RNA-seq analysis of developing pecan (Carya illinoinensis) embryos reveals parallel expression patterns among allergen and lipid metabolism genes

Authors: Mattison, Chris; RAI, RUHI - Virginia Biotechnology Institute; SETTLAGE, ROBERT - Virginia Biotechnology Institute; Hinchliffe, Doug; Madison, Crista; Bland, John; Brashear, Suzanne; GRAHAM, CHARLES - Louisiana State University Agcenter; TARVER, MATTHEW - Bayer Cropscience; Florane, Christopher; Bechtel, Peter

Submitted to: Journal of Agricultural and Food Chemistry
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/25/2017
Publication Date: 1/25/2017
Citation: Mattison, C.P., Rai, R., Settlage, R.E., Hinchliffe, D.J., Madison, C.A., Bland, J.M., Brashear, S.S., Graham, C.J., Tarver, M.R., Florane, C.B., Bechtel, P.J. 2017. RNA-seq analysis of developing pecan (Carya illinoinensis) embryos reveals parallel expression patterns among allergen and lipid metabolism genes. Journal of Agricultural and Food Chemistry. 65:1443-1455. doi:10.1021/acs.jafc.6b04199.

Interpretive Summary: Pecan nuts and other tree nuts can be a nutrient rich part of a healthy diet full of beneficial fatty acids and antioxidants, but can also cause allergic reactions in people suffering from food allergy to the nuts. We characterized the genes expressed during the development of a pecan nut using modern sequencing methods to identify genes that were highly expressed. We highlighted genes involved in fatty acid metabolism and those that commonly act as food allergens. Pecan samples were collected at several time points during nut development so that we could generate a time line for the expression of specific genes. We sequenced gene expression within the developing pecan nuts at 4 time points during the growing season between August and September 2012. We identified 133,000 potential genes, and approximately 50,000 of these were similar to genes from other life forms. We grouped the gene expression of some of these genes into clusters to identify those that were turned on or off at similar times. This analysis allowed us to determine that pecan nut seed storage proteins that commonly act as allergens were significantly upregulated during the time course. In some cases there were fatty acid metabolism genes that had expression patterns similar to the allergen genes. Our findings suggest the possibility of coordinated accumulation of lipids and allergens during pecan nut embryogenesis.

Technical Abstract: Pecan nuts and other tree nuts can be a nutrient rich part of a healthy diet full of beneficial fatty acids and antioxidants, but can also cause allergic reactions in people suffering from food allergy to the nuts. We characterized the transcriptome of a developing pecan nut to identify the gene expression occurring during the process of nut development and to highlight those genes involved in fatty acid metabolism and those that commonly act as food allergens. Pecan samples were collected at several time points during the embryo development process including the water, gel, dough, and mature nut stages. Library preparation and sequencing was performed using Illumina based mRNA HiSeq with RNA from 4 time points during the growing season during August and September 2012. Sequence analysis with Trinotate software following the Trinity protocol identified 133,000 unigenes with 52,267 named transcripts and 45,882 annotated genes. A total of 27,312 genes were defined by GO annotation. Gene expression clustering analysis identified 12 different gene expression profiles, each containing a number of genes. Three pecan seed storage proteins that commonly act as allergens, Car i 1, 2, and 4 were significantly upregulated during the time course. We identify upregulated fatty acid metabolism genes, including acyl-[ACP] desaturase and omega-6 desaturase genes involved in oleic and linoleic acid metabolism. Notably, a few of the upregulated acyl-[ACP] desaturase and omega-6 desaturase genes we have identified have expression patterns similar to the allergen genes based upon gene expression clustering and qPCR analysis. Our findings suggest the possibility of coordinated accumulation of lipids and allergens during pecan nut embryogenesis, provides a valuable genetic resource, and could aid in the development of improved pecan cultivars through breeding.