THB1, a putative transmembrane protein that causes hybrid breakdown in rice.

Hybrid breakdown is a post-zygotic reproductive isolation that hinders genetic exchange between species or populations in both animals and plants. Two complementary recessive genes, () and , cause hybrid breakdown in rice (). The present study delimited the locus to a 9.1-kb sequence, containing a single gene encoding a putative transmembrane protein with unknown functions. Haplotype analysis of in the two core collections of 119 accessions revealed that these accessions were divided into 22 haplotypes. A test cross with carrier showed that haplotype2 (H2) was assigned to and was restricted to . A nonsynonymous nucleotide polymorphism (SNP) specific to H2 was identified as a causal mutation in . A test cross with carrier indicated that six accessions, including , , and , carried . These results suggest that has recently evolved in , whereas arose in an ancient and introgressed into the present three subgroups. Furthermore, we developed a derived cleaved amplified polymorphic sequence (dCAPS) marker to detect causal SNP in . Our findings provide new insights into reproductive isolation and may benefit rice breeding.