Divergent selection and genetic introgression shape the genome landscape of heterosis in hybrid rice

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 117; no. 9; pp. 4623 - 4631
• Main Authors: Lin, Zechuan, Qin, Peng, Zhang, Xuanwen, Fu, Chenjian, Deng, Hanchao, Fu, Xingxue, Huang, Zhen, Jiang, Shuqin, Li, Chen, Tang, Xiaoyan, Wang, Xiangfeng, He, Guangming, Yang, Yuanzhu, He, Hang, Deng, Xing Wang
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 03.03.2020
• Subjects: Biological Sciences; Divergence; Genomes; Genotypes; Heterosis; Hybrids; Loci; Phenotypes; Plant breeding; Population studies; Rice; Single-nucleotide polymorphism; Subpopulations; heterosis; divergent selection; genetic introgression; hybrid rice
• ISSN: 0027-8424; 1091-6490; 1091-6490
• DOI: 10.1073/pnas.1919086117

The successful application of heterosis in hybrid rice has dramatically improved rice productivity, but the genetic mechanism for heterosis in the hybrid rice remains unclear. In this study, we generated two populations of rice F₁ hybrids with present-day commercial hybrid parents, genotyped the parents with 50k SNP chip and genome resequencing, and recorded the phenotype of ∼2,000 hybrids at three field trials. By integrating these data with the collected genotypes of ∼4,200 rice landraces and improved varieties that were reported previously, we found that the male and female parents have different levels of genome introgressions from other rice subpopulations, including indica, aus, and japonica, therefore shaping heterotic loci in the hybrids. Among the introgressed exogenous genome, we found that heterotic loci, including Ghd8/DTH8, Gn1a, and IPA1 existed inwild rice, but were significantly divergently selected among the rice subpopulations, suggesting these loci were subject to environmental adaptation. During modern rice hybrid breeding, heterotic loci were further selected by removing loci with negative effect and fixing loci with positive effect and pyramid breeding. Our results provide insight into the genetic basis underlying the heterosis of elite hybrid rice varieties, which could facilitate a better understanding of heterosis and rice hybrid breeding.