Genome-wide identification and expression pattern analysis of CCT genes in Brassica rapa

The term “CCT genes” refer to the genes encoding proteins containing CCT (CONSTANS, CONSTANS-LIKE and TOC1) domains, widely found in higher plants, and they are a pivotal gene family linked to flowering traits in plants. In-depth investigations have revealed that these genes not only participate in the photoperiodic response of plants but also play significant roles in abiotic stress responses and plant hormone signal transduction. Our study successfully identified 69 CCT family genes in Brassica rapa using bioinformatics and comparative genomics techniques and subsequently investigated their physicochemical properties, phylogenetic relationships, conserved domains, gene structures, syntenic relationships, cis-acting elements, KEGG enrichment, and expression patterns across diverse tissues/organs. Our findings revealed that the 69 BrCCTs genes are non-uniformly distributed across 10 chromosomes. We categorized them into four distinct subfamilies based on their conserved domains. Members belonging to the same subfamily exhibit remarkable similarity in their conserved motifs but display considerable differences in their gene structures. Notably, the majority of these genes harbor light-responsive and hormone-responsive elements, which is an indication of their potential roles in regulating plant flowering and growth development. KEGG enrichment analysis revealed that these genes are primarily enriched in cellular functions and nucleic acid binding sites. Additionally, transcriptome analysis showed the distinct expression patterns of the 69 BrCCTs in roots, stems, leaves, flowers, and callus tissues. Members of the COL subfamily displayed particularly prominent expression levels. Overall, this study offers profound insights into the functionalities and roles of the CCT gene family in B. rapa and thus provides a solid foundation for the selection and improvement of early-maturing B. rapa varieties.