Genomic characterization of miR156 and SQUAMOSA promoter binding protein-like genes in sweet orange (Citrus sinensis)

Abstract

miR156, as one of the first discovered and most conserved microRNAs (miRNAs) in plants, was known to play versatile roles in plants, through regulation of the target SBP-box genes, a plant-specific transcription factor family. In this study, four MIR156 and 15 SQUAMOSA promoter binding protein-like (SPL) genes were retrieved from Citrus sinensis genome. According to the phylogenetic grouping with plant SPLs, synteny analysis with Arabidopsis SPLs, characterization of exon–intron structure and motif organization, the CsSPL genes were clustered into two major groups, and one major group was further divided into seven subgroups. The possible function of CsSPLs was inferred based on their likely orthologous relationship to SPLs in Arabidopsis. The precursor of csi-miR156a was isolated and overexpressed in citrus callus. The transformed callus cells were found to over-accumulate amyloids, resulting in increased starch content. Among the nine CsSPLs targeted by csi-miR156a/b, only CsSPL2 and CsSPL14 showed downregulated transcript level in miR156 overexpressed lines, suggesting the involvement of ‘miR156-CsSPL’ module in starch accumulation. In this study, genomic analysis of miR156 and SPL gene family of C. sinensis was conducted, and preliminary function of miR156-SPL was validated in citrus callus lines.