Application of genomics-based tools leading to the identification of markers on bovine chromosome 14 influencing milk production and carcass quality traits

Genetic improvements in beef and dairy cattle can bring significant advances in satisfying the global food demand, which is expected to double by 2050. Several DNA markers have been identified on bovine chromosome 14 (BTA14), but low mapping resolution prevents their refinement for identification of causal mutations. The objective of this research was to apply radiation hybrid mapping technique to correctly map available high density markers, enabling the accurate assessment of linkage disequilibrium and the scanning of quantitative trait loci across the chromosome. The research also applied these techniques to identify candidate markers on BTA14 contributing to the genetic variation observed in milk production and carcass quality traits in Holstein and Angus cattle, respectively. The first study aimed at correctly ordering genetic markers along BTA14 and comparing the order to the bovine sequence assembly to aid collaborative efforts in improving the future versions of the assembly. A 12K radiation hybrid map of BTA14 was constructed using 843 single nucleotide polymorphism markers. The second study assessed the extent of linkage disequilibrium along the chromosome identifying specific regions in both Angus and Holstein cattle where non-random association between alleles of different loci occurred. For both breeds, results showed that average linkage disequilibrium extends to moderate levels up to 100 kilo base pairs and falls to background levels after 500 kilo base pairs. Correlation analysis for marker pairs common to these two breeds confirmed that the same marker phase is maintained only up to distances of 10 kilo base pairs. Linkage analysis studies for both breeds identified markers on the basis of sire heterozygosity and linkage disequilibrium and reported quantitative trait loci affecting milk production and carcass quality traits. Finally, using marker function, association and linkage analysis results, several candidate markers demonstrating significant effects on these economically relevant traits were identified. The results from this study support the existence of considerable genetic variation for both milk production and carcass quality traits in Holstein and Angus cattle, respectively, demonstrating opportunities for genetic improvement.