Integrative analysis of transcriptome and physiological responses reveals lignin biosynthesis pathway and genes mediating salt-alkali tolerance in Sorghum

• Lignin biosynthesis genes are upregulated in saline-alkali tolerant sorghum LTR108. • MYB transcription factors are preferentially induced in response to saline-alkali stress and potentially prime early lignin biosynthesis. • Enhanced lignin deposition strengthens root cell walls in tolerant sorghum. • Saline-alkali tolerant variety LTR108 accumulates higher soluble sugars for osmotic adjustment. • Integrative transcriptomic and physio-biochemical analysis links lignin pathways to sorghum saline-alkali resilience. Salt-alkali stress (SAS) severely limits crop growth and development, posing a major challenge to global agricultural productivity. Sorghum bicolor L., a C4 crop with relatively strong salt-alkali tolerance, exhibits varying degrees of tolerance to severe SAS among varieties, and the molecular mechanisms underlying these differences remain unclear. To uncover these mechanisms, we performed comparative transcriptomic, phenotypic, physiological, and biochemical analyses on two contrasting sorghum genotypes, SAS-tolerant LTR108 and SAS-sensitive 654, under severe SAS conditions. Under severe SAS, LTR108 exhibited markedly enhanced resilience, maintaining a seedling height approximately 88 % higher, a shoot fresh weight nearly tenfold greater, and a chlorophyll content about 2.4-fold higher than 654 (all p < 0.05). Physiological analysis further demonstrated that LTR108 sustained significantly lower levels of malondialdehyde (MDA) and higher activity of catalase (CAT), consistent with its reinforced antioxidant capacity and membrane stability. Transcriptomic profiling revealed that key enzyme-coding genes in lignin biosynthesis pathways, such as PAL, 4CL , and C4H , were significantly up-regulated or expressed at higher levels in LTR108 than in 654. This transcriptional activation correlated with elevated lignin deposition in LTR108 roots, likely reinforcing cell wall integrity and contributing to its improved SAS tolerance. Strikingly, MYB transcription factors were preferentially upregulated in LTR108 during early SAS, potentially orchestrating the rapid activation of lignin biosynthesis and priming stress adaptation. Despite shared expression patterns in carbohydrate metabolism genes, LTR108 exhibits more genes with higher transcriptional levels and uniquely accumulated higher soluble sugar levels, suggesting transcriptional regulation favoring osmotic adjustment. Our findings demonstrate that LTR108 enhances SAS tolerance through coordinated activation of lignin biosynthesis and related regulation networks, offering novel strategies for breeding salt-alkali resilient crops.