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

• Published in: Nature communications Vol. 8; no. 1; pp. 1310 - 10
• Main Authors: Shen, Rongxin, Wang, Lan, Liu, Xupeng, Wu, Jiang, Jin, Weiwei, Zhao, Xiucai, Xie, Xianrong, Zhu, Qinlong, Tang, Huiwu, Li, Qing, Chen, Letian, Liu, Yao-Guang
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 03.11.2017; Nature Publishing Group; Nature Portfolio
• Subjects: 631/208/8; 631/449/2679; Abortion; Agricultural production; Alleles; Chromosomes; Copy number; CRISPR; Cultivars; Fertility; Gene dosage; Gene expression; Genetic diversity; Genomes; Genomics; Grain; Homology; Humanities and Social Sciences; Hybrids; Incompatibility; Laboratories; Male sterility; multidisciplinary; Oryza sativa indica; Oryza sativa japonica; Plant breeding; Pollen; Proteins; Rice; Science; Science (multidisciplinary)
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-017-01400-y

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. A reproductive barrier between japonica and indica rice subspecies hinders hybrid breeding. Here, the authors reveal that structural and copy number variations of a pollen-essential gene, which encodes a DUF1618-domain protein, result in allelic suppression and subsequently cause hybrid male sterility.