Molecular mapping of a thermosensitive genetic male sterility gene in rice using bulked segregant analysis

The thermosensitive genetic male sterility (TGMS) system is considered to be a more efficient alternative to the cytoplasmic male sterility (CMS) system for hybrid rice. An F-2 population from a cross between a TGMS mutant line (IR32364TGMS) and IR68 was used to map the TGMS gene tms3(t). Fertile and sterile bulks were constructed following the classification of F-3 plants into true breeding sterile, fertile, and segregating fertile plants based on Fg family studies. From the survey of 389 arbitrary primers in bulked segregant analysis, four RAPD markers were identified in which three, OPF18(2600), OPB19(750), and OPAA7(550), were linked to tms3(t) in repulsion phase and one, OPAC(640), was linked to tms3(t) in coupling phase. The tms3(t) gene was flanked by OPF18(2600) and OPAC3(640) on one side and by OPAA7(550) and OPB19(750) on the other side. All four markers were low-copy sequences and two of them (OPF18(2600) and OPAC3(640)) detected polymorphism when the markers were used to probe the genomic blots. Subsequently, OPAC3(640) was mapped to the short arm of chromosome 6 using a mapping population available at IRRI. However, no RFLP markers from this region showed linkage to tms3(t) owing to the lack of polymorphism between the parents. All RAPD fragments were cloned and partially sequenced from both ends. Thus, PCR primers can be designed to develop PCR markers for marker-assisted breeding to facilitate the transfer of tms3(t) from one genetic background to another.