Genomic characterization and expression analysis of TCP transcription factors in Setaria italica and Setaria viridis

The plant-specific TCP transcription factor plays important roles in plant development and environment adaptation. Setaria italica and Setaria viridis, the C4 model plants, can grow on drought or arid soils. However, there is no systematic information about the genomic dissection and the expression of Setaria TCP genes. A total of 22 TCP genes were both identified from S. italica and S. viridis genomes. They all contained bHLH domain and were grouped into three main clades (PCF, CIN, and CYC/TB1). The TCP genes in the same clades shared similar gene structures. Cis-element in the TCP promoter regions were analyzed and associated with hormones and stress responsiveness. Ten TCP genes were predicted to be targets of miRNA319. Moreover, gene ontology analysis indicated three SiTCP and three SvTCP genes were involved in the regulation of shoot development, and SiTCP16/SvTCP16 were clustered together with tillering controlling gene TB1. The TCP genes were differentially expressed in the organs, but SiTCP/SvTCP orthologs shared similar expression patterns. Ten SiTCP members were downregulated under drought or salinity stresses, indicating they may play regulatory roles in abiotic stresses. The study provides detailed information regarding Setaria TCP genes, providing the theoretical basis for agricultural applications.