Genetic characterization of Mangalarga Marchador horse

Mangalarga Marchador (MM) is the most important Brazilian horse breed, with 600 thousand animals registered. The aim of this study carry out the genetic characterization of the breed. Samples were collected from 355 horses [MM, n = 218; Andalusian n = 20; Purebred Lusitano n = 21; Sorraia (SOR) n = 16; Thoroughbred n = 21; Campolina (CAM) n = 21, and Mangalarga (MAN) n = 38] and genotyped with the SNP 70K BeadChip. Parameters were calculated, such as expected heterozygosities (He), Hardy-Weinberg equilibrium (HWE), linkage disequilibrium (r(2)), genetic differentiation, and principal component analysis (PCA); and haplotypes in common and population structure was assessed by Bayesian methods. The MM breed obtained reasonable He and deviations from HWE. The SOR breed had high r(2), and CAM and MM had low r(2). MAN and MM had a similar haplotype block. Analyses of population structure showed that, just as the other Brazilian breeds, the MM breed is not well defined, showing signs of substructure and possibly admixture. The analyses with PCA showed that Brazilian breeds clustered together, and well separated from the remaining breeds. A breeding program seeking to maximize the variability of MM and structure the breed as a more defined genetic entity should be implemented immediately.