In silico Identification of Genes for Combined Drought and Salinity Stress in Rice (Oryza sativa L.)

Abstract

The salinity and water stress are the important abiotic stresses which severely affect the rice growth, development and yield depending on degree of stress. Moreover, this stresses are inter-related and includes many crosstalk at genetically and physiologically. The identification of genes controlling both the stress would mean a lot in understanding molecular mechanism of tolerance, which in turn assist in development of stress resilient genotypes. In the present study, an in silico approach was used to identify genes commonly expressed under combined drought and salt stress using microarray data retrieved from NCBIGEO database. The meta-analysis of this transcriptome data revealed 35 candidate genes expressed under combined stress with 82.8% of the genes showing up regulation and 18.2% genes with down regulation. The functional annotation of candidate genes showed the expression of diverse stress responsive proteins mainly transcription factor, UDP-glucosyl transferase, glycosyl ptransferase 8, flavanone 3-hydroxylase, plant PDR ABC transporter associated domain and dehydrins. Among the expressed proteins, transcription factors shared major part in gene regulation. The key gene Os05g48650.1 which present on chromosome five at 28.8 Mb physical position encoded for HBP-1b protein. The earlier authors proved that the over expression of this HBP-1b gene in rice plant showed improved tolerance to salt and drought stress. Two more genes Os11g26780.1 and Os11g26790.1 co-localized on chromosome 11 encodes for an important stress responsive dehydrin protein which is positively correlated with the tolerance to cold, drought, and salt stress. Finally, in conclusion the genes Os11g26780.1, Os11g26790.1, Os06g27560.1 and Os05g48650.1 were directly related with salt and drought stress tolerance. The introgression of these genes in high yielding stress susceptible genotypes could assist in developing stress tolerant cultivars.