Genetic determinants of rice bran oil quantity and quality: genomic, proteomic and transcriptomic approaches

Any increase in the economic value of the rice crop could have a large impact on the economies of Asia. Rice bran can be used to produce rice bran oil (RBO) which is emerging as a major vegetable oil. In this research, new genetic targets to improve RBO quality have been investigated using genomic, proteomic and transcriptomic approaches. The first chapter gives a detailed background about rice grain structure, effect of lipases on lipids in rice and strategies to increase the quantity and quality of oil. In the second chapter, using the genomic approach 125 putative lipase gene sequences derived from Oryza sativa ssp. japonica genome were systematically analyzed using bioinformatics tools. Based on the analysis, LOC_Os11g43510 was selected and it was experimentally demonstrated to be highly expressed in rice bran.The transcript from LOC_Os11g43510 was cloned and expressed as a secretory protein in P. pastoris X-33 which retained demonstrated lipase activity. The third chapter describes the use of a proteomics approach based on fluorescence based lipase activity probes and liquid chromatography-tandem mass spectrometry (LC-MS/MS) detection analysis. The proteomics approach used identified Os01g0817700 as a novel putative lipase in rice bran. Bioinformatics and expression studies also suggested that Os01g0817700 has two lipase motifs and is also expressed in the bran and embryo of the rice grain. These data suggest that Os01g0817700 is a novel putative lipase expressed in rice. In the fourth chapter, a transcriptomic approach was used to study the subset of lipid-metabolism genes being affected when OsFAD2-1 is down-regulated by RNAi to produce high oleic (HO) rice. The transcriptomic analysis in the HO rice suggests that a suite of key genes (FatA, LACS, SAD) involved in fatty acid biosynthesis are concurrently down-regulated. Moreover, a decrease in the expression of oil body proteins (caleosin and steroleosin) was also observed in the HO lines. All of these genes are suitable targets for gene manipulation in order to further increase the oleic acid content. Very few plant lipases have been studied and reported so far. This study demonstrates an alternative route of identifying lipases in rice bran and also helps to identify additional genes involved in determining rice oil composition. Overall, this study has used different approaches to identify new genetic targets for further improvement of RBO