Transcriptome map for seedling stage specific salinity stress response indicates a specific set of genes as candidate for saline tolerance in Oryza sativa L.

Oryza sativa L. cv IR64 is a widely cultivated, salt-sensitive indica rice, while Pokkali is a well-known, naturally salt-tolerant relative. To understand the molecular basis of differences in their salinity tolerance, three subtractive cDNA libraries were constructed. A total of 1,194 salinity-regulated cDNAs are reported here that may serve as repositories for future individual gene-based functional genomics studies. Gene expression data using macroarrays and Northern blots gives support to our hypothesis that salinity tolerance of Pokkali may be due to constitutive overexpression of many genes that function in salinity tolerance and are stress inducible in IR64. Analysis of genome architecture revealed the presence of these genes on all the chromosomes with several distinct clusters. Notably, a few mapped on one of the major quantitative trait loci - Saltol - on chromosome 1 and were found to be differentially regulated in the two contrasting genotypes. The present study also defines a set of known abiotic stress inducible genes, including CaMBP, GST, LEA, V-ATPase, OSAP1 zinc finger protein, and transcription factor HBP1B, that were expressed at high levels in Pokkali even in the absence of stress. These proposed genes may prove useful as candidates in improving salinity tolerance in crop plants using transgenic approach.