Genome-wide identification, classification, and expression pattern analysis of the TCP transcription factor family in...

Carrot (Daucus carota L.) is an important root vegetable crop in the Apiaceae family, widely cultivated worldwide, with high nutritional and economic value. The TCP gene family is a plant-specific transcription factor family containing an atypical basic helix-loop-helix (bHLH) structure, which plays a crucial role in regulating plant growth and development and responding to stresses. In this study, genome-wide identification and systematic analysis of the TCP gene family in carrot were conducted using bioinformatics methods. The results showed that a total of 50 DcTCP family genes were identified in the carrot genome. The molecular weights of the proteins encoded by these genes ranged from 6056 to 53,512.5 Da, most of which were hydrophilic and unstable proteins, and all were localized in the nucleus. The DcTCP gene family had a relatively simple structure with a small number of introns, and 48 genes contained motif 1. Cis-acting element analysis revealed that DcTCP genes contained elements related to light response, stress response, and hormone response, participating in various physiological regulatory pathways. Phylogenetic analysis classified them into three subfamilies: PCF, CIN, and CYC/TB1. Among them, the PCF subfamily had the most members (36), accounting for 72% of the total family. Chromosomal localization indicated that the 50 DcTCP genes were unevenly distributed on 9 chromosomes, and whole-genome duplication (WGD) was the main driving force for the expansion of this family. Regulatory network prediction identified 12 regulatory miRNAs with targeting relationships to DcTCP genes, among which miR319 had the most target genes (7 target genes), and 28 DcTCP proteins could form 214 pairs of protein-protein interactions. Expression pattern analysis showed that DcTCP genes exhibited specific expression at different developmental stages of carrot roots. Some genes (such as DcTCP33 and DcTCP37) were highly expressed throughout the entire developmental process, while the expression levels of other genes gradually increased with the developmental stage, suggesting their involvement in the regulation of fleshy root formation and development. This study clarified the basic characteristics and potential regulatory mechanisms of the DcTCP gene family in carrot, enriched the research content of the plant TCP gene family, and provided a theoretical basis and gene resources for subsequent analysis of carrot growth and development rules and cultivation of stress-resistant and high-quality varieties.