Sunflower (Helianthus annuus L.), an important oilseed crop, is often used as a pioneer species for improving saline-alkali soils. However, the molecular mechanisms underlying sunflower seedling responses to combined saline-alkali stress remain unclear. This study aimed to elucidate the molecular basis of saline-alkali tolerance at the seedling stage by comparing physiological and transcriptomic responses between tolerant and sensitive sunflower hybrids. The saline-alkali tolerant hybrid K-27 and the sensitive hybrid K-7 were used as experimental materials. Root samples were collected at 0, 3, 12, 24, 48, and 96 h after exposure to combined saline-alkali stress (0.5% NaCl + Na₂CO₃, adjusted to pH 9.0). Physiological parameters, including antioxidant enzyme activities, osmolyte contents, ion concentrations, membrane damage levels, and cell wall components, were measured, followed by transcriptome sequencing analysis. Phenotypic analysis showed that the root length inhibition rate and fresh weight loss rate of K-27 were significantly lower than those of K-7, indicating stronger tolerance. Physiological analysis revealed that K-27 exhibited an inducible antioxidant enzyme response pattern. In addition, K-27 achieved osmotic adjustment through sustained proline accumulation (peaking at 12 h and remaining significantly higher than that of K-7 at 96 h) and exhibited higher basal levels of lignin and hemicellulose. Transcriptome analysis showed that the number of upregulated genes in K-27 was consistently higher than in K-7 at all time points, with 5,283 genes upregulated as early as 3 h after stress exposure. Venn analysis identified 44 core differentially expressed genes (cDEGs) shared between the two genotypes, which were mainly enriched in auxin biosynthesis regulation, phenylpropanoid biosynthesis, and glutathione metabolism. Among them, the benzoic acid carboxyl methyltransferase gene (BAMT) was continuously upregulated in K-27 but persistently downregulated in K-7. In addition, five other genes (encoding fatty aldehyde dehydrogenase, pectin methylesterase inhibitor, glutathione S-transferase, INPP5E, and HXXXD-type acyltransferase) exhibited significantly higher expression levels in K-27. K-27 tolerates combined saline-alkali stress through coordinated multi-layered response mechanisms, including inducible antioxidant defense, maintenance of ion homeostasis, sustained osmotic adjustment, and activation of the phenylpropanoid metabolic pathway. Candidate genes such as BAMT may provide potential targets for molecular breeding of saline-alkali tolerant sunflower, although their functions require further experimental validation.

Plant SABATH methyltransferases contribute to volatile formation, hormone homeostasis and stress responses, but their family-wide organization in sunflower remains poorly characterized. Using the HanXRQr2.0-SUNRISE reference genome, we identified 33 high-confidence HaSABATH genes and integrated phylogenetic, duplication, synteny, promoter and protein-structure analyses with expression profiles from 200 public RNA sequencing (RNA-seq) libraries representing 87 distinct conditions. Twelve genes belonged to the salicylic acid/jasmonic acid methyltransferase-related Clade I, 19 to the benzoic acid/salicylic acid methyltransferase-related Clade II, and two to other lineages. Tandem, proximal, dispersed and whole-genome/segmental duplication contributed to the family, with overlapping tandem and segmental evidence for HaSABATH4 and HaSABATH15. Eleven reliable nonsynonymous-to-synonymous substitution ratios were below one. Most predicted proteins showed high model confidence. Across the sampled conditions, Clade I members generally showed higher expression levels and broader expression, while many Clade II members were weakly expressed or condition-biased. HaSABATH4 and HaSABATH6 were prioritized for follow-up under combined saline–alkali stress. This integrated analysis links evolutionary context to expression divergence and provides candidates for targeted biochemical and genetic studies.