Comparative transcriptomic and metabolomic analyses reveal key genes and metabolic pathways underlying differential saline-alkali tolerance in triticale seedlings

Saline-alkali stress poses a significant threat to global agricultural productivity, necessitating the development of stress-resilient crop varieties. In this study, a comprehensive multi-omics approach was employed to elucidate the adaptive mechanisms of triticale under single salt (SS), mixed alkali (MB), and mixed saline-alkali (MSA) stress conditions. Through the evaluation of 178 germplasms, M25 was identified as stress-tolerant and QT-22 as stress-sensitive. M25 exhibited higher germination rate, enhanced antioxidant capacity, and sustained photosynthetic performance. Transcriptomic analyses revealed 1,200 conserved differentially expressed genes enriched in caffeine and sulfur metabolism and photosynthesis and 82 conserved differentially accumulated metabolites associated with anthocyanin biosynthesis. Notably, we identified and validated several key candidate genes, including transcript25361, transcript61050, transcript22731, and transcript20253, using qRT-PCR. MB treatment predominantly activated alkaloid biosynthesis, whereas MSA treatment triggered diterpenoid-related pathways. These results underscore the importance of anthocyanin biosynthesis and phosphonate metabolism in triticale stress adaptation. This study established molecular targets for breeding, standardized phenotyping protocols (200 mM SS, 150 mM MB, 250 mM MSA), and a conceptual framework for the development of saline-alkali-resilient crop varieties. Overall, this study advances the understanding of plant stress adaptation and offers practical insights for crop improvement in marginal environments.