Use of Genetic Polymorphisms to Assess the Genetic Structure and Breed Composition of Crossbred Animals

Abstract

This thesis explores the accuracy of methods to estimate the breed composition of crossbred animals which have unknown pedigree. Herein I present the use of SNP technologies to estimate the breed composition of small-holder crossbred dairy cattle in developing countries for the first time. Before this could be done there was a need to determine: what are the accuracies of different methods for estimating breed composition? The genetic structure of animals, the design of reference populations, the number of SNP markers and the model selected has possible consequences for estimation of breed composition. Once the effect of the above factors on the accuracy of estimation of breed composition is identified, it is possible to estimate with confidence the breed composition of crossbred animals that have no recorded pedigree. The overall aim of this thesis was to investigate the use of high-density SNP data to understand the livestock breed's population structure and estimate the breed composition of crossbred animals.