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

• Author / Creator

  Foroutannaddafi, Aidin

• 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.

• Subjects / Keywords

  • Omega-3
  • Beef
  • Gene-expression

• Graduation date

  Fall 2015

• Type of Item

  Thesis

• Degree

  Master of Science

• DOI

  https://doi.org/10.7939/R3B27PX0P

• License

  This thesis is made available by the University of Alberta Libraries with permission of the copyright owner solely for non-commercial purposes. This thesis, or any portion thereof, may not otherwise be copied or reproduced without the written consent of the copyright owner, except to the extent permitted by Canadian copyright law.