Identification and analysis of the structure, expression and nucleotide polymorphism of the GPAT gene family in rice

Abstract Glycerol-3-phosphate acyltransferase (GPAT), a family of membrane-bound enzymes, is involved in the initial step of glycerolipid biosynthesis in plant cells. In this study, we performed an in-silico genome-wide analysis of rice (Oryza sativa) and identified 26 GPAT genes annotated according to their chromosomal locations. Putative orthologs of the rice genes were identified in five monocot and dicot plant species. The study characterized the rice GPAT gene structures, genome localization, gene duplications, conserved motifs, and cis-elements in their promoter regions. Segmental duplication contributed to the expansion of the GPAT family in rice with purifying selection pressure. We analyzed the phylogeny between six different monocots and dicot GPAT genes and compared them with rice orthologs and their exon-intron structure to understand their evolutionary relationships. Based on RNA-seq data, we found rice GPAT genes have diverse expression patterns. Some genes had high expression in specific tissues, including; OsGPAT2,13 and 8 in the root; OsGPAT3 and 10 in the shoot; OsGPAT4 in panicle; OsGPAT25 in the leaf; OsGPAT8, 25, and 26 in the anther and OsGPAT10, and 25 in the seed. Expression analysis under salt, cold, and heat conditions showed that GPAT genes positively respond to abiotic stress conditions. Some genes demonstrated sustained up-regulation in specific stresses including; OsGPAT2, OsGPAT18, OsGPAT19, OsGPAT5, and OsGPAT12 in cold stress; OsGPAT6, 11, 13, 18, 19 and 21 in heat stress; and OsGPAT5, 14, 18, 19 and 24 during salt stress. Moreover, we used the 3000 rice genomes project (3 K RGP) data to analyze nucleotide polymorphism at each rice GPAT locus among hundred Chinese rice varieties. This study will provide a framework for future studies and further broaden our insights into the evolution and functional elucidation of GPAT genes in rice.