Date of Award

2024

Document Type

Doctoral Thesis

Degree Name

Doctor of Philosophy

Department

BIOLOGICAL SCIENCES

First Advisor

Dr. Deirdre Purfield

Second Advisor

Prof. Donagh Berry

Abstract

Genotype information is now available for over 4 million Irish dairy and beef cattle, and is primarily used for parent verification and genomic evaluations. Additional benefits that can be generated from genomic data should be explored to maximise the respective return-on- investment. This thesis investigated novel approaches that leverage genome-wide genomic information in cattle, focusing on using the genotype data to accurately determine breed composition, to quantify the association between major genes and performance traits, and to identify karyotype abnormalities. Furthermore, the value of genotyping for the purpose of identifying genetically superior animals depends largely on the accuracy of the breeding value; this, in turn, relies on integrity of data in the evaluations. The motivation for this thesis was also to establish data quality control pipelines to improve the integrity of the genomic data especially in relation to animal sex and breed composition. The single nucleotide polymorphism (SNP) used in this thesis all originated from different versions of the bespoke Irish genotyping panels containing between 48,502 to 49,213 autosomal SNPs across the genome. Genotypes on up to 779,138 juvenile cattle were available; genotype intensity metrics were also available. The breed composition of purebred and crossbred cattle was accurately predicted using SNP-BLUP. These breed estimates can be readily integrated into the SNP- BLUP pipelines used for genomic evaluations, serving as both an adjustment factor and as a genotype quality control measure. The observed interaction effect on calving difficulty between the myostatin genotypes of the dam and the sire could be incorporated into a sire- advice tool, thereby providing a more accurate estimate of the expected calving difficulty. Furthermore, genotype intensity information was used to identify aneuploidy at no additional cost; the incidence of sex-chromosomal and autosomal aneuploidy in the cattle population was 0.045% and 0.017%, respectively. By employing more data quality control strategies along with broadening genomic applications, this research will maximise the benefits of genotyping for producers and accelerate the rate of genetic improvement in Irish cattle.

Access Level

info:eu-repo/semantics/openAccess

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