Pedigree reconstruction, relationship and population structure using SNP markers in Gir cattle

• Ano de defesa: 2021
• Autor(a) principal: Garcia, Arielly Oliveira
• Tipo de documento: Dissertação
• Tipo de acesso: Acesso aberto
• Idioma: eng
• Instituição de defesa: Universidade Federal de Viçosa; Zootecnia
• Palavras-chave em Português: Gir (bovino); Funções Verossimilhança; Paternidade; Animais - População; Genética e Melhoramento dos Animais Domésticos
• Link de acesso: https://locus.ufv.br//handle/123456789/30254

Over time estimates of genetic values and studies of the structure and genetic diversity of animal populations have been carried out using traditional methods. Using only pedigree records, it was possible to obtain valuable information on their productive potential, history of population and genetic diversity. Consequently, incorrect or incomplete pedigree information could considerably reduce the accuracy of the analyzes. Currently, the use of markers has allowed the correction of information contained in the pedigree, in addition to estimating the relationship between animals more accurately, including in the absence of a pedigree. More accurate estimates of population parameters, such as inbreeding, linkage disequilibrium and effective size are also possible. With these parameters, we can evaluate the population structure and genetic diversity, guiding management and mating strategies in herds and the population as a whole. In this context, our general objectives were i. Identify a set of at least 1000 SNP markers, present in the main commercial chips, that accurately allow parentage assignment to be carried out in Gir breed; ii. Estimate relationship coefficients in Gir cattle based on SNP markers; iii. Estimate the inbreeding coefficients in Gir animals through runs of homozygosity; iv. Estimate the effective population size based on linkage disequilibrium in Gir cattle. We used the likelihood ratio approach to reconstruct the pedigree of Gir cattle, in order to correct any errors in annotation and to deepen the information contained in the pedigree records. The approach proved to be satisfactory, improving the depth of the pedigree and showing that it is well established in terms of recent information. The relationship coefficients allowed us to assess the distribution of values for each relationship category of the reconstructed pedigree. The population structure of the Gir breed was analyzed using effective size, linkage disequilibrium and inbreeding based on runs of homozygosity (ROH). In which a decrease in effective size and levels of inbreeding were detected, especially those based on short segments of ROH, with moderate to high values, suggesting the presence of bottlenecks in the genome of Gir cattle. On the other hand, a lower percentage of ROH resided in the longest ROH classes. The present study provides important information that can be added to the Brazilian Dairy Gir Breeding Program (PNMGL) to increase the accuracy and volume of records, in addition to assisting in the development of mating management strategies. Keywords: Likelihood approach. Parentage analysis. Population parameters. Probability.