Delimitation of the fgr gene for rice fragrance to a 28-kb DNA fragment

The fragrance gene plays an important role in high-quality rice varieties and has been widely used in breeding programs. Using a random sample of 370 individuals from an F2 segregating population developed from a cross between a japonica rice variety 9407 with fragrant flavor and an indica variety IRBB60, the fgr locus was mapped on chromosome 8 between SSR markers, PSM465 and RM1109, with genetic distances of 0.3 cM and 0.1 cM to respective markers. These mapping efforts confirmed the previous mapping results. A large F3 mapping population with 7300 individuals was then developed from F2 plants, in which a small chromosomal region defined by the SSR markers, PSM465 and RM1109, was heterozygous. The analysis of recombinants in the fgr region anchored the gene locus to an interval of 28 kb flanked by the left marker NS9 and the right marker L06. Sequence analysis of this fragment predicted three open reading frames encoding putative 3-methylcrotonyl-CoA carboxylase, putative isoleucyl-tRNA synthetase, and betaine aldehyde dehydrogenase (BADH2). The latter was presumed to be the candidate gene for fragrance. This result will be very useful in molecular cloning of the fgr gene and marker-assisted transfer of the fgr gene in rice breeding programs.