Comparative transcriptomic analysis reveals distinct drought-response patterns in Chrysanthemum morifolium ‘Jinsihuangju’ and Chrysanthemum chanetii

Abstract

To elucidate the differential responses of chrysanthemum materials to drought stress and their underlying molecular regulatory mechanisms, this study used Chrysanthemum chanetii H. Lév. (XHJ) and Chrysanthemum morifolium ‘Jinsihuangju’ (JSHJ). Phenotypic observation, physiological measurements, transcriptome sequencing, GO/KEGG enrichment analyses, and qRT-PCR validation were integrated to systematically compare their drought-response characteristics. The results showed that drought stress induced more severe wilting and canopy shrinkage in JSHJ, whereas XHJ maintained a relatively intact canopy structure. Physiological analysis showed that the activities of POD, SOD, and APX, as well as the contents of Pro, SS, and SP, increased in both materials, indicating that antioxidant defense and osmotic adjustment jointly participated in drought responses. Transcriptome analysis generated 60,531 nonredundant transcripts, with 3,502 and 3,792 drought-responsive DETs in JSHJ and XHJ, respectively. A factorial material × treatment analysis further identified 630 transcripts with significantly different drought responses. KEGG enrichment showed that DETs were mainly involved in photosynthesis, carbon and carbohydrate metabolism, antioxidant defense, energy metabolism, and signal transduction. Major candidate regulatory families included AP2/ERF, bHLH, MYB, NAC, WRKY, bZIP, and RLK-Pelle. qRT-PCR showed overall consistency with RNA-seq expression patterns for the selected genes. Integrated analysis showed that XHJ maintained lower absolute MDA levels and better canopy integrity, whereas JSHJ exhibited stronger antioxidant and transcriptional responses. These findings provide candidate transcript resources and a comparative framework for genetic mapping and breeding-oriented evaluation of drought-associated traits in chrysanthemum.