Genome-wide Identification and Characterization of TCP Gene Family in and Their Role in Perianth Development

Overview

Journal Front Plant Sci

Date 2024 Feb 20

PMID 38375086

Authors

Xinrui Wei

Meng Yuan

Bao-Qiang Zheng

Lin Zhou

Yan Wang

Affiliations

Soon will be listed here.

Abstract

TCP is a widely distributed, essential plant transcription factor that regulates plant growth and development. An in-depth study of genes in , a crucial parent in genetic breeding and an excellent model material to explore perianth development in , has not been conducted. We identified 23 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 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 genes contained many developmental stress-, light-, and phytohormone-responsive elements in their promoter regions. Distinct expression patterns were observed among the 23 genes, suggesting that these genes have diverse regulatory roles at different stages of perianth development or in different organs. For instance, and play a role in early perianth development, and and are significantly expressed during late perianth development. , , , and are the most likely to be involved in perianth and leaf development. was significantly expressed in the gynandrium. Specially, MADS-specific binding sites were present in most 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.

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References

Hugouvieux V, Zubieta C . MADS transcription factors cooperate: complexities of complex formation. J Exp Bot. 2018; 69(8):1821-1823. PMC: 6019057. DOI: 10.1093/jxb/ery099. View

Li X, Zhang G, Liang Y, Hu L, Zhu B, Qi D . TCP7 interacts with Nuclear Factor-Ys to promote flowering by directly regulating SOC1 in Arabidopsis. Plant J. 2021; 108(5):1493-1506. DOI: 10.1111/tpj.15524. View

Zhang L, Zhou L, Yung W, Su W, Huang M . Ectopic expression of Torenia fournieri TCP8 and TCP13 alters the leaf and petal phenotypes in Arabidopsis thaliana. Physiol Plant. 2021; 173(3):856-866. DOI: 10.1111/ppl.13479. View

Liu D, Zhang C, Zhao X, Ke S, Li Y, Zhang D . Genome-wide analysis of the TCP gene family and their expression pattern in . Front Plant Sci. 2022; 13:1068969. PMC: 9772009. DOI: 10.3389/fpls.2022.1068969. View

Kaufmann K, Muino J, Jauregui R, Airoldi C, Smaczniak C, Krajewski P . Target genes of the MADS transcription factor SEPALLATA3: integration of developmental and hormonal pathways in the Arabidopsis flower. PLoS Biol. 2009; 7(4):e1000090. PMC: 2671559. DOI: 10.1371/journal.pbio.1000090. View

Liu D, Luo Y, Han H, Liu Y, Alam S, Zhao H . Genome-wide analysis of citrus TCP transcription factors and their responses to abiotic stresses. BMC Plant Biol. 2022; 22(1):325. PMC: 9258177. DOI: 10.1186/s12870-022-03709-3. View

Zhao Y, Broholm S, Wang F, Rijpkema A, Lan T, Albert V . TCP and MADS-Box Transcription Factor Networks Regulate Heteromorphic Flower Type Identity in . Plant Physiol. 2020; 184(3):1455-1468. PMC: 7608168. DOI: 10.1104/pp.20.00702. View

Yuan C, Huang D, Yang Y, Sun M, Cheng T, Wang J . CmCYC2-like transcription factors may interact with each other or bind to the promoter to regulate floral symmetry development in Chrysanthemum morifolium. Plant Mol Biol. 2020; 103(1-2):159-171. DOI: 10.1007/s11103-020-00981-5. View

Alem A, Ariel F, Cho Y, Hong J, Gonzalez D, Viola I . TCP15 interacts with GOLDEN2-LIKE 1 to control cotyledon opening in Arabidopsis. Plant J. 2022; 110(3):748-763. DOI: 10.1111/tpj.15701. View

10.

Tilly J, Allen D, Jack T . The CArG boxes in the promoter of the Arabidopsis floral organ identity gene APETALA3 mediate diverse regulatory effects. Development. 1998; 125(9):1647-57. DOI: 10.1242/dev.125.9.1647. View

11.

Valsecchi I, Guittard-Crilat E, Maldiney R, Habricot Y, Lignon S, Lebrun R . The intrinsically disordered C-terminal region of Arabidopsis thaliana TCP8 transcription factor acts both as a transactivation and self-assembly domain. Mol Biosyst. 2013; 9(9):2282-95. DOI: 10.1039/c3mb70128j. View

12.

Mitoma M, Kanno A . The Greenish Flower Phenotype of (Orchidaceae) Is Caused by a Mutation in the -Like MADS-Box Gene . Front Plant Sci. 2018; 9:831. PMC: 6018480. DOI: 10.3389/fpls.2018.00831. View

13.

Yu H, Goh C . Identification and characterization of three orchid MADS-box genes of the AP1/AGL9 subfamily during floral transition. Plant Physiol. 2000; 123(4):1325-36. PMC: 59091. DOI: 10.1104/pp.123.4.1325. View

14.

Lan J, Qin G . The Regulation of CIN-like TCP Transcription Factors. Int J Mol Sci. 2020; 21(12). PMC: 7349945. DOI: 10.3390/ijms21124498. View

15.

Pan Z, Chen Y, Du J, Chen Y, Chung M, Tsai W . Flower development of Phalaenopsis orchid involves functionally divergent SEPALLATA-like genes. New Phytol. 2014; 202(3):1024-1042. PMC: 4288972. DOI: 10.1111/nph.12723. View

16.

Sun B, He X, Long F, Yu C, Fei Y . The Role of in the Lobed Leaf Formation of var. . Int J Mol Sci. 2022; 23(21). PMC: 9653974. DOI: 10.3390/ijms232113296. View

17.

Yang F, Zhu G, Wang Z, Liu H, Xu Q, Huang D . Integrated mRNA and microRNA transcriptome variations in the multi-tepal mutant provide insights into the floral patterning of the orchid Cymbidium goeringii. BMC Genomics. 2017; 18(1):367. PMC: 5426072. DOI: 10.1186/s12864-017-3756-9. View

18.

Lucero L, Manavella P, Gras D, Ariel F, Gonzalez D . Class I and Class II TCP Transcription Factors Modulate SOC1-Dependent Flowering at Multiple Levels. Mol Plant. 2017; 10(12):1571-1574. DOI: 10.1016/j.molp.2017.09.001. View

19.

Viola I, Alem A, Jure R, Gonzalez D . Physiological Roles and Mechanisms of Action of Class I TCP Transcription Factors. Int J Mol Sci. 2023; 24(6). PMC: 10049435. DOI: 10.3390/ijms24065437. View

20.

Liu M, Fu Q, Ma Z, Sun W, Huang L, Wu Q . Genome-wide investigation of the MADS gene family and dehulling genes in tartary buckwheat (Fagopyrum tataricum). Planta. 2019; 249(5):1301-1318. DOI: 10.1007/s00425-019-03089-3. View