Identification and functional analysis of miR156 family and its target genes in foxtail millet (Setaria italica)

miR156s, one of the most conserved miRNA families, are widely involved in multiple growth and development processes in plants. However, the MIR156 gene family has not yet been identified in foxtail millet. In this study, a total of 11 MIR156 genes, named as Sit-MIR156a to Sit-MIR156k, were identified in foxtail millet. A comprehensive bioinformatics analysis of the Sit-MIR156 gene family was presented, including chromosomal locations, phylogenetic relationships, base conservativeness and secondary structures. Eleven Sit-MIR156s were distributed on seven chromosomes. Phylogenetic analysis showed that the Sit-MIR156 family can be roughly divided into two clusters, and MIR156 in foxtail millet were more closely related to those in rice compared to Arabidopsis and tomato. All the precursors of Sit-MIR156 can form into the stable stem-loop secondary structures, and the mature sequences are highly conserved. The expression profile analysis showed that Sit-miR156s were expressed in flowers, leaves and roots with obvious tissue-specific patterns. The target genes of Sit-miR156s are mainly SPL transcription factor genes, as well as the genes encoding Acyl-CoA N-acyltransferase, UDP-Glycosyltransferase, DNA-glycosylase, and so on. The diverse expression patterns of these target genes in various tissues suggested that miR156 may play essential roles in plant growth and development and response to environments in foxtail millet. Our results provide an overview and lay the foundation for future functional characterization of the foxtail millet Sit-MIR156 gene family.