Identification of differentially-expressed genes in response to salt stress in the salt-tolerant Sri Lankan rice variety At354

Rice is highly sensitive to salt stress, an expanding abiotic stress factor that limits rice yield improvement. Development of salt tolerant rice varieties based on molecular breeding methods requires identification of genes responsible. for various mechanisms and responses that contribute to salt tolerance. The objective of the present work was to identify genes, which are differentially-expressed in response to salt stress in the salt-tolerant Sri Lankan rice variety, At354. Two cDNA libraries were constructed from mRNA of shoot samples of salt-stressed (100 mM NaCl) At354 at Phase I and Phase II (24 hours and 10 days, respectively after increasing salt stress up to 100 mM) of salt stress development. A total of 3192 and 960 cDNA clones respectively were screened from Phase I and II libraries. Differential hybridization of the cDNA clones with probes prepared from salt-stressed and unstressed At354 shoot samples enabled identification of up and down-regulated genes in response to salt stress in Phase I and Phase II. The identified, differentially-expressed cDNA clones were re-confirmed by another round of differential hybridization and through Northern hybridization by the RNA dot blot method. Relative reverse transcription polymerase chain reaction (RT-PCR) was performed to compare the expression levels of selected differentially-expressed genes. Sequencing and subsequent homology search in databases identified 14 up-regulated genes and 17 down-regulated genes during Phase I in At354. Similarly, 11 up-regulated genes and 2 down-regulated genes were identified during Phase II. Possible functions of the identified, differentially-expressed genes in conferring salt tolerance in At354 is discussed extensively. These genes may enable exploration of newer avenues for engineering salt tolerance in rice.