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

Abstract

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 F2 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 F2 plants into true breeding sterile, fertile, and segregating fertile plants based on F3 family studies. From the survey of 389 arbitrary primers in bulked segregant analysis, four RAPD markers were identified in which three, OPF182600, OPB19750, and OPAA7550, were linked to tms3(t) in repulsion phase and one, OPAC3640, was linked to tms3(t) in coupling phase. The tms3(t) gene was flanked by OPF182600 and OPAC3640 on one side and by OPAA7550 and OPB19750 on the other side. All four markers were low-copy sequences and two of them (OPF182600 and OPAC3640) detected polymorphism when the markers were used to probe the genomic blots. Subsequently, OPAC3640 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.

Fine mapping and candidate gene prediction of the photoperiod and thermo-sensitive genic male sterile gene pms1(t) in rice

“…Localization studies showed that the TGMS genes from different sources may be located in different chromosomes. Examples include reports that tms1 (Wang et al, 1995), tms2 (Lopez et al, 2003), tms3 (Subudhi et al, 1997), tms4 (Dong et al, 2000), tms5 (Yang et al, 2007a), rtms1 (Jia et al, 2001), ms-h (Koh et al, 1999), and tms6 (Lee et al, 2005) were located on chromosomes 8, 7, 6, 2, 2, 10, 9, and 5, respectively. However, these TGMS materials are not to be applied in rice production because of the non-stability of their sterility.…”

Photoperiod- and thermo-sensitive genic male sterility in rice are caused by a point mutation in a novel noncoding RNA that produces a small RNA

“…To date, a number of loci that control PGMS or TGMS, including reverse PGMS or reverse TGMS, in different rice lines have been mapped to different chromosomes: photoperiod-sensitive genic male sterile genes pms1 [15,16], pms2 [15], pms3 [17][18][19][20]; reverse photoperiod-sensitive genic male sterile genes rpms1 [21], rpms2 [21]; thermo-sensitive genic male-sterile genes tms1 [22], tms2 [23,24], tms3 [25,26], tms4 [27], tms5 [5,[28][29][30][31], tms6 [32], tms6(t) [33]; photoperiod-thermosensitive genic male sterile genes ptgms2-1 [34], pms1(t) [35]; and reverse thermo-sensitive genic male-sterile genes rtms1 [36]. Despite the wide application of PGMS and TGMS lines in hybrid rice breeding, the genes responsible for PGMS and TGMS in these lines have not been cloned, and the molecular mechanisms underlying these traits remain unclear.…”

A TGMS-linked nuclear DNA marker as originated from the mitochondrial genome in rice (Oryza sativa L.)

“…It was therefore concluded that pF18 was transferred from the mitochondrion into the nuclear genome. A mapping study indicated that the insertion point was on the short arm of chromosome 6 (Subudhi et al, 1997).…”

“…The TGMS mutant line, IR32364TGMS, showed complete male-sterility at day/night temperatures of 32°/24°C but partial fertility at 27°/21°C in an IRRI phytotron. A RAPD marker, OPF18 2600 , amplified by the random primer OPF18 (5-TTCCCGGGTT-3) was found to be linked to tms3 (Subudhi et al, 1997).…”

“…We initiated a study on this TGMS line with the final objective to elucidate the molecular basis of TGMS and to apply it to rice hybrid seed production. We identified four RAPD markers linked to tms3 and located tms3 on the short arm of chromosome 6 (Subudhi et al, 1997). One of the RAPD markers, OPF18 2600 was very peculiar.…”