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Identification and Expression Analysis of TCP Genes in Saccharum spontaneum L

  • Jishan Lin
  • Mengting Zhu
  • Mingxing Cai
  • Wenping Zhang
  • Mahpara Fatima
  • Haifeng Jia
  • Feifei Li
  • Ray MingEmail author
Article
  • 25 Downloads

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.

Keywords

Sugarcane S. spontaneum TCP genes Gene expression 

Notes

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.

Supplementary material

12042_2019_9238_MOESM1_ESM.docx (220 kb)
ESM 1 (DOCX 220 kb)

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Jishan Lin
    • 1
  • Mengting Zhu
    • 1
    • 2
  • Mingxing Cai
    • 1
    • 2
  • Wenping Zhang
    • 1
  • Mahpara Fatima
    • 1
    • 3
  • Haifeng Jia
    • 1
    • 3
  • Feifei Li
    • 1
    • 2
  • Ray Ming
    • 1
    • 4
    Email author
  1. 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 BiologyFujian Agriculture and Forestry UniversityFuzhouChina
  2. 2.College of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
  3. 3.College of Crop SciencesFujian Agriculture and Forestry UniversityFuzhouChina
  4. 4.Department of Plant BiologyUniversity of Illinois at Urbana-ChampaignUrbanaUSA

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