comparative studies on tolerance of the extremely tolerant and extremely sensitive recombinant inbred lines bulks of rice to salt stress

Identification of the novel genes is an indispensable prerequisite for developing rice varieties with increased salinity tolerance. to this end, a comparative transcriptome analysis of the extremely tolerant and extremely sensitive recombinant inbred lines (rils) bulks derived from a cross between salt-tolerant variety csr 27 and salt-sensitive variety mi 48 was carried out using microarray data analysis and motif promoter analysis. according to the results, 417 and 169 genes showed differential expression in the tolerant bulk and sensitive bulk respectively under salt stress conditions. among degs, 6 degs were significantly up-regulated in salt sensitive rils but were significantly down-regulated in salt tolerant rils.  it points to their role as negative regulators of the salinity tolerance mechanism. using meme, we detected seven significant motifs. moreover, the majority of motifs have relationship with ap2/erf domain transcription factor. it shows that erf family transcription factor is the upstream components in a transcriptional cascade that modulate gene expression in response to salinity stress. the gomo analysis for the motifs discovered by meme identified several interesting biological functions such as regulation of transcription, dna-dependent, dna replication, mismatch repair and translation. moreover, these motifs were involved in molecular functions, including transcription factor activity and structural constituent of ribosome. this analysis provides useful information about cis-elements in the genes associated with salinity stress in rice.