Genetic dissection of hybrid breakdown in an indica/japonica cross and fine mapping of a quantitative trait locus qSF-12 in rice (Oryza sativa L.)

Hybrid breakdown is an important form of post-zygotic reproductive barriers, often arising from hybrid progeny between two varietal groups of Asian cultivated rice (Oryza sativa L.), indica and japonica. However, the genetic mechanism underlying the hybrid breakdown remains unclear. In the present study, a chromosomal segment substitute line (CSSL) population together with a backcross inbred line population, derived from the same cross of Sasanishiki/Habataki, were employed for genetic analysis of rice hybrid breakdown (spikelet fertility as index). Quantitative trait locus mapping results showed that, in both populations, qSF-12 was stably detected across different locations and growing seasons, which was found to interact with qSF-8. Subsequently, a CSSL line SL438 with low spikelet fertility was used to cross with Sasanishiki to generate the secondary F2 population for the mapping of qSF-12. The results showed that qSF-12 was restricted to a 137-kb long region on BAC clone AL928774, containing 11 predicted ORFs in total. The DNA sequencing revealed that a 3-bp insertion/deletion exists between two parents in the coding region of LOC_Os12g38850. Together with the RNA-seq data, it is suggested that LOC_Os12g38850is the putative candidate of qSF-12, which encodes a DUF1336 domain containing protein. These results provide an important clue to further dissect the mechanism of hybrid breakdown in rice and the linked markers will be useful in rice cross breeding.