Investigating the role of host genetics and genomics in beef cow efficiency
Date
2023-09-28
Authors
Journal Title
Journal ISSN
Volume Title
Publisher
ORCID
0009-0004-1591-6123
Type
Thesis
Degree Level
Masters
Abstract
The ability to utilize forage to produce vigorous offspring annually contributes to a beef cow’s lifetime efficiency. This study aimed to identify genetic and genomic variation associated with beef cow efficiency using a novel weighted percentile scoring system. Ninety-eight Black Angus cows were raised under extensive feeding management over two years and cow efficiency was determined using a scoring system based on back fat at calving, day within the calving season, and calf weaning weight represented as a function of cow body weight (adjusted for sex and age). Eighty-three of these cows were retained for genetic analysis. Five genes (LEP, NPY, CCKBR, GHRL, and GHR) were selected for a candidate gene study to identify variants associated with the efficiency phenotype. Three genome-wide association studies (GWAS) were conducted using differing subpopulations and phenotypic classifications, including the efficiency ranking phenotype and a qualitative efficiency phenotype (HD-Quantitative, HD-Qualitative, and FULL). Based on the GWAS, a positional candidate study was conducted for two genes: SNX29 and RITA1. Results of the GWAS identified regions on BTA 10, 17, 25, and 27 as loci suggestively associated with efficiency in the GWAS, despite associations not reaching significance (Bonferroni threshold). Sequencing of the candidate genes identified two SNP in GHR and 11 SNP in RITA1 significantly associated with cow efficiency. Further study of associated RITA1 SNP identified five associated SNP are non-synonymous, causing four amino acid substitutions. This study has identified genetic variation with potential functional consequences associated with efficiency. Further validation is needed to confirm these preliminary findings if these markers are to be used for selection of efficient beef cows.
Description
Keywords
Genome-wide association study, beef cows, efficiency
Citation
Degree
Master of Science (M.Sc.)
Department
Animal and Poultry Science
Program
Animal Science