Genome-wide identification, characterization, interaction network and expression profile of GRAS gene family in sweet orange (Citrus sinensis)

Abstract

GRAS genes are suggested to be grouped into plant-specific transcriptional regulatory families that have been reported to participate in multiple processes, including plant development, phytohormone signaling, the formation of symbiotic relationships, and response to environmental signals. GRAS genes have been characterized in a number of plant species, but little is known about this gene family in Citrus sinensis. In this study, we identified a total of 50 GRAS genes and characterized the gene structures, conserved motifs, genome localizations and cis-elements within their promoter regions. According to their structural and phylogenetic features, the identified sweet orange GRAS members were divided into 11 subgroups, of which subfamily CsGRAS34 was sweet orange-specific. Based on publicly available RNA-seq data generated from callus, flower, leaf and fruit in sweet orange, we found that some sweet orange GRAS genes exhibited tissue-specific expression patterning. Three of the six members of subfamily AtSHR, particularly CsGRAS9, and two of the six members of subfamily AtPAT1 were preferentially expressed in leaf. Moreover, protein-protein interactions with CsGRAS were predicted. Gene expression analysis was performed under conditions of phosphate deficiency, and GA3 and NaCl treatment to identify the potential functions of GRAS members in regulating stress and hormone responses. This study provides the first comprehensive understanding of the GRAS gene family in the sweet orange genome. As such, the study generates valuable information for further gene function analysis and identifying candidate genes to improve abiotic stress tolerance in citrus plants.