Yinting Wang, Zixuan Li, Bi Wu, Xueqiang Wang, Wenyan Yang, Danjing Lou, Jinyue Ge, Ziran Liu, Wenlong Guo, Neng Zhao, Jun Yang, Weiya Fan, Kai Wang, Fei Li, Weihua Qiao, Hongbo Pang, Leina Zhou, Qingwen Yang, Chenwu Xu, Dingyang Yuan, Yang Xu, Qian Qian, Xiaoming Zheng

Molecular Plant; 2025; IF: 24.1

DOI: 10.1016/j.molp.2025.10.004

Abstract

Hybrid rice has made significant contributions to global food security. However, the efficient utilization of landraces to further enhance heterosis remains a key challenge in rice breeding. In this study, we collected a set of 1,392 landraces and 696 hybrid rice parental lines. A total of 770 hybrid combinations were constructed by crossing of 517 accessions selected from 2,088 rice accessions and seven key yield-related traits were collected. Nearly 500,000 potential hybrid combinations were predicted, comprehensive analysis revealed that landraces from South Asia played a significant role in improving multiple traits. Further investigation revealed substantial variation in the landraces contribution to the optimal hybrid combinations for various traits, with landraces particularly contributing to improvements in grain width. We identified 171 QTLs for seven traits using three association analysis methods. Of these QTLs, 77 known genes were identified within 66 QTLs and 105 novel QTLs without any known genes nearing to them. Gene editing based on CRISPR/Cas9 method showed that OsGRW5.1 plays a critical role in regulating grain width and grain weight. Additionally, a strong correlation was also observed between advantageous haplotypes accumulating and phenotypic performance enhancing in our findings. More than 45% of the advantageous haplotypes derived from landraces are likely to play a significant role in future hybrid rice improvement. A predictive platform was developed that can output all the seven phenotypes of potential hybrid combinations with a given genotype of both parents. This research provides valuable data and practical insights for enhancing heterosis through the efficient utilization of landraces.