The breeding effects and genetic mysteries of a milestone variety (Fengbazhan) of modern indica rice in China

Huanghuazhan and Huazhan are the most widely used indica conventional rice and restorer line in China, respectively. In fact, both of them are all derivatives of Fengbazhan (FBZ), and many other FBZ-derived varieties have been widely planted in China, accounting 22% of China’s rice paddy fields. Therefore, evaluating the breeding effects of FBZ and clarifying its genetic mysteries is an effective strategy to interpret the history of modern rice breeding. Here, we report FBZ could be regarded as a milestone for the renewal of China’s modern indica rice. By comparing the variant information of genes that underlie quantitative traits (QTGs), we identified 48 QTGs showing allelic differences among different types of varieties. Further research found that favorable genes were gradually optimized during the breeding of the FBZ-series varieties, while the selection and utilization of Hd1-Pi2-Pid3-Pid2 segment, directly contributed to the breeding of FBZ. Importantly, the application of favorable genes on chromosome 6 solves the problem of ‘high-quality but susceptible to rice blast’, enabling the FBZ-series varieties to achieve high and stable yield, good quality, and wide adaptability in production. We put forward thinking and insights from the perspectives of fertility restoration, defense and growth, germplasm resources, variety replacement and future breeding goals. Our study provides useful gene targets for molecular breeding, as well as a valuable reference for the development of breakthrough varieties.