Submitted to: Association for the Advancement of Industrial Crops Conference
Publication Type: Abstract Only
Publication Acceptance Date: 7/15/2014
Publication Date: 9/13/2014
Citation: Chen, G.Q. 2014. Mining lesquerella seed transcriptome for oil and meal improvement and translational research. Association for the Advancement of Industrial Crops Conference. http://www.aaic.org/meetings.htm#Past_programs: 2014, page 31..
Technical Abstract: Lesquerella (Physaria fendleri), a member of the Brassicaceae family, is currently being developed as a new industrial oilseed. Lesquerella is valued for its unusual hydroxy fatty acid (HFA) lesquerolic acid (20:1OH). The conventional source of HFA is ricinoleic acid (18:1OH) from castor oil. Ricinoleic acid and its derivatives are used as raw materials for numerous industrial products, such as lubricants, plasticizers and surfactants. The production of castor oil, however, is hampered by the presence of the toxin ricin and hyper-allergenic 2S albumins in castor seeds. Lesquerella on the other hand, does not have such biological toxic compounds; thus its oil represents a safe source of HFA. As a step towards genetic engineering of lesquerella, we report here building a lesquerella seed transcriptome reference and identification of candidate genes that provide genetic targets for seed quality improvement. We used 454 GX FLX pyrosequencing and acquired 651 megabases of raw sequences from an mRNA sample of developing seeds. Bioinformatic analysis of these sequences revealed 59,914 transcripts representing 26,995 unique genes that include nearly all known seed expressed genes, suggesting a high level of completeness and usefulness of the reference. When these unique genes were searched against the NCBI NR database, 19,861 genes (74%) matched annotated coding genes. In addition, about 18,868 coding genes (95%) matched genes from Arabidopsis, a model dicot plant, with the highest homology. The transcriptome analysis indicates that lesquerella is closely related to Arabidopsis, which allows for translating genetic findings from Arabidopsis to lesquerella. We identified lesquerella genes involved in acyl-lipid metabolism based on information from the Arabidopsis acyl-lipid metabolism database. We found a total 615 lesquerella genes with representatives from each sub acyl-lipid metabolism group. To understand hydroxy fatty acid biosynthesis and metabolism in lesquerella, we further searched the transcriptome assembly for genes involved in fatty acid and TAG biosynthesis and found almost all lesquerella homologues of these genes. Moreover, we characterized the expression profiles of key lipid biosynthesis genes in various tissues of lesquerella, including developing seeds, leaf, stem, root, and flower buds using quantitative real-time PCR (qRT-PCR) assays. Our results provide information on key target genes that can be useful in the design of future applications to control HFA production in plants.