Gene identification and expression analysis of the TCP gene family of Arundo donax under salt stress

Arundo donax has a short growth cycle and high cellulose and crude protein contents. A. donax is a new economic energy forage with broad application prospects. TCP is a plant-specific transcription factor that plays an important role in regulating plant growth and development. However, the distribution and biological functions of this gene family in A. donax have not yet been reported. In this study, the basic physical and chemical properties, chromosome localization, collinearity, gene structure, conserved motifs of proteins, multiple sequence alignment, and phylogenetic relationships with other species of the AdTCP gene family were systematically analyzed using bioinformatics. The relative expression levels of the seven AdTCP genes under salt stress were determined by real-time fluorescence quantitative PCR. Our results showed that the 37 AdTCP genes were distributed on different chromosomes. The physical and chemical properties of different proteins differ. All proteins were hydrophilic and unstable, and most of them were in the nucleus. The gene structure of this family contains only exons and no introns, and 22 fragment-replicating gene pairs were identified by collinear analysis. The protein family contains 15 conserved motifs with a sequence similarity of 30.52%. Compared with TCP genes of Arabidopsis thaliana and Oryza sativa, 82 AdTCPs were divided into two subfamilies, TCP-P and TCP-C, in which TCP-P contained only the PCF branch and TCP-C contained the CYC and CIN branches. With an increase in the salt stress concentration, the expression levels of seven AdTCP genes first increased and then decreased, indicating that AdTCP was involved in the salt stress response. This study could lay the foundation for the analysis of gene function and the creation of new germplasms of Arundo donax