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Identifying Gene Expression Differences Induced by Diets that Lead to Higher Omega-3 Fatty-Acid Deposition in Beef Cows Open Access


Other title
Gene Expression
Type of item
Degree grantor
University of Alberta
Author or creator
Foroutannaddafi, Aidin
Supervisor and department
Fitzsimmons, Carolyn (Agricultural, Food & Nutritional Science)
Examining committee member and department
Stothard, Paul (Agricultural, Food & Nutritional Science)
Mazurak, Vera (Agricultural, Food & Nutritional Science)
Department of Agricultural, Food, and Nutritional Science
Animal Science
Date accepted
Graduation date
Master of Science
Degree level
A strong emphasis on the type of fatty acids (FAs) consumed in the human diet has emerged in recent years. In this context, the various health benefits of consuming omega-3 (n-3) polyunsaturated fatty acids (PUFAs) have been widely reported. Supplementation of beef cattle diets with flaxseed, a rich source of alpha-linolenic acid (ALA), has been shown to increase n-3 FAs content of muscle and fat tissues. Towards the goal of enhancing beef FA composition, 64 crossbred cull cows (~30 months of age) with similar breed composition were randomized by weight/body condition, and fed one of four 50:50 forage:concentrate diets on a DM basis (16 cows/treatment), containing ground barley grain with either hay or silage, supplemented with 0 or 15% ground flaxseed (DM basis). Cows were slaughtered after spending 140 days on the treatment diets. For the initial transcriptional analysis, five cows from each of the four diets (20 in total), were selected using an index equation (Index=0.40(18:3n-3) + 0.60(Long Chain:3n)) which ranked cows based on the amount of alpha-linolenic acid (18:3n-3) and long chain omega-3 (3n) FAs in kidney fat collected at slaughter. Cattle scoring the highest indexes were selected from diets which included flax and those scoring the lowest indexes were selected from diets which did not contain flax. RNA was isolated from Longissimus thoracis (LT) muscle, subcutaneous fat (SC), and kidney fat (KF) tissues of each of the 20 cows, and hybridized in duplicate to BOMC 24K 70-mer microarrays. Differentially expressed (DE) genes (contrast: Flax-high index vs. No-Flax-low index) were identified using linear modeling and the empirical Bayes approach within Limma to produce moderated t-statistics and associated p-values (Limma package, Biocoductor), incorporating the BH significance correction for multiple tests. Sixty-eight and 166 transcripts with p-value < 0.05 and < 0.10 respectively, were found to be DE in the two tissues, LT muscle and SC fat combined (no DE genes were found in KF), between Flax-high index, and No-Flax-low index groups. DE genes (p-value < 0.1) were imported to DAVID and IPA software, and resulted in identifying eight DE genes associated with FA metabolism. Fidelity of microarray results were tested for the eight DE genes by traditional real-time PCR. Subsequently 40 genes related to FA metabolism were selected for high-throughput real-time PCR gene expression analysis in all LT and SC samples collected from cattle in the feeding trial (31 and 61 samples for LT and SC, respectively) to identify expression differences in the flax-supplemented cattle versus non-supplemented. Out of 40 genes, eight were those DE associated with FA metabolism (p-value < 0.1) identified from the analysis of microarray data, while the remaining 32 genes were selected from a combination of the results of the microarray experiment (genes with p-value ≥ 0.1), literature, and in consultation with an Alberta Livestock and Meat Agency (ALMA) funded project 2010R038R - Identifying DNA markers for enhancing beneficial fatty acids in beef. Correlation analysis was performed between 40 genes and FA profiles of LT and SC tissues and resulted in identifying strong candidate genes for selection of cattle with a healthier FA profile in meat.
Permission is hereby granted to the University of Alberta Libraries to reproduce single copies of this thesis and to lend or sell such copies for private, scholarly or scientific research purposes only. The author reserves all other publication and other rights in association with the copyright in the thesis and, except as herein before provided, neither the thesis nor any substantial portion thereof may be printed or otherwise reproduced in any material form whatsoever without the author's prior written permission.
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