongyao Xie () and Letian Chen ()
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Zhe Zhao: South China Agricultural University
Zhi Ding: South China Agricultural University
Jingjing Huang: South China Agricultural University
Hengjun Meng: South China Agricultural University
Zixu Zhang: South China Agricultural University
Xin Gou: South China Agricultural University
Huiwu Tang: South China Agricultural University
Xianrong Xie: South China Agricultural University
Jingyao Ping: South China Agricultural University
Fangming Xiao: University of Idaho
Yao-Guang Liu: South China Agricultural University
Yongyao Xie: South China Agricultural University
Letian Chen: South China Agricultural University

Nature Communications, 2023, vol. 14, issue 1, 1-14

Abstract: Abstract Cytoplasmic male sterility (CMS) lines are important for breeding hybrid crops, and utilization of CMS lines requires strong fertility restorer (Rf) genes. Rf4, a major Rf for Wild-Abortive CMS (CMS-WA), has been cloned in rice. However, the Rf4 evolution and formation of CMS-WA/Rf system remain elusive. Here, we show that the Rf4 locus emerges earlier than the CMS-WA gene WA352 in wild rice, and 69 haplotypes of the Rf4 locus are generated in the Oryza genus through the copy number and sequence variations. Eight of these haplotypes of the Rf4 locus are enriched in modern rice cultivars during natural and human selections, whereas non-functional rf4i is preferentially selected for breeding current CMS-WA lines. We further verify that varieties carrying two-copy Rf4 haplotype have stronger fertility restoration ability and are widely used in three-line hybrid rice breeding. Our findings increase our understanding of CMS/Rf systems and will likely benefit crop breeding.

Date: 2023
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DOI: 10.1038/s41467-023-43009-4

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