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.

中文翻译：

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Mangalarga Marchador 马品种近交率、纯合度和全基因组杂合度水平的精细估计

随着高密度 SNP 面板的可用性以及用于表征纯合性和杂合性位点的方法的建立，可以访问有关基因组的精细信息，提供的不仅仅是不同近交系数的比较。这是第一项旨在在基因组规模上获取 Mangalarga Marchador (MM) 马品种此类信息的研究。为此，我们旨在使用不同的系数评估近亲繁殖水平，并表征群体中的纯合子和杂合子运行。使用 Axiom ® Equine Genotyping Array-670k SNP (Thermo Fisher)，对 192 匹马进行了基因分型。我们的结果显示了不同的估计：基因组系数近亲繁殖 (FROH) = 0.16；基于谱系 (FPED) = 0.008；以及基于过度纯合度 (FHOM) = 0.010 的方法。近亲繁殖系数之间的相关性从低到中等，一些比较显示负相关，几乎为零。总共对 31 条马的常染色体进行了 85,295 次纯合性 (ROH) 运行和 10,016 次杂合性 (ROHet) 运行的表征。ROH 百分比最高的类别为 0-2 Mbps，占观测值的 92.78%。在 ROHet 结果中，只有 0-2 类显示了观察结果，其中 11 号染色体突出显示在具有高遗传变异性的区域。ROHet 分析的三个区域显示了具有已知功能的基因：含三联基序的 37 (TRIM37)、蛋白磷酸酶、Mg2+ /Mn2+ 依赖性 1E (PPM1E) 和碳酸酐酶 10 (CA10)。因此，我们的研究结果表明适度近亲繁殖，可能归因于品种形成，取消了最近可能的近亲繁殖。