Characterization of Fatty Acid Metabolism and Allergen Genes during Pecan Nut Development.

Pecan nuts (Carya illinoinensis) are a nutrient rich part of a heart healthy diet, full of beneficial fatty acids, including oleic and linoleic acid, and high in antioxidants. However, seed storage proteins in pecan can cause severe allergic reactions in people suffering from food allergy to the nuts. To further our understanding, genes expressed during pecan nut development were sequenced and evaluated for changes in expression to identify and characterize fatty acid metabolism and allergen genes. Pecan samples were collected at several time points during embryo development including water, gel, dough, and mature stages. Library preparation and mRNA sequencing was performed using Illumina based HiSeq with RNA from 4 time points during the growing season from August through 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. The expression of over 3000 genes was observed to be significantly altered during embryogenesis. Nearly 300 unique transcripts potentially involved in fatty acid metabolism were identified. Upregulated fatty acid metabolism genes that were identified included acyl-[ACP] desaturase and omega-6 desaturase genes involved in oleic and linoleic acid metabolism. Three pecan seed storage proteins that commonly act as allergens, Car i 1, 2, and 4 were significantly upregulated too. Gene expression clustering analysis identified 12 different gene expression profiles, each containing a number of genes. Notably, a few of the upregulated acyl-[ACP] desaturase and omega-6 desaturase genes have expression patterns similar to the allergen genes based upon gene expression clustering and qPCR analysis. These findings suggest the possibility of coordinated gene expression and accumulation of lipids and allergens during pecan embryogenesis. Application of these findings could enable better solutions for relieving allergies and improving the nutritional or sensory qualities of pecan.