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In-Silico Prediction and Functional Analysis of Salt Stress Responsive Genes in Rice (Oryza sativa)

Jyotika Bhati, Pavan Chaduvula K, Anil Rai1, Kishore Gaikwad, Soma Marla S and Sanjeev Kumar

The area for cultivation of rice on salt affected soil is increasing at very fast rate due to insensitivity towards following proper package and practices of crops production in order to increasing productivity of rice due to high population pressure in Asian countries. Therefore, it is important to identify genes and their regulatory elements for development of salt stress tolerance variety of rice. In order to identify genes responsible for salt stress in rice 7746 expressed sequence tags (ESTs), expressed in salinity stress condition, were mined from the different web recourses. The downloaded ESTs were clustered and assembled into 672 contigs. Biological functions were obtained only for 424 out of 672 contigs through Gene Ontology (GO). The remaining contigs were used for reconstruction, validation and annotation of salt stress genes. These contigs were mapped on to rice genome and full length gene sequences were designed. These designed candidate genes were further validated by means of a) Integrating with known salt stress related quantitative trait loci (QTL) on rice genome and b) Promoter analysis. In this study novel candidate genes were identified which may have a possible involvement in regulation of salt stress mechanism and may be useful in molecular breeding programme in rice for development of salt tolerance varieties through Molecular Assisted Breeding.