Two complementary genes in a presence-absence variation contribute to indica-japonica reproductive isolation in rice

Daiqi Wang, Hongru Wang, Xiaomei Xu, Man Wang, Yahuan Wang, Hong Chen, Fei Ping, Huanhuan Zhong, Zhengkun Mu, Wantong Xie, Xiangyu Li, Jingbin Feng, Milan Zhang, Zhilan Fan, Tifeng Yang, Junliang Zhao, Bin Liu, Ying Ruan, Guiquan Zhang, Chunlin Liu and Ziqiang Liu ()
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Daiqi Wang: South China Agricultural University
Hongru Wang: Chinese Academy of Agricultural Sciences
Xiaomei Xu: South China Agricultural University
Man Wang: South China Agricultural University
Yahuan Wang: South China Agricultural University
Hong Chen: South China Agricultural University
Fei Ping: South China Agricultural University
Huanhuan Zhong: South China Agricultural University
Zhengkun Mu: South China Agricultural University
Wantong Xie: South China Agricultural University
Xiangyu Li: South China Agricultural University
Jingbin Feng: South China Agricultural University
Milan Zhang: South China Agricultural University
Zhilan Fan: Guangdong Academy of Agricultural Sciences
Tifeng Yang: Guangdong Academy of Agricultural Sciences
Junliang Zhao: Guangdong Academy of Agricultural Sciences
Bin Liu: Guangdong Academy of Agricultural Sciences
Ying Ruan: Hunan Agricultural University
Guiquan Zhang: South China Agricultural University
Chunlin Liu: Hunan Agricultural University
Ziqiang Liu: South China Agricultural University

Nature Communications, 2023, vol. 14, issue 1, 1-12

Abstract: Abstract Understanding the evolutionary forces in speciation is a central goal in evolutionary biology. Asian cultivated rice has two subspecies, indica and japonica, but the underlying mechanism of the partial reproductive isolation between them remains obscure. Here we show a presence-absence variation (PAV) at the Se locus functions as an indica-japonica reproductive barrier by causing hybrid sterility (HS) in indica-japonica crosses. The locus comprises two adjacent genes: ORF3 encodes a sporophytic pollen killer, whereas ORF4 protects pollen in a gametophytic manner. In F1 of indica-japonica crosses, pollen with the japonica haplotype, which lacks the sequence containing the protective ORF4, is aborted due to the pollen-killing effect of ORF3 from indica. Evolutionary analysis suggests ORF3 is a gene associated with the Asian cultivated rice species complex, and the PAV has contributed to the reproductive isolation between the two subspecies of Asian cultivated rice. Our analyses provide perspectives on rice inter-subspecies post-zygotic isolation, and will promote efforts to overcome reproductive barriers in indica-japonica hybrid rice breeding.

Date: 2023
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DOI: 10.1038/s41467-023-40189-x

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