Rice genome sequence accelerates the discovery of commercially important genes and polymorphisms

Traditionally, identification of genes which control important traits has been labour intensive and time consuming. We have demonstrated the annotated rice genome sequence used in combination with re-sequencing by PCR greatly facilitates the discovery of both genes and polymorphisms within genes, which control commercially important traits. Identification of the gene which controls fragrance was achieved using a relatively small mapping population of 168 F2 individuals. Analysis of the recombination data and the relatively large tract (385 kbp) of annotated genome sequence between the flanking markers revealed a candidate gene in this region which plausibly explained the known biochemistry of fragrance. Re-sequencing the gene in a fragrant variety found a mutation which was in accord with the known genetics of fragrance. In the absence of a genome sequence, a much larger mapping population, a genome library and more sequencing would have been necessary. Likewise, availability of the rice genome sequence greatly simplified the task of re-sequencing the SSIIa encoding gene which allowed us to identify single nucleotide polymorphisms (SNP) in soluble starch synthase IIa which explain gelatinisation temperature (GT). This important quantitative trait seems to be determined by two SNP in the 3’ end of the coding sequence. Because starch bio-synthetic genes display high levels of interspecific conservation, it is likely this knowledge will have utility in other species.