Rice Science ›› 2023, Vol. 30 ›› Issue (6): 552-565.DOI: 10.1016/j.rsci.2023.06.004

• Research Papers • Previous Articles     Next Articles

Genome-Wide Dissection of Quan 9311A Breeding Process and Application Advantages

Li Qianlong2, Feng Qi1, Wang Heqin3, Kang Yunhai2, Zhang Conghe2,3, Du Ming2, Zhang Yunhu3, Wang Hui2,3, Chen Jinjie3, Han Bin1, Fang Yu2,3,4(), Wang Ahong1()   

  1. 1Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
    2Shanghai ZKW Molecular Breeding Technology Co. Ltd, Shanghai 200234, China
    3Win-all Hi-tech Seed Co. Ltd / Key Laboratory for New Variety Creative of Hybrid Rice, Ministry of Agriculture and Rural Affairs, Hefei 230088, China
    4Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China


Germplasm resource innovation is a crucial factor for cultivar development, particularly within the context of hybrid rice breeding based on the three-line system. Quan 9311A, a cytoplasmic male sterile (CMS) line, has been successfully cultivated using rice restoration materials and extensively employed as a female parent in hybrid breeding program in China. This line was developed by crossing the CMS line Zhong 9A with a two-line restorer line 93-11, with the intention of eliminating the restoring ability of 93-11 while retaining the sterility gene WA352c from Zhong 9A. Quan 9311A effectively amalgamates the most favorable agronomic traits from both parental lines. In this study, the relationship between phenotypic characteristics and the known functional genes of Quan 9311A were analyzed using the rice genome navigation technology based on whole-genome sequencing. The findings revealed that Quan 9311A harbors multiple superior alleles from both 93-11 and Zhong 9A, providing exceptional agronomic traits that are unavailable in earlier CMS lines. Despite the removal of the fertility restorer gene Rf3 from 93-11, numerous chromosomal segments from 93-11 persist in the Quan 9311A genome. Furthermore, the hybrid rice Quanyousimiao (QYSM) and the restorer line Wushansimiao (WSSM) were used as examples to illustrate the important role of Quan 9311A as the female parent in heterosis. It was found that QYSM carries a great number of superior alleles, which accounts for its high grain yield and wide adaptability. These insights not only advanced the utilization of hybrid rice pairing groups but also provided guidance for future breeding endeavors. The study introduced innovative concepts to further integrate genomics with traditional breeding techniques. Ultimately, Quan 9311A signified a significant milestone in rice breeding technology, opening up novel avenues for hybrid rice development.

Key words: breeding, hybrid rice, phenotype, quantitative trait nucleotide locus, rice genome navigation system, whole-genome sequencing