Summary• A sex-independent transmission ratio distortion (siTRD) system detected in the interspecific cross in rice was analyzed in order to understand its significance in reproductive barriers. The S 1 gene, derived from African rice Oryza glaberrima, induced preferential abortion of both male and female gametes possessing its allelic alternative ( ), from Asian rice O. sativa, only in the heterozygote.• The siTRD was characterized by resolving it into mTRD and fTRD occurring through male and female gametes, respectively, cytological analysis of gametophyte development, and mapping of the S 1 locus using near-isogenic lines. The allelic distribution of the S 1 locus in Asian and African rice species complexes was also analyzed.• The siTRD system involved at least two components affecting male and female gametogeneses, respectively, including a modifier(s) that enhances fTRD. The chromosomal location of the major component causing the mTRD was delimited within an approx. 40 kb region. The S 1 locus induced hybrid sterility in any pairwise combination between Asian and African rice species complexes.• The allelic state of the S 1 locus has diverged between Asian and African rice species complexes, suggesting that the TRD system has a significant role in the reproductive barriers in rice.

Transmission ratio distortion (TRD) is frequently observed in inter-and intraspecific hybrids of plants, leading to a violation of Mendelian inheritance. Sex-independent TRD (si TRD) was detected in a hybrid between Asian cultivated rice and its wild ancestor. Here we examined how si TRD caused by an allelic interaction at a specific locus arose in Asian rice species. The si TRD is controlled by the S 6 locus via a mechanism in which the S 6 allele acts as a gamete eliminator, and both the male and female gametes possessing the opposite allele (S 6 a ) are aborted only in heterozygotes (S 6 /S 6 a ). Fine mapping revealed that the S 6 locus is located near the centromere of chromosome 6. Testcross experiments using near-isogenic lines (NILs) carrying either the S 6 or S 6 a alleles revealed that Asian rice strains frequently harbor an additional allele (S 6 n ) the presence of which, in heterozygotic states (S 6 /S 6 n and S 6 a /S 6 n ), does not result in si TRD. A prominent reduction in the nucleotide diversity of S 6 or S 6 a carriers relative to that of S 6 n carriers was detected in the chromosomal region. These results suggest that the two incompatible alleles (S 6 and S 6 a ) arose independently from S 6 n and established genetically discontinuous relationships between limited constituents of the Asian rice population.