Masters Theses

Date of Award

8-2024

Degree Type

Thesis

Degree Name

Master of Science

Major

Animal Science

Major Professor

Phillip R Myer, Brynn H Voy

Committee Members

Phillip R Myer, Brynn H Voy, Jon Beever, Troy Rowan

Abstract

In beef cattle production, the skeletal muscle is the primary product. Animals with greater efficiency use fewer resources to produce muscle. However, there are very few studies about the relationship between the molecular pathways in muscle and animal efficiency. The objective of the study was to determine relationships between animal efficiency at the molecular level and how those genes regulate growth in the skeletal muscle of beef cattle. Our hypothesis was there are increased number of genes involved in muscle growth in association with greater ADG or increased feed efficiency. One-hundred Angus steers were enrolled in 70d feed efficiency trials using the Vytelle GrowSafe 8000 individual feed intake monitoring system. Around 500µg of muscle tissue were collected via needle biopsy during the last 30 days of the feed efficiency trial. RNA was extracted from ~50mg/sample using a modified TRIzol method. Libraries were constructed using SMART Seq v4 3’ DE Kit and were sequenced using a Novaseq 6000. Reads were mapped to the bos taurus genome (ARS-UCD 2.0) using STAR RNA-seq aligner. For all ADG and feed efficiency analyses, animals were ranked according to ADG or feed efficiency and grouped by the greatest to least 20th percentile; greater or less ADG, respectively. DESeq2 in R (version 3.5) was used to examine the differential expression with an LRT test for the analysis of the linear model. A total of 4,162 and 55 genes were identified as differentially expressed (fdr p-value < 0.05) respectively for the grouped and linear models. Gene sets were functionally annotated using clusterProfiler package in R (version 3.14) and found expression at higher levels in greater ADG steers were significantly enriched (fdr p-value < 0.01) in BP Gene Ontology (GO) and KEGG functions relating to ribosomal biogenesis and mitochondrial function, which has been associated with muscle growth. Genes that were expressed at higher levels in less ADG steers were significantly enriched in GO terms and KEGG pathways relating to lysosome degradation and which have been associated with muscle atrophy. In conclusion, these results support that animals with greater ADG expressed more genes associated with muscle growth and energy metabolism.

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