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Application of Multi-Omics Approaches to Maximize Beef Production

  • Author / Creator
    Foroutan Naddafi, Aidin
  • Approximately 70% of the cost of beef production is impacted by dietary intake. Maximizing production efficiency of beef cattle requires not only genetic selection to maximize feed efficiency (i.e. residual feed intake - RFI), but also adequate nutrition throughout all stages of growth and development to maximize efficiency of growth and reproductive capacity - even during gestation. Nutrient restriction during gestation has been shown to negatively affect postnatal growth and development as well as fertility of the offspring. This, when combined with RFI, may significantly affect energy partitioning in the offspring and subsequently important performance traits. Therefore, we decided to conduct a comprehensive multi-omics study (metabolomics, transcriptomics, epigenomics) to understand the biological mechanisms impacted by prenatal nutrition (normal-diet or Ndiet versus low-diet or Ldiet) and/or parental RFI (high-RFI or HRFI versus low-RFI or LRFI) in young Angus bulls. Four different tissues (Longissimus thoracis (LT) muscle, semimembranosus (SM) muscle, liver, and testis) and three biofluids (serum, semen, and ruminal fluid) were analyzed. Through the metabolomics study, we created the Bovine Metabolome Database (BMDB; www.bovinedb.ca) which contains 51,801 metabolites with unique compound structures in various tissues and biofluids. We also identified two serum candidate biomarker panels ((1) formate and leucine; (2) C4 (butyrylcarnitine) and LysoPC(28:0)), which can distinguish HRFI from LRFI animals with high sensitivity and specificity (area under the curve from receiver-operator characteristic (ROC) or AUROC > 0.85). Through the transcriptomics study, we found that differences in selection for parental RFI altered gene expression level of myocyte enhancer factor 2A [MEF2A] in tissues (LT muscle, SM muscle, liver, and testis) of young Angus bulls. Furthermore, the mRNA abundance of protocadherin 19 [PCDH19] in liver, and MEF2A in LT muscle were affected by prenatal undernutrition. We also detected correlations between gene expression in tissues with phenotypic measures of feed efficiency and body weight. Through the epigenomics study, we found 652 and 1400 differentially methylated regions (DMRs) that were affected by maternal diet and parental RFI, respectively. Through pathway analysis of the identified DMRs using the Ingenuity Pathway Analysis (IPA) tool, three networks associated with “cell survival and growth”, “disease or abnormalities”, and “connective tissue development” were identified as being overrepresented in the DMRs when comparing the Ndiet group to the Ldiet group. Similar pathway analysis for the HRFI and LRFI bulls showed overrepresentation of the number of DMRs in four networks involved in “embryonic development”, “DNA replication, DNA repair, and RNA processing”, “growth control and homeostasis”, as well as “lipid metabolism”. These findings provided new knowledge regarding underlying biological mechanisms regulating postnatal responses to prenatal nutrition and feed efficiency in beef bulls.

  • Subjects / Keywords
  • Graduation date
    Spring 2021
  • Type of Item
    Thesis
  • Degree
    Doctor of Philosophy
  • DOI
    https://doi.org/10.7939/r3-dmka-4k42
  • 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.