Introgression of a Complex Genomic Structural Variation Causes Hybrid Male Sterility in GJ Rice ( Oryza sativa L.) Subspecies.

Hybrids between different subspecies of rice Oryza   sativa L. commonly show hybrid sterility. Here we show that a widely planted commercial japonica / GJ variety, DHX2, exhibited hybrid sterility when crossing with other GJ varieties. Using the high-quality genome assembly, we identified three copies of the Sc gene in DHX2, whereas Nipponbare (Nip) had only one copy of Sc . Knocking out the extra copies of Sc in DHX2 significantly improved the pollen fertility of the F 1 plant of DHX2/Nip cross. The population structure analysis revealed that a slight introgression from Basmati1 might occur in the genome of DHX2. We demonstrated that both DHX2 and Basmati1 harbored three copies of Sc . Moreover, the introgression of GS3 and BADH2 / fgr from Basmati1 confers the slender and fragrance grain of DHX2. These results add to our understanding of the hybrid sterility of inter-subspecies and intra-subspecies and may provide a novel strategy for hybrid breeding.