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Genetic and genomic studies in small ruminants

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Title: Genetic and genomic studies in small ruminants
Author: Brito, Luiz Fernando
Department: Department of Animal Biosciences
Program: Animal and Poultry Science
Advisor: Schenkel, Flávio
Abstract: Genomic selection (GS) has revolutionized livestock breeding programs around the world by increasing rates of genetic gain compared to traditional methods. Despite all the work done in species such as dairy cattle, there is still a lack of information for goats and sheep. Therefore, this thesis aimed to investigate topics that are needed for the successful use of genomic information into goat and sheep breeding programs. A total of 1,151 goats from nine breeds and 14,845 sheep from New Zealand Terminal Sire composite breeds genotyped using the Illumina Goat 50K BeadChip and Ovine Infinium® HD SNP Beadchip (600K), respectively, were used in the investigations. Goats were recorded for traditional production and conformation traits and sheep were recorded for over 30 growth, carcass and meat quality traits. Studies on basic parameters for genomic applications were first carried out, including linkage disequilibrium, consistence of gametic phase, admixture, population structure, runs of homozygosity, effective population size, inbreeding and signatures of selection. All sheep and goat breeds were shown to have high levels of genetic variability, nevertheless regions of their genomes displaying selection signatures were identified. Furthermore, genetic parameters for various growth, carcass and meat quality traits were estimated using a large and unique data set from a large range of New Zealand Terminal Sire sheep composite breeds. Next, the accuracy of genomic predictions of breeding values for all the traits was evaluated, using different genomic relationship matrices, validation designs, and genomic prediction scenarios. Based on the several genomic parameters evaluated, it seems that for the majority of the goat breeds genomic evaluation could potentially be implemented with reasonable accuracy within breed, using the current Illumina 50k panel and a large enough training population. For multi-breed genomic evaluation in goats, a denser SNP panel seems to be required. On the other hand, a multi-breed training population was shown to increase the prediction accuracy in New Zealand sheep. In conclusion, this thesis provides potentially valuable genetic and genomic parameters to serve as future reference for designing and/or updating sheep and goat breeding programs and for future genomic researches and applications.
Date: 2016-08
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