Genetic diversity and population structure of locally adapted Brazilian horse breeds assessed using genome-wide single nucleotide polymorphisms

Abstract

Animals first introduced in Brazil with the discovery were submitted to various selective pressures over five centuries, developing adaptive traits specific to the hostile environments found in the country. A high quantity of genotypic information can be generated quickly and with high repeatability and reliability using genome-wide Single Nucleotide Polymorphism (SNP) panels. Blood samples from 285 horses belonging to eight Brazilian breeds (Baixadeiro, Lavradeiro, Marajoara, Puruca, Campeiro, Crioulo, Mangalarga Marchador and Pantaneiro) and two commercial breeds sampled in Brazil (Arabian and English Thoroughbred) were genotyped focusing on elucidating the genetic structure and composition within and among Brazilian horse breeds and some of their possible founders. Data from the GGP Equine BeadChip (GeneSeek® Genomic Profiler™ Equine, 65.157 SNPs) was used to assess basic diversity parameters, genetic distance (pairwise FST and Nei), Principal Component Analysis (PCA), Analysis of Molecular Variance (AMOVA) and population structure (ADMIXTURE). Results showed that Crioulo (few animals), Pantaneiro, Mangalarga Marchador, and Campeiro breeds possess distinct genetic bases from the others and each other. The Lavradeiro, Baixadeiro, Puruca, and Marajoara breeds have a shared genetic basis, hindering their differentiation. The results also reflected a geographic division of the Brazilian equine breeds, with those originally from the North and Northeast regions (Lavradeiro, Marajora, Puruca and Baixadeiro) grouped. On the other hand, animals from the South and Southeast regions (Crioulo, Campeiro and Mangalarga Marchador) were genetically closer although distinguished. The Pantaneiro breed originating from Pantanal Matogrossense in the Midwest region of Brazil, separated from all the others. Overall, high values of genetic variability and low values of FIS were observed for the Brazilian naturalized breeds. Both Arabian and English Thoroughbred sampled in Brazil presented a similar genetic variability to the Brazilian breeds but were genetically differentiated. This study aims to understand better the genetic variability and relation among Brazilian naturalized horse breeds and their possible origins. This information helps establish and maintain conservation nuclei and programs for each horse breed. Results found here can be used as a base for backup decisions regarding management to optimize conservation programs and other support sampling strategies for the National Animal Germplasm Program.