Rapidly creating indica-japonica hybrid compatibility materials by molecular detection and genome editing

Objective By molecular detection and genome editing, a rapid and precise creation of artificial hybrid-compatible lines is carried out to break the indica-japonica hybrid sterility and provide a new paradigm for realizing the utilization of indica-japonica hybrid vigor.

Method In this study, an elite indica rice variety ‘Huanghuazhan’ (HHZ) and an elite japonica rice variety ‘Zhongjia 8’ (ZJ8) were used as test materials. The genotypes of the major indica-japonica hybrid sterility loci in HHZ and ZJ8 were detected by molecular detection. Then, the genome editing was carried out to knock out the major hybrid sterility gene(s) conferring HHZ-ZJ8 hybrid fertility, thereby rapidly and precisely creating indica-japonica hybrid F₁ with high fertility.

Result The HHZ-ZJ8 hybrid F₁ plants showed strong hybrid vigor, but exhibited spikelet semi-sterility. According to genetic mechanism of intersubspecific hybrid sterility in indica and japonica rice, molecular detection revealed that one known major locus S5 exists in the HHZ-ZJ8 hybrids. Then, genome editing was used to knockout S5-ORF5⁺ (killer gene) in HHZ and S5-ORF4⁺ (partner gene) in ZJ8. Compared with the wild type, several important agronomic traits of these edited materials had no obvious changes. However, the spikelet fertility of the F₁ plants derived from crossing these edited materials with wild type ZJ8 or HHZ were fully restored.

Conclusion Rational design of indica-japonica hybrid breeding can be achieved by molecular detection and genome editing, enabling rapid cultivation of indica-japonica artificial hybrid-compatible lines and maximizing the retention of genetic diversity in indica and japonica rice. This study provides a new example for breaking the indica-japonica hybrid sterility and utilizing indica-japonica hybrid vigor.