Functional genomics of drought stress response in rice: transcript mapping of annotated unigenes of an indica rice (Oryza sativa L. cv. Nagina 22)

Abstract

Rice being one of the widely cultivated cereals across diverse agroecological systems, is prone to high yield losses due to recurring droughts. In India, drought is a major constraint of rice production and accounts for as much as 15% of yield losses during some years. Conventional plant breeding techniques though cumbersome and time-consuming, have been immensely helpful in releasing drought-tolerant varieties. However, this is not adequate to cope up with the future demand for rice, as drought seems to spread to more regions and seasons across the country. Understanding the genes that govern rice plant architecture and response to drought stress is urgently needed to enhance breeding rice with improved drought tolerance. In order to identify genes associated with drought stress response and their temporal and spatial regulation, we took the genomic approach. By generating a large set of expressed sequence tags (EST_s) from cDNA libraries of drought-stressed seedlings and transcript profiling, we identified 589 genes presumed to be involved in drought stress. These 5814 EST_s are assembled into 2094 contigs and localized onto chromosome arms. We present here the physical map of the 2094 unigene set along with 589 annotated putative stress responsive genes of rice. Further, using EST_s, a few of drought quantitative trait loci (QTL_s) have been dissected and putative candidate genes identified. This will be useful to rice researchers as ready reference source for breeding through developing candidate gene markers, molecular dissection of QTL_s associated with drought stress and map-based cloning.