Identification of stress-responsive genes in an indica rice (Oryza sativa L.) using ESTs generated from drought-stressed seedlings

The impacts of drought on plant growth and development limit cereal crop production worldwide. Rice (Oryza sativa) productivity and production is severely affected due to recurrent droughts in almost all agroecological zones. With the advent of molecular and genomic technologies, emphasis is now placed on understanding the mechanisms of genetic control of the drought-stress response. In order to identify genes associated with water-stress response in rice, ESTs generated from a normalized cDNA library, constructed from drought-stressed leaf tissue of an indica cultivar, Nagina 22 were used. Analysis of 7794 cDNA sequences led to the identification of 5815 rice ESTs. Of these, 334 exhibited no significant sequence homology with any rice ESTs or full-length cDNAs in public databases, indicating that these transcripts are enriched during drought stress. Analysis of these 5815 ESTs led to the identification of 1677 unique sequences. To characterize this drought transcriptome further and to identify candidate genes associated with the drought-stress response, the rice data were compared with those for abiotic stress-induced sequences obtained from expression profiling studies in Arabidopsis, barley, maize, and rice. This comparative analysis identified 589 putative stress-responsive genes (SRGs) that are shared by these diverse plant species. Further, the identified leaf SRGs were compared to expression profiles for a drought-stressed rice panicle library to identify common sequences. Significantly, 125 genes were found to be expressed under drought stress in both tissues. The functional classification of these 125 genes showed that a majority of them are associated with cellular metabolism, signal transduction, and transcriptional regulation

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

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 (ESTs) from cDNA libraries of drought-stressed seedlings and transcript profiling, we identified 589 genes presumed to be involved in drought stress. These 5814 ESTs 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 ESTs, a few of drought quantitative trait loci (QTLs) 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 QTLs associated with drought stress and map-based cloning

Isolation and characterization of expressed sequence tags (ESTs) from subtracted cDNA libraries of Pennisetum glaucum seedlings

Pearl millet (Pennisetum glaucum), used as forage and grain crop is a stress tolerant species. Here we identify differentially regulated transcripts in response to abiotic (salinity, drought and cold) stresses from subtracted cDNA libraries by single-pass sequencing of cDNA clones. A total of 2,494 EST sequences were clustered and assembled into a collection of 1,850 unique sequences with 224 contigs and 1,626 singleton sequences. By sequence comparisons the putative functions of many ESTs could be assigned. Genes with stress related functions include those involved in cellular defense against abiotic stresses and transcripts for proteins involved in stress response signaling and transcription in addition to ESTs encoding unknown functions. These provide new candidate genes for investigation to elucidate their role in abiotic stress. The relative mRNA abundance of 38 selected genes, quantified using real time quantitative RT-PCR, demonstrated the existence of a complex gene regulatory network that differentially modulates gene expression in a kinetics-specific manner in response to different abiotic stresses. Notably, housekeeping and non-target genes were effectively reduced in these subtracted cDNA libraries constructed. These EST sequences are a rich source of stress-related genes and reveal a major part of the stress-response transcriptome that will provide the foundation for further studies into understanding Pennisetum's adaptability to harsh environmental conditions