Transcriptome and Expression Analysis of Genes Related to Regulatory Mechanisms in Holly (Ilex dabieshanensis) under Cold Stress

Ilex dabieshanensis (K. Yao and M. B. Deng) is not only an important economic tree species, but also has the characteristics of evergreens in all seasons, as well as strong cold resistance. In order to understand the molecular mechanism of holly’s response to cold stress, we used transcriptome analysis to identify the main signaling pathways and key genes involved in cold stress. The result showed that 5750 differentially expressed genes (DEGs) were identified under different cold treatment times compared with the control (cold—0 h). The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of DEGs showed that seven phytohormone signal transduction were the most highly enriched, including abscisic acid (ABA), ethylene (ET), cytokinin (CK), auxin (IAA), gibberellin (GA), jasmonate (JA), and brassinosteroids (BR). In addition, proline metabolism, arginine metabolism, flavonoid biosynthesis, and anthocyanin biosynthesis were also implicated in response to cold stress. The weighted gene co-expression network analysis (WGCNA) showed that the genes in two modules were significantly up-regulated after 12 h and 24 h treatments, suggesting these two module genes may participate in the cold stress. The gene ontology (GO) results of the two module genes showed that calcium, scavenging reactive oxygen species, and nitric oxide might act as signaling molecules to regulate cold tolerance in holly. By calculating the connectivity and function prediction of genes in the two modules, five genes (evm.TU.CHR2.244, evm.TU.CHR1.1507, evm.TU.CHR1.1821, evm.TU.CHR2.89, and evm.TU.CHR2.210) were identified as the key hub genes of I. dabieshanensis response to cold stress. These results provided candidate genes and clues for further studies on the molecular genetic mechanism of cold stress in holly.