Transcriptome analysis identifies novel gene(s) and pathways for salt stress responses in Dandi cultivar

Salinity tolerance has been documented as one of the main abiotic stresses, disapprovingly impeding the growth and fertility of core food crops including rice in the ecosphere. We have evaluated 24 varieties exposed to salt stress (150–300 mM NaCl; for 48–72 h) at the vegetative stage. The cellular-level physiological response was observed by assessing the morphophysiological parameters and significant differences were observed in the rice varieties of the Gujarat region of the Indian continent. Additionally, we have performed a comparative transcriptome analysis of the shoots and roots of rice varieties at the vegetative stage (Dandi, salinity-tolerant; and GR-11, Salinity-sensitive) in response to salinity. Based on transcriptome analysis, the genes specifically activated and differentially over-expressed during salinity stress belong to different functional categories mostly located on chromosomes 1, 2, 3, 4, 8, and 11 in both cultivars. A total of 617 and 676 significant DEGs with log2-fold change in the range of ≥  + 2.0 to ≤  − 2.0 were identified from the comparative analysis of the two data sets DS (Dandi Shoot) and GS (GR-11Shoot) (Dandi vs. Control, GR-11 vs. Control) in the shoot sample. Similarly, a total of 510 and 508 significant DEGs DR (Dandi Root) and GR (GR-11 Root) (Dandi vs. Control, GR-11 vs. Control) in the root samples. The DEGs were examined against the KEGG database to explore the biological pathways of Dandi (226) and GR-11 (397) in the shoot as well as root (218,285) samples. Further PageMan analysis showed that there was a significantly higher number of DEGs (p < 0.05, ≥  ± 2.0-fold) involved in signalling pathways including secondary metabolism, hormone metabolism, abiotic stresses, and development which have significant regulatory functions in shoot and root of Dandi and GR-11 variety of rice.