Genome-wide identification of the TCP gene family in Chrysanthemum lavandulifolium and its homologs expression patterns during flower development in different Chrysanthemum species

Genome-wide identification and expression analysis of the TCP transcription factor family and its response to abiotic stress in rapeseed (Brassica napus L.)

The study used 80 BnTCP genes (Brassica napus TCP genes) in rapeseed, which were identified and designated with nomenclature based on their chromosomal locations. A systematic analysis encompassed the evolutionary relationships, classifications, gene structures, motif compositions, chromosome localization, and gene replication events within these BnTCP genes. These 80 BnTCP proteins were categorized into three subfamilies, with the PCF subfamily showing significant expansion during evolution. Segmental duplications were identified as a major driver of TCP family amplification. To comprehensively assess the evolutionary relationships of the TCP family across diverse plant species, nine comparative genomic maps were constructed, elucidating homologous genes between B. napus and representative monocotyledonous and dicotyledonous plants. In the final phase of the study, the gene expression response characteristics of 15 selected BnTCP genes across various biological processes and stress responses were examined. Noteworthy candidates, including BnTCP28, BnTCP30, and BnTCP76, were identified as potentially crucial in tissue development and environmental stress responses.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-025-04273-x.

Identification and expression responses of TCP gene family in Opisthopappus taihangensis under abiotic stress

The TCP gene family plays pivotal roles in the development and abiotic stress responses of plants; however, no data has been provided for this gene family in Opisthopappus taihangensis. Based on O. taihangensis genome, 14 TCP genes were identified and divided into two classes (I and II). After tandem and segmental duplication/whole-genome duplication (WGD), more loss and less gain events of OtTCPs occurred, which might be related with the underwent purifying selection during the evolution. The conserved motifs and structures of OtTCP genes contained light response, growth and development, hormone response, and stress-related cis-acting elements. Different OtTCP genes, even duplicated gene pairs, could be expressed in different tissues, which implied that OtTCP genes had diverse function. Among OtTCPs, OtTCP4, 9 and 11 of CYC clade (Class II) presented a relative wide expression pattern with no or one intron. The three TCP genes could be regarded as important candidate factors for O. taihangensis in growth, development and stress response. These results provided some clues and references for the further in-depth exploration of O. taihangensis resistance mechanisms, as well as those of other unique eco-environment plants.

TaTCP21-A negatively regulates wheat cold tolerance via repressing expression of TaDREB1C

Cold stress is one of the important harmful factors that seriously affect wheat (Triticum aestivum) yield and quality. TCP transcription factor plays important roles in the process of plant cell proliferation and growth. In this study, we identified 60 TaTCP genes expressed in strong cold resistant winter wheat variety Dongnongdongmai1 (Dn1) under cold stress by previous transcriptome data, of which 13 TaTCPs showed significant differences in expression. The evolution of TaTCPs was analyzed, and the results showed that there were 2 homologous pairs in TaTCPs with AtTCPs and 90 homologous pairs in TaTCPs with OsTCPs. Expression patterns of 20 TaTCPs under cold stress were analyzed by qRT-PCR, and TCP21-A with significant expression differences was screened. We obtained tcp21-A mutant from the EMS mutant library of winter wheat Kenong9204. We observed that the mutation of TaTCP21-A significantly improved its cold resistance. Subsequently, transcriptome analysis revealed that TCP21-A inhibited expression of cold responsive gene TaDREB1C. Finally, subcellular localization and yeast one hybrid were used to verify that TCP21-A can act as a transcription factor to bind to the GGTCCC promoter element. Luciferase reporter gene experiment showed that TCP21-A inhibits the transcriptional activity of the TaDREB1C promoter. In summary, we systematically analyzed the expression patterns of TaTCP family members in Dn1 under cold stress and demonstrated that TaTCP21-A negatively regulated wheat cold tolerance by inhibiting expression of TaDREB1C. These results provide new insights into the functional mechanism of TaTCP transcription factors in response to cold stress.

ECE-CYC1 Transcription Factor CmCYC1a May Interact with CmCYC2 in Regulating Flower Symmetry and Stamen Development in Chrysanthemum morifolium

BACKGROUND

The attractive inflorescence of Chrysanthemum morifolium, its capitulum, is always composed of ray (female, zygomorphy) and disc (bisexual, actinomorphy) florets, but the formation mechanism remains elusive. The gene diversification pattern of the ECE (CYC/TB1) clade has been speculated to correlate with the capitulum. Within the three subclades of ECE, the involvement of CYC2 in defining floret identity and regulating flower symmetry has been demonstrated in many species of Asteraceae, including C. morifolium. Differential expression of the other two subclade genes, CYC1 and CYC3, in different florets has been reported in other Asteraceae groups, yet their functions in flower development have not been investigated.

METHODS

Here, a CYC1 gene, CmCYC1a, was isolated and its expression pattern was studied in C. morifolium. The function of CmCYC1a was identified with gene transformation in Arabidopsis thaliana and yeast two-hybrid (Y2H) assays were performed to explore the interaction between CmCYC1 and CmCYC2.

RESULTS

CmCYC1a was expressed at higher levels in disc florets than in ray florets and the expression of CmCYC1a was increased in both florets during the flowering process. Overexpression of CmCYC1a in A. thaliana changed flower symmetry from actinomorphic to zygomorphic, with fewer stamens. Furthermore, CmCYC1a could interact with CmCYC2b, CmCYC2d, and CmCYC2f in Y2H assays.

CONCLUSIONS

The results provide evidence for the involvement of CmCYC1a in regulating flower symmetry and stamen development in C. morifolium and deepen our comprehension of the contributions of ECE genes in capitulum formation.

Chrysanthemum lavandulifolium homolog CYCLIN A2;1 modulates cell division in ray florets

The morphology of ray florets in chrysanthemums is tightly associated with cell division and expansion, both of which require proper progression of the cell cycle. Here, we identified a Chrysanthemum lavandulifolium homolog, CYCLIN A2;1 (CYCA2;1), the expression of which in ray florets is negatively correlated with petal width. We found that CYC2a, a TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) transcription factor in the CYCLOIDEA2 (CYC2) family, interacts with and stabilizes CYC2b, and the latter can bind to the promoter of CYCA2;1 to activate its transcription. Overexpression of CYCA2;1 in C. lavandulifolium reduced the size of capitula and ray florets. Cytological analysis revealed that CYCA2;1 overexpression inhibited both cell division and expansion via repression of the mitotic cell cycle in ray florets, the latitudinal development of which was more relatively negatively influenced, thereby leading to increased ratios of petal length to width at later developmental stages. Yeast two-hybrid library screening revealed multiple proteins that interacted with CYCA2;1 including ACTIN-RELATED PROTEIN7 (ARP7), and silencing ARP7 inhibited the development of ray florets. Co-immunoprecipitation assays confirmed that CYCA2;1 could induce the degradation of ARP7 to inhibit the development of ray florets. Taken together, our results indicate the presence of a regulatory network in ray floret development in chrysanthemum consisting of CYC2b-CYCA2;1-ARP7 that acts via governing mitosis. The identification of this network has the potential to facilitate breeding efforts targeted at producing novel ornamental traits in the flowers.

Genome-wide identification and characterization of TCP gene family in Dendrobium nobile and their role in perianth development

TCP is a widely distributed, essential plant transcription factor that regulates plant growth and development. An in-depth study of TCP genes in Dendrobium nobile, a crucial parent in genetic breeding and an excellent model material to explore perianth development in Dendrobium, has not been conducted. We identified 23 DnTCP genes unevenly distributed across 19 chromosomes and classified them as Class I PCF (12 members), Class II: CIN (10 members), and CYC/TB1 (1 member) based on the conserved domain and phylogenetic analysis. Most DnTCPs in the same subclade had similar gene and motif structures. Segmental duplication was the predominant duplication event for TCP genes, and no tandem duplication was observed. Seven genes in the CIN subclade had potential miR319 and -159 target sites. Cis-acting element analysis showed that most DnTCP genes contained many developmental stress-, light-, and phytohormone-responsive elements in their promoter regions. Distinct expression patterns were observed among the 23 DnTCP genes, suggesting that these genes have diverse regulatory roles at different stages of perianth development or in different organs. For instance, DnTCP4 and DnTCP18 play a role in early perianth development, and DnTCP5 and DnTCP10 are significantly expressed during late perianth development. DnTCP17, 20, 21, and 22 are the most likely to be involved in perianth and leaf development. DnTCP11 was significantly expressed in the gynandrium. Specially, MADS-specific binding sites were present in most DnTCP genes putative promoters, and two Class I DnTCPs were in the nucleus and interacted with each other or with the MADS-box. The interactions between TCP and the MADS-box have been described for the first time in orchids, which broadens our understanding of the regulatory network of TCP involved in perianth development in orchids.