Transcriptomic Analysis Based on RNA-Seq Technology Reveals the Molecular Mechanisms of Sunflower (Helianthus annuus...

Background/Objectives: Sunflower (Helianthus annuus L.) is one of the four major oil crops worldwide and possesses strong stress tolerance. However, salt stress remains limiting in the improvement of sunflower yield and quality. Methods: In this study, the salt-tolerant cultivar P50 and salt-sensitive cultivar P29 were used as experimental materials to conduct transcriptome sequencing on root and leaf samples treated with NaCl. Subsequently, the molecular mechanisms underlying salt tolerance in sunflower were revealed through assembly and splicing, functional annotation, differential expression analysis, enrichment analysis, and transcription factors (TFs) prediction. Results: Results showed that 54,860,184 and 60,601,572 high-quality clean reads were obtained from the two cultivars, respectively. A total of 110,751 all-unigenes were generated after assembly and clustering, of which 77,536 were functionally annotated. A total of 21,332 differentially expressed genes (DEGs) were identified, including 10,306 upregulated and 11,026 downregulated genes. Quantitative real-time PCR validation of 15 DEGs showed a 93.33% consistency rate with the sequencing data. GO enrichment analysis indicated that DEGs were significantly enriched in pathways related to antioxidant enzyme activities. KEGG enrichment analysis demonstrated that DEGs were primarily involved in 15 carbohydrate metabolism pathways, especially starch and sucrose metabolism. In addition, 67 differentially expressed TF families containing 528 DEGs were identified, including bHLH, AP2/ERF-ERF, MYB, C3H, WRKY, EREBP, B3-ARF, and NAC. Conclusions: Our study constructed a comprehensive transcription map of the sunflower response to salt stress and systematically elucidated the molecular mechanisms underlying salt tolerance. The salt-tolerant sunflower cultivar P50 exhibits an efficient salt stress defense system via three core strategies: (i) activating the antioxidant system to rapidly scavenge excess reactive oxygen species and mitigate oxidative damage; (ii) regulating carbohydrate metabolism through starch and sucrose redistribution to provide energy and osmotic protection against physiological drought; and (iii) mobilizing multiple TF families to establish a complex regulatory network for the precise control of downstream functional genes.