Population structure and genetic characterization of the Mangalarga Marchador horse breed

Abstract

Mangalarga Marchador (MM) is the largest equine breed in Brazil, and the analysis of pedigree and molecular markers has made possible the best genetic research in the breed. The objectives of this work were to evaluate the population structure and to pre-characterize the MM with pedigree and genotyping data. Pedigree of 514,283 animals were used for estimates of inbreeding (F), probability of gene origin and breed structuring. Genotyped 3193 equines for 13 microsatellites (SSR) and in chip of the single nucleotide polymorphism, SNP70K, 244 animals of the breeds MM, Andalusian (AND), Lusitano (LUS), Thoroughbred (THO), Arabian (ARA), Campolina (CAM), Mangalarga (MAN), Puro Sangue Espanhol (PSE) and Sorraia (SOR). Thus, calculated the number of rare alleles (RA), expected heterozygosities (He) and observed (Ho), expected homozygosity (Home) and observed (Homo), minor allele frequency (MAF), F statistics (Fis, Fit e Fst), genetic distance (GD), principal component analysis (PCA), Hardy-Weinberg equilibrium (HWE), linkage disequilibrium (LD), population differentiation, population structuring by clustering and presence of common haplotypes between breeds. By pedigree analysis in the MM, the generation interval was from 9.48 to 10.43, F from 1.02% to 1.10, additive genetic ratio from 0.0023 to 0.0045, effective numbers of ancestors, founders, and genomes founders were from 198 to 1038, 225 to 1062 and 133 to 150, numbers of founders who presented 50% and 10% of the genetic pool accounted for 7.94% to 19.09% and 0.69% to 6.64% of the founders. For SSR analysis, the mean RA in the MM was two alleles/locus, He and Ho mean values ranged from 0.5767 to 0.8450 and 0.5331 to 0.7949, Fis averages (-0.0195), Fit (0.0566) and Fst (0.0748) and deviations of HWE were observed such as population differentiation in the loci and 60.26% of the alleles had strong LD. The GD were higher in the ARA and THO with the other breeds and minors between the MM, MAN and CAM and these with the AND and LUS, a result corroborated by the PCA. The MM was a substructured genetic entity, however with some more structured farms. With the SNP, in the MM the highest value of Homo (34,916.70) was found, 51% of the animals had loss of heterozygosity, mean MAF of 0.2010, there were deviations of EHW in the chromosomes, He ranged from 0.2940 to 0.3231 and smaller extensions of DL. A similar haplotype block was found between MAN and MM. The lowest differentiation occurred between CAM and MM (Fst = 0.0411), and the highest between THO and SOR (Fst = 0.2284). The MM was poorly defined unlike the LUS, PSE, THO and SOR, and the alleles sharing between MM and MAN was observed. PCA discriminated to a greater extent the SOR and THO of the other breeds, moderately the LUS and PSE, and smaller between MM, MAN and CAM. The MM is not in severe endogamy, which does not affect its evolution as a species. However, continuous monitoring of genetic diversity is necessary with the use of molecular and accurate pedigree records.