Genome-wide identification, classification, and expression analysis of TCP transcription factors in carrot

Abstract

Carrot (Daucus carota L.) is a crop with rich nutritional value and is one of the most important economical horticulture crops worldwide. The TEOSINTE BRANCHED 1, CYCLOIDEA, PROLIFERATING CELL FACTORS (TCP) transcription factor (TF) family plays important roles in several physiological processes; However, TCP TFs in carrot are rarely reported. In this study, 36 D. carota TCP (DcTCP) TFs were identified from the carrot genome database. On the basis of phylogenetic relationship with TCP TFs in Arabidopsis, the DcTCP family was divided into two classes, namely class I and class II (including CIN and CYC/TB1 subclass). The number of DcTCP TFs in classes I and II were 22 and 14, respectively. Motif analysis and chromosome location of DcTCP TFs were also conducted. All of the DcTCP genes were distributed on nine chromosomes of carrot. The distribution of TCP TFs in different species indicates that the number of TCP TFs is consistent with plant evolution. Quantitative real-time PCR assay was performed to further understand the expression patterns of DcTCP genes during the development of carrot. The expression levels of DcTCP33 and DcTCP36 increased with the germination of carrot seed. The CIN subclass of DcTCPs (DcTCP1, DcTCP4, and DcTCP5) was primarily expressed in leaf blades, whereas the DcTCP26 gene was mainly expressed in roots. These results can provide potentially useful information about TCP TF identification and help explain the roles of TCP TFs in carrots.