Identification and Expression Analysis of TCP Genes in Saccharum spontaneum L

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.