Identification and functional annotation of drought-induced molecular pathways in sugarcane using suppression subtractive hybridization.

BACKGROUND: Wild ancestors of sugarcane, in particular Saccharum spontaneum, are inherently tolerant to abiotic stress. Interspecific hybrids derived from S. spontaneum possess agronomically desirable traits in addition to their potential for sustaining themselves in drought-stressed conditions. METHODS AND RESULTS: In our study, suppression subtractive hybridisation was used to identify drought-responsive candidate transcripts (DRCTs) under water deficit conditions in AS 04-1687 and TS-GS 2024, which were validated by physiological and molecular expression analysis. The amplicon size of the subtraction libraries ranged from 200 bp to 1.6 kb for AS 04-1687, whereas for TS-GS 20-24, it ranged from 250 bp to 1.1 kb. The sequenced raw reads were processed, assembled, and functionally annotated. A total of 452 and 625 differentially expressed drought-induced transcripts were identified in AS 04-1687 and TSGS 20-24, respectively. Functional annotation revealed that the expression of a substantial portion of these transcripts was associated with protein modification. In AS 04-1687, drought tolerance was associated with coumarin-mediated stress responses, whereas in TSGS 20-24, drought response was regulated by ABA-mediated signalling cascade and the ascorbate biosynthetic pathway. CONCLUSION: Transcripts belonging to the MYB, NAC, bZIP, SPL, and WRKY were identified as key regulators of drought stress in both genotypes, while in TSGS 20-24, additional transcriptional regulation via JAZ families contributed to coordinating plant defence via ABA signalling, osmotic adjustment, and physiological remodelling. These findings offer valuable insights for identifying novel genes that enhance drought resistance in sugarcane.