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Identification and Expression Analysis of TCP Genes in Saccharum spontaneum L

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Abstract

The TCP family genes have been under selection during domestication in maize and related andropogoneae crops. They encode plant-specific transcription factors involved in growth and development, especially in shaping the plant morphology and architecture. Sugarcane (Saccharum spp.) is the most productive in harvesting tonnage and 5th economically valuable crops worldwide for supporting world’s sugar and fuel ethanol production. Based on recently published sugarcane genome, we performed a genome-wide analysis of this gene family in the sugarcane genome and identified 22 TCP genes (SsTCPs), with 1–4 alleles each. They distributed across 28 chromosomes of S. spontaneum. Phylogenetic analysis showed that all 22 SsTCP genes can be classifed into two major groups: class I and class II. All 22 groups of SsTCPs showed species-specific clustering with TCPs of sorghum which indicate close relationship between sorghum and Saccharum. Structural organization of SsTCP genes showed that 37 SsTCPs are intronless and of the 22 SsTCPs with introns exist in coding region, which are different with TCPs of sorghum and wheat that located in UTR region. Expression study showed that transcripts of class I SsTCPs were more abundant than transcripts of class II SsTCPs. Moreover, the expression of SsTCP5–4, SsTCP6–2, SsTCP8–1, SsTCP12, SsTCP13, SsTCP15–1, SsTCP17–1 and SsTCP17–6 displayed significant change after plant hormones treatments, which suggest their function related to plant hormones. Cis-element analysis of SsTCPs’s promoter suggests that subfunctionalization may have occurred for homoeologous genes. Taken together, our analysis of TCPs in S. spontaneum provide a good starting for further studies to elucidate their specific function in sugarcane.

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References

  • Baba K, Nakano T, Yamagishi K, Yoshida S (2001) Involvement of a nuclear-encoded basic helix-loop-helix protein in transcription of the light-responsive promoter of psbD. Plant Physiol 125(2):595–603

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bicknell AA, Cenik C, Chua HN, Roth FP, Moore MJ (2012) Introns in UTRs: why we should stop ignoring them. Bioessays 34(12):1025–1034

    Article  CAS  PubMed  Google Scholar 

  • Braun N, de Saint Germain A, Pillot JP, Boutet-Mercey S, Dalmais M, Antoniadi I et al (2012) The pea TCP transcription factor PsBRC1 acts downstream of strigolactones to control shoot branching. Plant Physiol 158(1):225–238

    Article  CAS  PubMed  Google Scholar 

  • Chen C, Xia R, Chen H, He Y (2018) TBtools, a toolkit for biologists integrating various biological data handling tools with a user-friendly interface. BioRxiv, 289660

  • Chow CN, Lee TY, Hung YC, Li GZ, Tseng KC, Liu YH et al (2018) PlantPAN3. 0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants. Nucleic Acids Res 47(D1):D1155–D1163

    Article  PubMed Central  Google Scholar 

  • Cubas P, Lauter N, Doebley J, Coen E (1999) The TCP domain: a motif found in proteins regulating plant growth and development. Plant J 18:215–222

    Article  CAS  PubMed  Google Scholar 

  • Davière JM, Wild M, Regnault T, Baumberger N, Eisler H, Genschik P, Achard P (2014) Class I TCP-DELLA interactions in inflorescence shoot apex determine plant height. Curr Biol 24(16):1923–1928

    Article  CAS  PubMed  Google Scholar 

  • Doebley J, Stec A, Gustus C (1995) Teosinte branched1 and the origin of maize: evidence for epistasis and the evolution of dominance. Genetics 141:333–346

    CAS  PubMed  PubMed Central  Google Scholar 

  • Francis A, Dhaka N, Bakshi M, Jung KH, Sharma MK, Sharma R (2016) Comparative phylogenomic analysis provides insights into TCP gene functions in Sorghum. Sci Rep 6:38488

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Giraud E, Ng S, Carrie C, Duncan O, Low J, Lee CP, ..., Whelan J (2010) TCP transcription factors link the regulation of genes encoding mitochondrial proteins with the circadian clock in Arabidopsis thaliana. The Plant Cell, tpc-110

  • Hubbard L, McSteen P, Doebley J, Hake S (2002) Expression patterns and mutant phenotype of teosinte branched1 correlate with growth suppression in maize and teosinte. Genetics 162(4):1927–1935

    CAS  PubMed  PubMed Central  Google Scholar 

  • Jeffares DC, Penkett CJ, Bähler J (2008) Rapidly regulated genes are intron poor. Trends Genet 24(8):375–378

    Article  CAS  PubMed  Google Scholar 

  • Kebrom TH, Burson BL, Finlayson SA (2006) Phytochrome B represses teosinte Branched1 expression and induces sorghum axillary bud outgrowth in response to light signals. Plant Physiol 140(3):1109–1117

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kieffer M, Master V, Waites R, Davies B (2011) TCP14 and TCP15 affect internode length and leaf shape in Arabidopsis. Plant J 68(1):147–158

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kim SH, Son GH, Bhattacharjee S, Kim HJ, Nam JC, Nguyen PDT, Hong JC, Gassmann W (2014) The A rabidopsis immune adaptor SRFR 1 interacts with TCP transcription factors that redundantly contribute to effector-triggered immunity. Plant J 78(6):978–989

    Article  CAS  PubMed  Google Scholar 

  • Koyama T, Furutani M, Tasaka M, Ohme-Takagi M (2007) TCP transcription factors control the morphology of shoot lateral organs via negative regulation of the expression of boundary-specific genes in Arabidopsis. Plant Cell 19(2):473–484

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y et al (2002) PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res 30(1):325–327

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li S (2015) The Arabidopsis thaliana TCP transcription factors: a broadening horizon beyond development. Plant Signal Behav 10(7):e1044192

    PubMed  PubMed Central  Google Scholar 

  • Li S, Zachgo S (2013) TCP3 interacts with R2R3-MYB proteins, promotes flavonoid biosynthesis and negatively regulates the auxin response in Arabidopsis thaliana. Plant J 76(6):901–913

    Article  CAS  PubMed  Google Scholar 

  • Liu C, Teo ZWN, Bi Y, Song S, Xi W, Yang X, Yin Z, Yu H (2013) A conserved genetic pathway determines inflorescence architecture in Arabidopsis and rice. Dev Cell 24(6):612–622

    Article  CAS  PubMed  Google Scholar 

  • Lopez JA, Sun Y, Blair PB, Mukhtar MS (2015) TCP three-way handshake: linking developmental processes with plant immunity. Trends Plant Sci 20(4):238–245

    Article  CAS  PubMed  Google Scholar 

  • Lucero LE, Uberti-Manassero NG, Arce AL, Colombatti F, Alemano SG, Gonzalez DH (2015) TCP15 modulates cytokinin and auxin responses during gynoecium development in Arabidopsis. Plant J 84(2):267–282

    Article  CAS  PubMed  Google Scholar 

  • Manassero, N. G. U., Viola, I. L., Welchen, E., & Gonzalez, D. H. (2013). TCP transcription factors: architectures of plant form. Biomolecular concepts, 4(2), 111-127.

  • Martín-Trillo M, Cubas P (2010) TCP genes: a family snapshot ten years later [J]. Trends Plant Sci 15(1):31–39

    Article  CAS  PubMed  Google Scholar 

  • Mukhopadhyay P, Tyagi AK (2015) OsTCP19 influences developmental and abiotic stress signaling by modulating ABI4-mediated pathways. Sci Rep 5:9998

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Navaud O, Dabos P, Carnus E, Tremousaygue D, Hervé C (2007) Tcp transcription factors predate the emergence of land plants. J Mol Evol 65(1):23–33

    Article  CAS  PubMed  Google Scholar 

  • Nicolas M, Cubas P (2015) The role of TCP transcription factors in shaping flower structure, leaf morphology, and plant architecture. In Plant Transcription Factors (pp. 249-267)

    Chapter  Google Scholar 

  • Nicolas M, Cubas P (2016) TCP factors: new kids on the signaling block. Curr Opin Plant Biol 33:33–41

    Article  CAS  PubMed  Google Scholar 

  • Resentini F, Felipo-Benavent A, Colombo L, Blázquez MA, Alabadí D, Masiero S (2015) TCP14 and TCP15 mediate the promotion of seed germination by gibberellins in Arabidopsis thaliana. Mol Plant 8(3):482–485

    Article  CAS  PubMed  Google Scholar 

  • Rueda-Romero P, Barrero-Sicilia C, Gómez-Cadenas A, Carbonero P, Oñate-Sánchez L (2011) Arabidopsis thaliana DOF6 negatively affects germination in non-after-ripened seeds and interacts with TCP14. J Exp Bot 63(5):1937–1949

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sarvepalli K, Nath U (2011) Hyper-activation of the TCP4 transcription factor in Arabidopsis thaliana accelerates multiple aspects of plant maturation. Plant J 67(4):595–607

    Article  CAS  PubMed  Google Scholar 

  • Takeda T, Suwa Y, Suzuki M, Kitano H, Ueguchi-Tanaka M, Ashikari M, Matsuoka M, Ueguchi C (2003) The OsTB1 gene negatively regulates lateral branching in rice. Plant J 33(3):513–520

    Article  CAS  PubMed  Google Scholar 

  • Takeda T, Amano K, Ohto MA, Nakamura K, Sato S, Kato T et al (2006) RNA interference of the Arabidopsis putative transcription factor TCP16 gene results in abortion of early pollen development. Plant Mol Biol 61(1–2):165–177

    Article  CAS  PubMed  Google Scholar 

  • Waclawovsky AJ, Sato PM, Lembke CG, Moore PH, Souza GM (2010) Sugarcane for bioenergy production: an assessment of yield and regulation of sucrose content. Plant Biotechnol J 8(3):263–276

    Article  CAS  PubMed  Google Scholar 

  • Wang M, Zhao P, Cheng H, Han L, Wu X, Gao P, ..., Xia G (2013) The cotton transcription factor GhTCP14 functions in auxin-mediated epidermal cell differentiation and elongation. Plant physiology, pp-113

  • Yao X, Ma H, Wang J, Zhang D (2007) Genome-wide comparative analysis and expression pattern of TCP gene families in Arabidopsis thaliana and Oryza sativa. J Integr Plant Biol 49(6):885–897

    Article  CAS  Google Scholar 

  • Zhang J, Zhou M, Walsh J, Zhu L, Chen Y, Ming R (2014) Sugarcane genetics and genomics. In: Sugarcane: physiology, biochemistry, and functional biology. Edited by Moore PH, Botha FC. Wiley-Blackwell physiology, biochemistry, and functional biology. Edited by Moore PH, Botha FC. Wiley-Blackwell Publishing, p 623–43

  • Zhang J, Zhang X, Tang H, Zhang Q, Hua X, Ma X et al (2018) Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. Nat Genet 50(11):1565–1573

    Article  CAS  PubMed  Google Scholar 

  • Zhao J, Zhai Z, Li Y, Geng S, Song G, Guan J, ..., Kong X (2018) Genome-wide identification and expression profiling of the TCP family genes in spike and grain development of wheat (Triticum aestivum L.). Frontiers in Plant Science, 9

  • Zhou Y, Zhang D, An J, Yin H, Fang S, Chu J, Zhao Y, Li J (2018) TCP transcription factors regulate shade avoidance via directly mediating the expression of both PHYTOCHROME INTERACTING FACTORs and auxin biosynthetic genes. Plant Physiol 176(2):1850–1861

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This project was supported by startup fund from Fujian Agriculture and Forestry University, the International Consortium for Sugarcane Biotechnology project #35 to R.M., US DOE DE-SC0010686, and EBI BP2012OO2J17.

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Author notes

  1. Jishan Lin and Mengting Zhu contributed equally to this work.

Authors and Affiliations

  1. FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, National Sugarcane Engineering Technology Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China

    Jishan Lin, Mengting Zhu, Mingxing Cai, Wenping Zhang, Mahpara Fatima, Haifeng Jia, Feifei Li & Ray Ming

  2. College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China

    Mengting Zhu, Mingxing Cai & Feifei Li

  3. College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China

    Mahpara Fatima & Haifeng Jia

  4. Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA

    Ray Ming

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  1. Jishan Lin
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Correspondence to Ray Ming.

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Lin, J., Zhu, M., Cai, M. et al. Identification and Expression Analysis of TCP Genes in Saccharum spontaneum L. Tropical Plant Biol. 12, 206–218 (2019). https://doi.org/10.1007/s12042-019-09238-y

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