Genes involved in fatty acids biosynthesis, modification and oil body formation are expected to be conserved in structure and function in different plant species. However, significant differences in the composition of fatty acids and total oil contents in seeds have been observed in different plant species. Comparative genomics was performed on 261 genes involved in fatty acids biosynthesis, TAG synthesis, and oil bodies formation in Arabidopsis, Brassica rapa, castor bean and soybean. In silico expression analysis revealed that stearoyl desaturase, FatB, FAD2, oleosin and DGAT are highly abundant in seeds, thereby considered as ideal candidates for mining of favorable alleles in natural population. Gene structure analysis for major genes, ACCase, FatA, FatB, FAD2, FAD3 and DGAT, which are known to play crucial role in oil synthesis revealed that there are uncommon variations (SNPs and INDELs) which lead to varying content and composition of fatty acids in seed oil. The predicted variations can provide good targets for seed oil QTL identification, understanding the molecular mechanism of seed oil accumulation, and genetic modification to enhance seed oil yield in plants. 1. Introduction A major challenge mankind is facing in this century is the gradual exhaustion of the fossil energy resources. The combustion of those fossil fuels used in transportation is one of the key factors responsible for global warming and environment pollution due to large-scale carbon dioxide emissions. Thus, alternative energy sources based on sustainable and ecologically friendly processes are urgently required. At present gasoline or diesel are being largely substituted by two biofuels, bioethanol and biodiesel, capturing ~90% of the market [1]. Biodiesel is made from renewable biomass mainly by alkali-catalysed transesterification of triacylglycerols (TAGs) from plant oils [2]. Manipulation of biosynthetic pathways offers a number of exciting opportunities for plant biologists to redesign plant metabolism toward production of specific TAGs. The biosynthesis of fatty acids in plants begins with the formation of acetyl Co-A from pyruvate. The acetyl CoA produced in plastids is activated to malonyl CoA; the malonyl group is subsequently transferred to acyl carrier protein (ACP) giving rise to malonyl ACP, the primary substrate of the fatty acid synthase complex. The formation of malonyl CoA is the committed step in fatty acid synthesis and is catalyzed by the highly regulated plastidic acetyl CoA carboxylase complex [3]. De novo fatty acid synthesis in the plastids occurs
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