Genome-wide scan for selection signature and estimates of levels of autozygosity in Mangalarga Marchador horses

• Ano de defesa: 2020
• Autor(a) principal: Santos, Wellington Bizarria dos
• Tipo de documento: Dissertação
• Tipo de acesso: Acesso aberto
• Idioma: eng
• Instituição de defesa: Universidade Estadual Paulista (Unesp)
• Palavras-chave em Português: iHS; ROHet; ROH islands; FPED; Tajima’s D
• Link de acesso: http://hdl.handle.net/11449/193259

The Brazilian Mangalarga Marchador horse has dominated the attention of many horse breeders for their gaited phenotype over decades. A particularity of this breed is its intermediate-speed gait known as "marcha" in Brazil, which is subdivided into “marcha batida” and “marcha picada”. Considering the few studies focused on the genetic improvement of the breed, with so many potentials for the economy of the country, the objective of this study was to analyze through molecular/genomic information, the occurrences of signatures of selection using different statistics, featuring runs of homozygosity and heterozygosity, as well as accessing the inbreeding levels by measurements of genomics coefficients, and based on pedigree. To achieve these objectives, 192 animals were genotyped using the platform: Axiom ® Equine Genotyping Array - 670.796 SNP (Thermo Fisher, USA). To study the selection signatures, three methods already established in the literature were used: Tajima’s D, Runs of Homozygosity (ROH) islands, and Integrated Haplotype Score (iHS). For the evaluation of inbreeding were investigated the characterization of Runs of Homozygosity (ROH) and Heterozygosity (ROHet), and genomics coefficients (FHOM, and FROH), and those based on Pedigree (FPED) were calculated. As a final result, our findings reveal evidence of signals of selection associated with athletic performance, gait type, and energy muscle activity. The other potential signatures were associated with energy metabolism, bronchodilator response, NADH regeneration, reproduction, keratinization, and immunological system. The observed inbreeding coefficients were considered low to moderate. For FROH the results were considered moderate (0.16). However, its levels were low in the method based on pedigree information (FPED) (0.008), as well as for the genomic method based on the differences between the observed and expected number of homozygous genotypes (FHOM) (0.010). Besides, the correlations between the inbreeding coefficients were also of low to moderate. The availability of high-density SNP chips made it possible to improve estimates of inbreeding coefficients. The calculation of FROH allowed access to information on the demographic history and genetic relationships in the population based on molecular information, and therefore estimates were higher than those observed in the classical approach.