Gene Discovery Of The Rice Drought Resistant QTLs

Rice is an important food staple for millions of people globally. Drought, like many other environmental stresses, limits crop yield. Genetic improvement for drought stress tolerance in rice must deal with the quantitative nature of the trait, which reflects the additive effects of several genetic loci throughout the genome, each making a modest contribution towards the phenotype, through a variety of physiological mechanisms, perhaps conditionally in different environments.To facilitate the discovery of the candidate rice genes underlying Quantitative Trait Loci (QTL) for drought tolerance, we assayed yield components and related traits under stressed and well-water conditions in mapping populations derived from an introgression line of a cross between Azucena, a traditional tropical Japonica variety, and IR64, an elite Indica variety, backcrossed to IR64. This population segregates for height due to allelic variation in the region around sdl, the semi-dwarf gene. We found that yield components also mapped to this region.To facilitate identification of candidate genes, single nucleotide polymorphisms (SNPs) represent a rich source for molecular markers and are valuable for association genetics and fine scale map validation of candidate genes. We have developed IR1SNP as a flexible tool using the two varieties of public rice genome sequence -International Rice Genome Sequence Project (IRGSP) Japonica and Beijing Genome Institute (BGI) Indica - to identify putative SNPs in candidate genes using in silico alignment. IRISNP has been successful used to identify the SNPs in the rice semi-dwarf (SD1) candidate genes region as an example. To discovery of the SNPs in these candidate genes, this thesis describe the overall process that leads to the set up of a SNP database, a pipeline for SNP discovery and a web accessible interface collects the SNP information.We arc presently focusing on the region flanked by the genetic markers RM212 and RM319 on chromosome 1 proximal to the sdl locus. A total of 175 annotated genes were identified from this region and classified based on the genefunctions. These included 48 genes annotated by functional homology to known genes, 23 pseudogenes, 24 ab initio predicted genes supported by an alignment match to an EST of unknown function, and 80 hypothetical genes predicted solely by ab initio means. Among the 48 well-annotated genes, we identified a subset of genes that could be implicated in drought-tolerance, based on other supporting experimental evidence or literature support. In addition, we found 16 candidate genes matching with some literature support for involvement in drought stress response.