Genetic diversity and structure of livestock breeds
This thesis addresses the genetic characterisation of livestock breeds, a key aspect of the long-term future breed preservation and, thus, of primary interest for animal breeders and management in the industry. First, the genetic diversity and structure of breeds were investigated. The application of individual-based population genetic approaches at characterising genetic structure was assessed using the British pig breeds. All approaches, except for Principle Component Analysis (PCA), found that the breeds were distinct genetic populations. Bayesian genotypic clustering tools agreed that breeds had little individual genetic admixture. However, inconsistent results were observed between the Bayesian methods. Primarily, BAPS detected finer genetic differentiation than other approaches, producing biologically credible genetic populations. BAPS also detected substructure in the British Meishan, consistent with prior known population information. In contrast, STRUCTURE detected substructure in the British Saddleback breed that could not wholly be explained. Further analysis of the British Saddleback revealed that the genetic subdivision did not reflect its historical origin (union of Essex pig and Wessex Saddleback) but was associated with herds. The Rainbarrow appeared to be moderately differentiated from the other herds, and relatively lower allelic diversity and higher individual inbreeding, a possible result of certain breeding strategies. The genetic structure and diversity of the British traditional chicken breeds was also characterised. The breeds were found to be highly distinctive populations with moderately high levels of within-breed genetic diversity. However, majority of the breeds had an observed heterozygote deficit. Although individuals clustered to their origin for some of the breeds, genetic subdivision of individuals was observed in some breeds. For two breeds the inferred genetic subpopulations were associated with morphological varieties, but in others they were associated with flock supplier. As with the British Saddleback breed, gene flow between flocks within the chicken breeds should be enhanced to maintain current levels of genetic diversity. Second, the thesis focused on breed identification through the assignment of individuals to breed origin. Dense genome-wide assays provide an opportunity to develop tailor-made panels for food authentication, especially for verifying traditional breed-labelled products. In European cattle breeds, the prior selection of informative markers produced higher correct individual identification than panels of randomly selected markers. Selecting breed informative markers was more powerful using delta (allele frequency difference) and Wright's FST (allele frequency variation), than PCA. However, no further gain in power of assignment was achieved by sampling in excess of 200 markers. The power of assignment and number of markers required was dependent on the levels of breed genetic distinctiveness. Use of dense genome-wide assays and marker selection was further assessed in the British pig breeds. With delta, it was found that 96 informative SNP markers were sufficient for breed differentiation, with the exception of Landrace and Welsh pair. Assignment of individuals to breed origin was high and few individuals were falsely assigned, especially for the traditional breeds. The probability that a sample of a presumed origin actually originated from that breed was high in the traditional breeds. Validation of the 96-SNP panel using independent test samples of known origin and market samples revealed a high level of breed label conformity.
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