Novel investigations into the genomic architecture affecting the muscle growth and development of Irish beef and dairy cattle

Abstract

Muscle growth and development in livestock is an important indicator of carcass yield and performance. Investigating the complex polygenic nature of carcass traits may yield additional knowledge and important insights into the role of genomic variation in muscle growth and development. This thesis describes the approaches undertaken to dissect the genomic variation and biological processes governing bovine muscle growth and development. Chapter two describes the estimation of the frequency and effects of genomic polymorphisms in Myostatin (MSTN) on milk, fertility and carcass performance in a population of dairy cows. The role of MSTN in muscle growth and development is long established however the aim here was to estimate both the beneficial and possible antagonistic effects on production traits of economic importance in the dairy industry. Similarly, the role μ-calpain (CAPN1) and Calpastatin (CAST) in post-mortem tenderisation is widely reported and in chapter three, the frequency and effects of genomic polymorphisms in CAPN1 and CAST on fertility and carcass performance were estimated in a population of beef cows. Chapter four describes the approaches taken to identify genomic polymorphisms with novel functional roles in bovine muscle growth and development and the disentanglement of their impact on gene function while also estimating the frequency of same polymorphisms in a large population of Irish cattle. Finally, the objective of chapter five was to identify novel associations between regions of the bovine genome with carcass performance using a GWAS in a population of beef cattle. Additionally, a functional genomics dataset in the form of gene expression data was integrated with GWAS results and subsequent gene ontology and pathway analysis contributed to an improved and enhanced understanding of the genomic variation underlying carcass performance. The project identified a number of gene polymorphisms, genomic regions and biological pathways significantly associated with carcass performance.