Identification of the TCP Gene Family in Actinidia chinensis var. Hongyang and Their Expression Analysis in Fruit

doi:10.13560/j.cnki.biotech.bull.1985.2024-0820

Abstract

Abstract:

Objective The members of TEOSINTE-BRANCHED1/CYCLOIDEA/PCF in kiwifruit ‘Hongyang’ (Actinidia chinensis var. Hongyang) (AcTCPs) gene family were identified based on whole-genome. Taxonomic and evolutionary relationships of the members were analyzed, and the expression profiles of the AcTCP genes in tissue-specific expression, fruit development process, and hormones treatments were explored. These findings provide a basis for further exploring the function of the AcTCP gene in kiwifruit. Method Bioinformatics methods were used to analyze the physicochemical properties, gene structure, conserved motifs, cis-acting elements and inter-species covariance of TCP transcription factors in kiwifruit ‘Hongyang’ were analyzed. RNA-seq and RT-qPCR were used to investigate the expression profiles of AcTCPs in different tissues, fruit development and in response to hormonal stimuli. Result A total of 40 AcTCP genes with complete TCP domains were identified on19 chromosomes in kiwifruit ‘Hongyang’ and named AcTCP1-AcTCP40. Using phylogenetic analyses, conserved motif, and gene structure analyses, the family members were divided into PCF (21), CIN (12) and CYC/TB1 (7). Synteny analysis showed that genome-wide or segment-based replication played an important role in the expansion of the kiwifruit ‘Hongyang’ TCP gene family. Analysis of tissue-specificity showed that the six candidate genes expressed significantly high in male flowers and fruits. The results of RT-qPCR experiments at different stages of fruit development found that AcTCP1 showed elevated expressions at later stages of fruit development, while AcTCP11, AcTCP35, AcTCP10, and AcTCP32 demonstrated high expression during the initial stages of fruit development, and the expression pattern was consistent with the transcriptomic results. In fruit, abscisic acid (ABA) and ethylene (ET) treatments to the fruits down-regulated six candidate AcTCPs, gibberellin (GA₃) treatment up-regulated the expressions of AcTCP1, AcTCP35 and AcTCP32, and the forchlorfenuron (CPPU) treatment up-regulated the expressions of AcTCP1, AcTCP35 and AcTCP32 in initial stages, whereas GA₃ and CPPU decreased the expressions of the others AcTCPs. Conclusion A total of 40 TCP members from kiwifruit ‘Hongyang’ were systematically identified. The expression patterns of six candidate genes highly express in the fruit and male flowers. The expressions of AcTCP35, AcTCP32, AcTCP1, AcTCP10, AcTCP11 and AcTCP20 in the fruit are involved in kiwifruit development and are regulated by various exogenous hormones (ABA, ET, GA₃, and CPPU).

Key words: Actinidia chinensis var. Hongyang, TCP transcription factors, genome-wide identification, bioinformatics, organizational differences, expression pattern analysis, hormone treatment

SONG Shu-yi, JIANG Kai-xiu, LIU Huan-yan, HUANG Ya-cheng, LIU Lin-ya. Identification of the TCP Gene Family in Actinidia chinensis var. Hongyang and Their Expression Analysis in Fruit[J]. Biotechnology Bulletin, 2025, 41(3): 190-201.

Figures/Tables 8

Fig. 1 Phylogenetic analysis (A) of TCP transcription factors in A. chinensis (Ac), A. thaliana (At), F. vesca (Fv), Ananas comosus (Aco) and P. Granatum L (Pg) and amino acid sequence comparison of conserved structural domains of AcTCPs (B)

Fig. 2 Phylogenetic tree (A), conserved motif (B) and genomic structure (C) analysis of AcTCPs

Fig. 3 Cis-element analysis of AcTCP genes promoter region

Fig. 4 Covariance analysis of AcTCPs genesPurple, green and black gene names indicate PFC genes, CIN genes and CYC/TB1 genes, respectively. Purple, green and black lines indicate intrachromosomal covariance of PFC genes, CIN genes and CYC/TB1 genes, respectively. The blue line indicates the intrachromosomal covariance between the CIN gene and the CYC/TB1 gene

Fig. 5 Expression analysis of TCP genes in fruits at different fruit developmental stages of A. chinensis var. Hongyang

Fig. 6 Analysis of tissue expression pattern of AcTCP genes in A. chinensis var. HongyangDifferent letters indicate significant difference at P<0.05 level. The same below

Fig. 7 Analysis of expression patterns of AcTCP genes in different stages of fruit development

Fig. 8 Expressions of AcTCP genes in different hormone treatmentsA: ABA treatment; B: ET treatment; C: GA3 treatment; D: CPPU treatment. Horizontal coordinates indicate different treatment times

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