Genome-Wide Identification and Expression Analysis of R2R3-MYB Gene Family in Chrysanthemum indicum Under Low-Temperature Stress

Low-temperature stress is a major factor limiting the development of the chrysanthemum industry. Chrysanthemum indicum L., wild germplasm with strong cold tolerance within the genus, is an ideal material for mining cold resistance genes. Through preliminary transcriptome analysis of C. indicum under low-temperature stress (PRJNA1391062), we found that multiple R2R3-MYB family members were significantly differentially expressed (|log2FC| &ge: 1, p &lt: 0.05), suggesting that this family may play important roles in cold stress responses. Within the C. indicum genome, we identified 63 R2R3-MYB members (CiMYBs) through HMMER and BLAST searches combined with domain validation. Phylogenetic analysis classified these genes into 19 subgroups, with most key nodes supported by bootstrap values &gt: 80%. Promoter cis-element analysis revealed enrichment of elements related to light responsiveness, hormone signaling, and stress responses, including 41 low-temperature responsive elements distributed across 28 genes and 32 drought-induced MYB-binding sites present in 23 genes. Synteny analysis identified 13 duplicated gene pairs within the C. indicum genome and 41 collinear gene pairs between C. indicum and Arabidopsis thaliana L. Transcriptome data under low-temperature stress showed that 22 of the 63 CiMYB members were differentially expressed under 4 &deg:C acclimation and &minus:4 &deg:C freezing stress, and they could be classified into three response patterns: acute stress-responsive (rapid upregulation upon initial stress), acclimation-induced (significant activation after 4 &deg:C acclimation), and freezing-suppressed (downregulation after &minus:4 &deg:C freezing). Six differentially expressed genes were randomly selected for RT-qPCR validation, and the results showed consistent trends with the transcriptome data. This study provides a comprehensive identification of R2R3-MYB family members in C. indicum and reveals their expression divergence under low-temperature stress, offering candidate gene resources for deciphering the cold adaptation mechanisms of C. indicum and breeding new cold-resistant chrysanthemum cultivars.