With the availability of high‐density SNP panels and the establishment of approaches for characterizing homozygosity and heterozygosity sites, it is possible to access fine‐scale information regarding genomes, providing more than just comparisons of different inbreeding coefficients. This is the first study that seeks to access such information for the Mangalarga Marchador (MM) horse breed on a genomic scale. To this end, we aimed to assess inbreeding levels using different coefficients, as well as to characterize homozygous and heterozygous runs in the population. Using Axiom ® Equine Genotyping Array—670k SNP (Thermo Fisher), 192 horses were genotyped. Our results showed different estimates: inbreeding from genomic coefficients (FROH) = 0.16; pedigree‐based (FPED) = 0.008; and a method based on excess homozygosity (FHOM) = 0.010. The correlations between the inbreeding coefficients were low to moderate, and some comparisons showed negative correlations, being practically null. In total, 85,295 runs of homozygosity (ROH) and 10,016 runs of heterozygosity (ROHet) were characterized for the 31 horse autosomal chromosomes. The class with the highest percentage of ROH was 0–2 Mbps, with 92.78% of the observations. In the ROHet results, only the 0–2 class presented observations, with chromosome 11 highlighted in a region with high genetic variability. Three regions from the ROHet analyses showed genes with known functions: tripartite motif‐containing 37 (TRIM37), protein phosphatase, Mg2+/Mn2+ dependent 1E (PPM1E) and carbonic anhydrase 10 (CA10). Therefore, our findings suggest moderate inbreeding, possibly attributed to breed formation, annulling possible recent inbreeding. Furthermore, regions with high variability in the MM genome were identified (ROHet), associated with the recent selection and important events in the development and performance of MM horses over generations.

This study aimed to evaluate population parameters and to describe the genetic diversity of Quarter Horse breed (QH) in Brazil, reported for the first time in the literature. The pedigree data comprised 131,716 animals representing the total population (TP), with records of animals born between 1747 and 2008. The reference population (RP) representing the last generation was applied in this study considering 47,861 animals born between 2000 and 2008. The average generation interval was 9.6 and 10.8 years in TP and RP, respectively. The average equivalent complete generations (EG) were 5.09 (TP) and 6.24 (RP). The inbreeding coefficient (F), average relatedness (AR) and the increase in inbreeding by generation (ΔF) was 1.07%, 0.95% and 0.24%, respectively, for TP. The effective population size (N e) based on ΔF was 195 and 164 for TP and RP, respectively. The effective number of founders (f e) was 1045 and 811 for TP and RP, respectively, that of ancestors (f a) was 156 and 113, and that of founder genomes (f g) was 105 and 66. The f e /f a and f e /f g ratios in TP were 6.70 and 9.95, respectively, and an increase was observed in RP, indicated a strong bottleneck effect. The total genetic diversity of the QH breed was explained by 4780 ancestors, with 50% of diversity being explained by only 121 and 72 ancestors in TP and RP, respectively. The thoroughbred stallion Three Bars is the most influential ancestor with the largest marginal genetic contribution for TP (5.73) and RP (5.94%). The results demonstrate a large number of founders and ancestors, but a small ancestor group was responsible for the continuity of the QH breed in Brazil. These finding highlight the importance of monitoring genetic diversity, including follow-up by breeding programs, to permit control of the next generations.

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