Systematic Investigation of TCP Gene Family: Genome-Wide Identification and Light-Regulated Gene Expression Analysis in Pepino (Solanum Muricatum)

Cheng Si; Deli Zhan; Lihui Wang; Xuemei Sun; Qiwen Zhong; Shipeng Yang

doi:10.3390/cells12071015

Systematic Investigation of TCP Gene Family: Genome-Wide Identification and Light-Regulated Gene Expression Analysis in Pepino (Solanum Muricatum)

Cells. 2023 Mar 26;12(7):1015. doi: 10.3390/cells12071015.

Authors

Cheng Si^{1

2}, Deli Zhan^{1

2}, Lihui Wang¹, Xuemei Sun¹, Qiwen Zhong¹, Shipeng Yang^{1

3}

Affiliations

¹ Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences Institute of Qinghai University, Xining 810016, China.
² College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China.
³ College of Life Sciences, Northwest A&F University, Yangling 712100, China.

Abstract

Plant-specific transcription factors such as the TCP family play crucial roles in light responses and lateral branching. The commercial development of S. muricatum has been influenced by the ease with which its lateral branches can be germinated, especially under greenhouse cultivation during the winter with supplemented LED light. The present study examined the TCP family genes in S. muricatum using bioinformatics analysis (whole-genome sequencing and RNA-seq) to explore the response of this family to different light treatments. Forty-one TCP genes were identified through a genome-wide search; phylogenetic analysis revealed that the CYC/TB1, CIN and Class I subclusters contained 16 SmTCP, 11 SmTCP and 14 SmTCP proteins, respectively. Structural and conserved sequence analysis of SmTCPs indicated that the motifs in the same subcluster were highly similar in structure and the gene structure of SmTCPs was simpler than that in Arabidopsis thaliana; 40 of the 41 SmTCPs were localized to 12 chromosomes. In S. muricatum, 17 tandem repeat sequences and 17 pairs of SmTCP genes were found. We identified eight TCPs that were significantly differentially expressed (DETCPs) under blue light (B) and red light (R), using RNA-seq. The regulatory network of eight DETCPs was preliminarily constructed. All three subclusters responded to red and blue light treatment. To explore the implications of regulatory TCPs in different light treatments for each species, the TCP regulatory gene networks and GO annotations for A. thaliana and S. muricatum were compared. The regulatory mechanisms suggest that the signaling pathways downstream of the TCPs may be partially conserved between the two species. In addition to the response to light, functional regulation was mostly enriched with auxin response, hypocotyl elongation, and lateral branch genesis. In summary, our findings provide a basis for further analysis of the TCP gene family in other crops and broaden the functional insights into TCP genes regarding light responses.

Keywords: RNA-seq; S. muricatum; TCP gene family; light response.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Amino Acid Sequence
Arabidopsis* / genetics
Gene Expression Profiling
Phylogeny
Plant Proteins / metabolism
Solanum* / genetics
Solanum* / metabolism

Substances

Plant Proteins

Grants and funding

This study was supported by the Basic Research Project of Qinghai Science and Technology Department (2023-ZJ-715), and the Qinghai Agriculture and Forestry Science Innovation Fund (2021-NKY-02).