Generation of simple, perfect markers for cereal quality traits

Commercially important traits including fragrance and starch gelatinisation temperature (GT) are difficult phenotypes for breeders to asses. We recently identified polymorphisms that control these key rice quality traits. The annotated rice genome sequence used in combination with re-sequencing by PCR facilitated the discovery of these polymorphisms and the design of perfect molecular markers for each of these traits. In the absence of a genome sequence, larger mapping populations, a genome library and more sequencing would have been necessary. Although these traits result from different classes of polymorphism, fragrance is due to an eight base pair deletion while gelatinisation temperature variation results from a polymorphism at a single nucleotide in combination with another polymorphism at two adjacent bases elsewhere in the gene, both have proven to be amenable to the development of a competitive allele specific PCR assay. Both are simple, cheap, robust, perfect genotyping assays for these difficult to measure and complex traits. Understanding the link between these polymorphisms and the resultant phenotype could be extended to other cereals and used for the identification and or generation of valuable phenotypes in these cereals. Similar assays could then be easily developed for use in breeding programs.