Thesis
Identification of genes and gene sets associated with residual feed intake in Hereford, Angus, and Simmental crossbred beef cattle
Washington State University
Master of Science (MS), Washington State University
2017
Handle:
https://hdl.handle.net/2376/100199
Abstract
This study identified genes and enriched gene sets associated with residual feed intake (RFI) in Hereford, Angus, and Simmental crossbred populations through Gene Set Enrichment Analysis using single nucleotide polymorphism data (GSEA-SNP). Eight hundred twenty-four Hereford steers, 1,460 Angus steers, and 1,100 Simmental crossbred steers underwent feeding trials where dry matter intake (DMI) was measured and average daily gain (ADG) and metabolic mid-test body weight (MMWT) were determined through body weight measurements. A genome-wide association analysis (GWAA) using the GRAMMAR mixed model method determined single nucleotide polymorphisms (SNPs) associated with RFI. The most significant SNPs from GWAA within 8.5 kb of a gene, reflective of the average haplotype block length for these populations, were selected as proxies for that respective gene for GSEA-SNP. Fifteen gene sets were enriched for RFI. Gene sets were involved in protein turnover and metabolism (n=5), cellular respiration (n=3), lipid metabolism (n=2), immune function (n=2), and cellular function (n=3). In the Hereford population, 87 leading edge genes (LEG) were involved in two enriched gene sets and two LEG (USP33 and PSEN2) were involved in both gene sets. In the Angus population, 108 LEG were identified within enriched gene sets (n=6), 79 of which were unique to one gene set while the others overlapped with at least one other gene set. In the Simmental crossbred population, 130 leading edge genes were identified within enriched gene sets (n=7). Of the 130 leading edge genes, 104 were unique to one gene set, while the others overlapped with as many as five gene sets. Many gene sets within the same population of animals contained the same leading edge genes and had similar function while few leading edge genes (n=5) overlapped across populations, showing the different genetic factors affecting feed efficiency across breeds. Protein turnover, energy metabolism, cellular function, immune function, and cellular respiration are important factors contributing to variation in the RFI phenotype among animals. Identification of genes and gene sets involved in these functions confirms their importance to RFI, metabolic function, and feed efficiency in beef cattle.
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Details
- Title
- Identification of genes and gene sets associated with residual feed intake in Hereford, Angus, and Simmental crossbred beef cattle
- Creators
- Jacob Levi Mutch
- Contributors
- Kristen A. Johnson (Degree Supervisor)
- Awarding Institution
- Washington State University
- Academic Unit
- Animal Sciences, Department of
- Theses and Dissertations
- Master of Science (MS), Washington State University
- Publisher
- Washington State University; [Pullman, Washington] :
- Identifiers
- 99900525071401842
- Language
- English
- Resource Type
- Thesis