Chromosomal translocations are a significant driver of hybrid sterility in rice.

Hybrid sterility is a major barrier in exploiting hybrid vigor in rice grains produced by crossing distantly related parents. While genetic mechanisms such as the killer-protector system have been extensively studied, novel systems underlying hybrid sterility remain poorly characterized. Here, a novel hybrid sterility system governed by two tightly pseudolinked loci SGA1 (on chromosome 1) and SGA2 (on chromosome 2) is reported, which induces semi-sterility in male and female gametes during hybridization between the indica and japonica subspecies. Chromosomal translocations were proposed as the basis for pseudolinkage and unbiased segregation, supported by cytological evidence of meiotic quadrivalent configurations and translocation breakpoint sequences. Gametophytic sterility was identified as the primary driver of dual male-female semi-sterility in translocated heterozygotes. Furthermore, large-segment chromosomal translocations are found to be widespread in rice. Analysis of 120 pangenomic rice accessions revealed that chromosomal translocations are prevalent among cultivars, with one-third exhibiting large translocations (>500 kb). Translocation breakpoints were mainly localized in intergenic and intronic regions, and the disrupted genes were identified as predominantly transposons and retrotransposons. Besides, large translocations were validated through sequence analysis and phenotypic assays. Overall, this study establishes chromosomal translocations as a critical driver of hybrid sterility and provides new insights into heterosis constraints.