Impact of foreign goat breeds on the genetic structure of Brazilian indigenous goats and consequences to intra-breed genetic diversity

Abstract

Brazilian goat breeds are at risk due to many threat factors including crossbreeding with exotic breeds. Genetic diversity, the genetic bottleneck hypothesis, and population genetic structure were examined in fourteen populations. The impact of crossbreeding exotic goats with indigenous Brazilian goat breeds was also studied. Twenty-three microsatellite markers were used to genotype 511 animals belonging to fourteen populations: six local from northeastern Brazil (BR), namely Azul (AZUL, n=40), Canindé (CAN, n=40), Graúna (GRAU, n=39), Marota (MAR, n=40), Moxotó (MOX, n=40) and Repartida (REPAR, n=40), and an undefined genotype standard group (UBS, n=40), four exotic breeds (EX), namely Alpina (ALP, n=40), Anglo-Nubian (ANG, n=26), Boer (BOER, n=40) and Saanen (SAAN, n=36), and three Spanish goat populations (ES), namely Murciana (MUR, n=35), Murciana-Granadina (MG, n=20) and Granadina (GRAN, n=35). The markers used displayed polymorphism (He=0.656) with suitable proportions of alleles. The populations showed a high proportion of markers in deviation from the Hardy Weinberg Equilibrium (HWE) and heterozygosity deficiency (FIS>0.10). The high value was found FST (0.27). Clear genetic structures were detected, indicating three genetically-similar groups (BR, EX, and ES). High genetic differentiation was observed mainly among EX and BR and between these and ES. Among the local population, a recent bottleneck has been detected only in the GRAU and MOX populations. The population substructure showed clear membership of individuals in thirteen groups. Up to 8% of this variability observed in BR is due to crossing of both crossing the Brazilian indigenous groups with exotic breeds, as well as crosses between indigenous breeds.