Genome-wide analysis of citrus TCP transcription factors and their responses to abiotic stresses

Abstract

Background: Citrus is one of the most important fruit crops in the world, and it is worthy to conduct more research on artificially controlling citrus plant growth and development to adapt to different cultivation patterns and environmental conditions. The plant-specific TEOSINTE BRANCHED1, CYCOLOIDEA, and PROLIFERATING CELL FACTORS (TCP) transcription factors are crucial regulators controlling plant growth and development, as well as responding to abiotic stresses. However, the information about citrus TCP transcription factors remains unclear. Results: In this study, twenty putative TCP genes (CsTCPs) with the TCP domain were explored from Citrus sinensis genome, of which eleven (CsTCP3, − 4, − 5, − 6, − 10, − 11, − 15, − 16, − 18, − 19, − 20), five (CsTCP1, − 2, − 7, − 9, − 13), and four genes (CsTCP8, − 12, − 14, − 17) were unevenly distributed on chromosomes and divided into three subclades. Cis-acting element analysis indicated that most CsTCPs contained many phytohormone- and environment-responsive elements in promoter regions. All of CsTCPs were predominantly expressed in vegetative tissues or organs (stem, leaf, thorn, and bud) instead of reproductive tissues or organs (flower, fruit, and seed). Combined with collinearity analysis, CsTCP3, CsTCP9, and CsTCP13 may take part in leaf development; CsTCP12 and CsTCP14 may function in shoot branching, leaf development, or thorn development; CsTCP15 may participate in the development of stem, leaf, or thorn. In mature leaf, transcript levels of two CsTCPs (CsTCP19, − 20) were significantly increased while transcript levels of eight CsTCPs (CsTCP2, − 5, − 6, − 7, − 8, − 9, − 10, − 13) were significantly decreased by shading; except for two CsTCPs (CsTCP11, − 19), CsTCPs’ transcript levels were significantly influenced by low temperature; moreover, transcript levels of two CsTCPs (CsTCP11, − 12) were significantly increased while five CsTCPs’ (CsTCP14, − 16, − 18, − 19, − 20) transcript levels were significantly reduced by drought. Conclusions: This study provides significant clues for research on roles of CsTCPs in regulating citrus plant growth and development, as well as responding to abiotic stresses.