Genomic structural variation-mediated allelic suppression causes hybrid male sterility in rice

Rongxin Shen, Lan Wang, Xupeng Liu, Jiang Wu, Weiwei Jin, Xiucai Zhao, Xianrong Xie, Qinlong Zhu, Huiwu Tang, Qing Li, Letian Chen and Yao-Guang Liu ()
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Rongxin Shen: State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources
Lan Wang: Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions
Xupeng Liu: State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources
Jiang Wu: State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources
Weiwei Jin: National Maize Improvement Center of China, Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University
Xiucai Zhao: State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources
Xianrong Xie: State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources
Qinlong Zhu: State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources
Huiwu Tang: State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources
Qing Li: State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources
Letian Chen: State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources
Yao-Guang Liu: State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources

Nature Communications, 2017, vol. 8, issue 1, 1-10

Abstract: Abstract Hybrids between divergent populations commonly show hybrid sterility; this reproductive barrier hinders hybrid breeding of the japonica and indica rice (Oryza sativa L.) subspecies. Here we show that structural changes and copy number variation at the Sc locus confer japonica–indica hybrid male sterility. The japonica allele, Sc-j, contains a pollen-essential gene encoding a DUF1618-domain protein; the indica allele, Sc-i, contains two or three tandem-duplicated ~ 28-kb segments, each carrying an Sc-j-homolog with a distinct promoter. In Sc-j/Sc-i hybrids, the high-expression of Sc-i in sporophytic cells causes suppression of Sc-j expression in pollen and selective abortion of Sc-j-pollen, leading to transmission ratio distortion. Knocking out one or two of the three Sc-i copies by CRISPR/Cas9 rescues Sc-j expression and male fertility. Our results reveal the gene dosage-dependent allelic suppression as a mechanism of hybrid incompatibility, and provide an effective approach to overcome the reproductive barrier for hybrid breeding.

Date: 2017
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DOI: 10.1038/s41467-017-01400-y

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