Identification of simple sequence repeat markers for utilizing wide-compatibility genes in inter-subspecific hybrids in rice (Oryza sativa L.)

Abstract

Although pronounced heterosis in inter-subspecific hybrids was known in rice for a long time, its utilization for hybrid rice breeding has been limited due to their hybrid sterility (HS). For the last two decades, however, a few inter-subspecific hybrids have been developed by incorporating wide-compatibility genes (WCG) that resolve HS, into parental lines of these inter-subspecific hybrids. For effective use of WCG, it is necessary to find convenient markers linked to WCG of practical importance. In this paper, initially a set of simple sequence repeat (SSR) markers in the vicinity of known WCG loci identified based on comparative linkage maps have been surveyed in a population derived from the three-way cross- IR36/Dular//Akihikari, where a known donor of WCG Dular was crossed to a representative indica and japonica cultivar. Of the five parental polymorphic markers, RM253 and RM276 were found to be closely linked to the WCG locus S5 at a distance of 3.0 and 2.8 cM, respectively. Later, loci for HS were examined in three F(2) populations derived from inter-subspecific crosses, with same set of SSR markers. The locus S8 was confirmed to have major influence on HS in the F(2 )population derived from CHMRF-1/Taichung65 since two SSR markers in its vicinity, RM412 and RM141, co-segregated with HS at a map distance of 7.6 and 4.8 cM, respectively. In the F(2) population derived from the cross BPT5204/Taipei309, three SSR markers in the vicinity of S5, RM50, RM276 and RM136 co-segregated with HS at a map distance of 4.2, 3.2 and 7.8 cM, respectively. In the third F(2 )population derived from Swarna/Taipei309, the SSR markers in the vicinity of S5, RM225, RM253, RM50, RM276 and RM136 were identified to co-segregate with HS at a map distance of 3.2, 2.6, 3.4, 2.6 and 6.6 cM, respectively. These results indicated a clear picture of WCG in Dular as well as the predominant role of HS alleles at S5 locus. The identified SSR markers are expected to be used for incorporation of WCG into parental lines in hybrid rice breeding to solve HS in inter-subspecific hybrids.

Validation of molecular markers linked to fertility restorer gene(s) for WA-CMS lines of rice

“…The reason for the failure to detect polymorphism with the CAPS marker RG140FL/RL in the parental lines of the BC 1 F 1 population could be due to lack of polymorphism between the parental lines in the genomic region amplified by the marker due to narrow genetic diversity. Another reason could be that the CMS line IR62829A is reported to possess hybrid sterility genes (Singh et al 2006).…”

Genomic changes at the early stage of somatic hybridization

“…Among these deleted fragments, the RM50 SSR locus is linked to S5, a gene that controls sterility in japonica x indica sexual hybrids (Singh et al, 2006), and that is located within a recombination hotspot. Given that the extent of chromatin elimination is higher in the more exotic somatic hybrids, such pressure could affect a number of genomic regions containing genes responsible for wide hybrid sterility, which merits further investigation.…”

The Evolution of Sex-Independent Transmission Ratio Distortion Involving Multiple Allelic Interactions at a Single Locus in Rice

“…Therefore, the developmental phase of the S 6 locus-mediated abortion and consequent segregation pattern are both unequivocally distinguished from those mediated by the Cif/cim genes, although the possibility cannot be ruled out that abortions at different developmental phases are caused by pleiotropic effects of a single gene, which would resemble a phenomenon caused by the Tcb1 locus in maize (Kermicle 2006). The hybrid sterility loci, S 1 (Sano 1990), S 5 (Yanagihara et al 1995), S 8 (Singh et al 2006), S 10 (Sano et al 1994, and S 26 (Kubo and Yoshimura 2001), have also been mapped to chromosome 6, a mapping procedure carried out using different pairs of crossing parents. These genes were mapped in chromosomal regions apart from the S 6 locus, and segregation analyses of marker genes tightly linked with these loci also indicated that the segregation distortion caused by these loci was independent of that by the S 6 locus (our unpublished data).…”