Transcriptome Profiling Reveals the Molecular Regulatory Network in Response to Salt Stress in Intervarietal Hybrids of Chrysanthemum × morifolium ‘Yannong Jinxia’ × ‘Yannong Qiujin’

Salinity stress is a major abiotic factor that significantly constrains plant growth and development. Hybridization within the genus Chrysanthemum produces hybrid offspring exhibiting salt tolerance levels that are intermediate between those of the parental. However, the molecular mechanisms underlying this phenomenon remain unreported. In this study, the salt-sensitive chrysanthemum variety ‘Yannong Jinxia’ (JX) and the salt-tolerant chrysanthemum variety ‘Yannong Qiujin’ (QJ) were selected as parents for hybridization, aiming to elucidate the molecular basis of this intermediate salt tolerance. The hybrid offspring ‘Yannong Xiutang’ (XT) were verified using SRAP-PCR. After salt stress treatment, physiological indicators—including antioxidant enzyme activity and malondialdehyde (MDA) content—were measured in both the parents and the offspring. Their differential responses to salt stress were systematically compared by integrating transcriptome sequencing with KEGG enrichment analysis. Additionally, the expression patterns of key genes in the SOS signaling pathway were analyzed. Results showed that under salt stress, the hybrid XT exhibited intermediate levels of antioxidant enzyme activity and MDA accumulation relative to its parents. Transcriptomic analysis revealed distinct pathway enrichments: comparisons between QJ and XT highlighted differences in galactose metabolism, whereas JX vs. XT showed specific enrichment in pathways such as isoflavonoid biosynthesis and fatty acid elongation. Additionally, the expression of the SOS pathway gene in XT was found to be intermediate between the two parental lines. This study elucidates the molecular regulatory network associated with salt tolerance in hybrid offspring of ground cover chrysanthemum, laying a theoretical foundation for the development of salt-tolerant chrysanthemum germplasm.