Identification of Up-regulated Transcripts in Salt Tolerant Rice (Oryza sativa L.) Cultivar using the cDNA-AFLP Technique

Salt stress is one of the main abiotic stresses for rice that causes negative effects on its growth and productivity. In present study, effects of salt stress on differential gene expression of some genes which are responsible in salt stress were investigated in two rice tolerant and sensitive genotypes (FL478 and IR29) by applying cDNA-AFLP technique. Among the TDFs (Transcript Derived Fragments (were generated by 2 restriction enzymes and 18 primer combination that displayed up-regulation expression in tolerant line with respect to the control treatment and sensitive line in response to salt stress, 28 TDF were separated and 21 of them were cloned, sequenced and submitted in gene bank and finally they were analyzed by BLAST algorithm. All known TDFs in current study were belonged to different groups of genes related to metabolism, signal transduction, transcription factors, detoxification, transport system and other mechanism related to salt stress which suggests a lot of process to be involved in salt stress responses. Some genes were further selected for validation of cDNA-AFLP expression patterns using real-time PCR. The results of real-time PCR confirmed the expression patterns that were detected using the cDNA-AFLP technique. The results of this research show that cDNA-AFLP is a powerful technique for investigating the expression pattern of rice genes under salt stress. Moreover our finding will help either elucidation the molecular basis of salt stress effects on rice rice or identification those genes that could increase the salt tolerance of rice plant.