Identification And Analysis Of The Structure,nucleotide Polymorphism And Expression Profile Of GPAT Gene Family In Rice

With the advent of high-throughput technologies,the volume of biological information,including the genomic data generated by massive sequencing platforms,is doubling roughly every six months.This data generation,including gene expression profiling and nucleotide polymorphisms,will increase more rapidly in the coming decades and needs to utilize and get meaningful results.The release of whole-genome sequencing platforms of rice provides an opportunity to analyze in detail,various known or unknown gene families.Glycerol-3-phosphate acyltransferase(GPAT),a family of membrane bound enzymes are involved in the initial and important step of glycerolipid biosynthesis in plant cells.In this study,an in-silico genome-wide analysis of rice(Oryza sativa)was performed(www.gramene.org),and we identified 26 GPAT genes annotated according to their chromosomal locations.Briefly,the study explored:1.The study identified 26 GPAT genes in rice and characterized the chromosomal localization of genes.Gene structure and conserved motifs were identified.Gene structure demonstrated variation in exon numbers ranged between one to a maximum of 13 exons.Gene duplication events were identified,and segmental duplication contributed to the expansion of the gene family,and duplicated genes underwent purifying selection pressure throughout evolution.According to phylogenetic analysis,GPAT members broadly divided into three major groups.Gene ontology annotation results allocated rice GPAT genes primarily in membranous part in the cellular component,involving in various lipid biosynthetic processes including dephosphorylation,phosphatidic acid and phosphatidylglycerol biosynthesis,and long-chain fatty acid synthesis.The presence of a majority of GPAT proteins in an integral part of the cellular membrane and Glycerol-3 phosphate transferase activity in molecular functions validate their role in glycerolipid biosynthesis as discussed in past studies.Functional interaction between GPAT proteins demonstrated they have functional diversity with involvement in cutin biosynthesis,suberin in seed coat synthesis,intracellular glycerolipids,and membrane lipid biosynthesis.Based on RNA-seq data,we found that GPAT genes had diverse expression patterns.Expression analysis was performed under salt,cold,heat conditions to identify the response of GPAT family under abiotic stresses,and found to be up regulated during stress conditions.Transcripts had positive relation in stress conditions,which also validate their role found in previous studies.Presences of the abiotic stress responsive cis-elements at a number of the putative GPAT promoter regions suggest these common elements might work synergistically to induce expression of stress responsive genes.2.Moreover,the data of 3,000 rice genomes project was used to analyze nucleotide polymorphism at each locus of GPAT genes among a hundred Chinese rice varieties from different geographical regions.Most genes tend to maintain low nucleotide diversity,most likely reflected by strong purifying selection pressure on genes,characterized by a low nonsynonymous and synonymous substitution ratio.Variation in terms of In Dels was retrieved that had high frequency in the cultivars.3.We also explored all the SNPs among hundred rice varieties from different geographical regions of China in 26 GPAT genes,identified 1056 SNPs,including important 98 coding ns SNPs that can change amino acid residues,and further explore the functionally significant SNPs with high damaging effects on protein structure using various insilico methods and computational approaches.These identified SNPs have high impact on the rice GPAT proteins.