Genome-wide identification, characterization and in-silico profiling of genes encoding FAD (fatty acid desaturase) proteins in chickpea (Cicer arietinum L.)

Abstract

Fatty acid desaturases (FADs) are involved in introducing double bonds into the hydrocarbon chains of fatty acids leading to the formation of unsaturated fatty acids. These unsaturated fatty acids are known to play important role in plant development and generating stress tolerance against various environmental stresses. In this study, 21 full-length FAD genes were identified in Desi chickpea (Cicer arietinum L.) and 18 FAD genes in Kabuli chickpea genome by a thorough annotation exercise. An extensive analysis was done to establish their chromosomal locations, construct a phylogeny, structure prediction, motif analysis, in-silico expression analysis and co-expression with other interconnected pathways. In desi chickpea, out of 21 FAD genes, 19 were located on seven chromosomes and two additional scaffolds whereas in Kabuli, out of 18 FAD genes, 17 were located on seven chromosomes and an additional scaffold. Identified soluble and membrane-bound CaFADs were phylogenetically clustered into four and eight subfamilies, respectively with their counterparts from other plants. It was observed that gene structures, motif composition and positions were highly conserved in each subfamily. Furthermore, in-silico gene expression analysis of CaFAD genes in various tissues as well as under abiotic stress conditions revealed differential expression patterns in different tissues and developmental stages. Nine FAD genes were down-regulated in all three abiotic stresses as compared to control. Whereas, five FAD genes were up-regulated in shoot tissue during drought, two FAD genes during salinity and three FAD genes were up-regulated during cold stress. In root tissue, 9 FAD genes were down-regulated and 3 FAD genes were up-regulated during all three abiotic stresses. In co-expression analysis, fatty acid synthesis, TAG synthesis genes and Jasmonic acid (JA) biosynthesis genes were expressed more during flower development and shoot apical meristem. JA signaling gene (CaJAR1) was also expressed more in bud, shoot apical meristem and seeds. No other relationship was observed with respect to modulation during abiotic stresses.