Transcriptome analysis of safflower (Carthamus tinctorius L.) reveals the roles of osmotic adjustment and regulatory mechanisms in response to drought stress

Although safflower (Carthamus tinctorius L.) is a momentous medicinal and industrial crop with intrinsic stress tolerance, molecular mechanism response to drought stress at the transcriptome level has been rarely scrutinized. Here, comprehensive transcriptome analysis was executed in the seedling stage to decipher responsive genes to drought stress. 138 M (90.9%) out of 152 M clean reads were mapped to the reference genome, generating 74,491 contigs. 1,096 differentially expressed genes (DEGs) were identified under drought stress, containing 454 genes up-regulated and 642 genes down-regulated. Transferases (n = 58), kinases (n = 51), and transcription factors (n = 47) were key genetic players under drought stress. Thirty-nine transcription factors (belonging to the HD-ZIP, ERF, CO-like, bZIP, TALE, NAC, C2H2, FAR1, GRAS, MYB-related, and Trihelix families) were upregulated, and 59 transcription factors (belonging to the bHLH, GATA, HD-ZIP, WRKY, G2-like, DBB and LBD families) were downregulated. The results illustrated that drought stress dramatically diminished photosynthesis rate and chlorophyll content. The functional enrichment analysis indicated that in addition to canonical pathways of response to drought stress (such as metabolic pathways and secondary metabolite biosynthesis), revealed reconnaissance of more specific pathways, including peroxisome, autophagy, photosynthesis, glycerolipid metabolism, beta-alanine biosynthesis, and protein processing. In addition to distinguishing the classical drought stress-responsive genes in safflower, several novel genes were recognized in drought stress transcriptome analysis that have not been reported in safflower and have been less studied in other plants. These candidate genes could be promising in future breeding programs for the extension of tolerant cultivars and as molecular markers.