Insilico analysis of drought tolerant genes in rice

Abstract

Rice (Oryza sativa L.) is the important cereal food crop and model crop for plant genome analysis. Drought remains as one of the major constraints limiting rice productivity. Conventional breeding approaches are slow in progress towards developing drought tolerant rice varieties due to complex nature of drought tolerance mechanism. The understanding of plant responses to abiotic stresses at the genomic level provides a foundation for gene discovery and genetic engineering of rice for drought tolerance. Identifying quantitative trait loci (QTLs) controlling drought tolerance related traits will help in precise introgression of desired genomic regions (QTLs) through marker assisted selection and genetic engineering. The genomic region on chromosome 9 (73 – 95 cM) controlling drought tolerant related traits were selected and attempts were made through insilico methods to understand the putative candidate genes controlling drought tolerance. Through literature survey and database search, QTL located on chromosome 9 (73 to 95 cM) linked to drought tolerance related traits was selected. About 145 drought responsive genes were found to be located in this region as reported in a publicly available microarray data. The drought responsive genes were classified according to their function and presence of cis elements. Detailed analyses revealed that majority of these drought responsive genes are involved in important cellular functions and enriched with DRE-cis elements. Aquaporin (OsPIP2; 7) and cytochromeP450 (OsCYP78A3) genes were selected for functional validation. Semi-quantitative RT-PCR analysis revealed the differential expression of these genes between contrasting rice genotypes IR64 and Nootripathu for drought tolerance at vegetative stage.