Structure and genetic relationships between Brazilian naturalized and exotic purebred goat domestic goat (Capra hircus) breeds based on microsatellites

Abstract

The genetic relationships and structure of fourteen goat (Capra hircus) populations were estimated based on genotyping data from 14 goat populations (n = 410 goats) at 13 microsatellite loci. We used analysis of molecular variance (AMOVA), principal component analysis (PCA) and F statistics (F IS , F IT and F ST ) to evaluate the genetic diversity (Ho, He and ad) of the goats. Genetic distances between the 14 goat populations were calculated from allelic frequency data for the 13 microsatellite markers. Moderate differentiation was observed for the populations of the undefined breeds (including the Anglo-Nubian-M breed), the naturalized Brazilian breeds (Moxotó, Canindé), the exotic purebred breeds (Alpine, Saanen, Toggenbourg and Anglo-Nubian) and the naturalized Brazilian Graúna group. Our AMOVA showed that a major portion (88.51%) of the total genetic variation resulted from differences between individual goats within populations, while between-populations variation accounted for the remaining 11.49% of genetic variation. We used a Reynolds genetic distance matrix and PCA to produce a phenogram based on the 14 goat populations and found three clusters, or groups, consisting of the goats belonging to the undefined breed, the naturalized breeds and the exotic purebred breeds. The closer proximity of the Canindé breed from the Brazilian state of Paraíba to the Graúna breed from the same state than to the genetically conserved Canindé breed from the Brazilian state of Ceará, as well as the heterozygosity values and significant deviations from Hardy-Weinberg equilibrium suggests that there was a high number of homozygotes in the populations studied, and indicates the importance of the State for the conservation of the local breeds. Cataloguing the genetic profile of Brazilian goat populations provides essential information for conservation and genetic improvements programs.

Genetic diversity and relatedness between Canindé and British Alpine goat breeds in Northeastern Brazil accessed by microsatellite markers

“…The mean observed heterozygosity estimation in this study for both Canindé and British Alpine (0.925 and 0.906, respectively) is higher than reported in Brazilian naturalized and exotic purebred domestic goats, from 0.320 to 0.460 (Oliveira et al, 2007), probably due to the fact that the choice for microsatellite markers was substantially different, which produced different results, and/or the presence of non-amplified alleles, as no test for the presence of nulls or scoring errors was performed in their study. Nevertheless, high H O values (i.e., 0.880 < H O < 0.980) are also reported in the literature for other goat breeds at different microsatellite loci (Araújo et al, 2006;Oliveira et al, 2010;Bulut et al, 2016).…”

“…HWE deviations have also been reported in other population genetic studies on goats (Menezes et al, 2006;Oliveira et al, 2007;Dixit et al, 2012).…”

“…These estimates, however, are higher than what has been reported between Alpine and Saanen dairy goats and the naturalized Brazilian Moxotó breed (Araújo et al, 2006), between Brazilian naturalized, exotic purebreds and crossbred goats (Oliveira et al, 2007), and between locally adapted Crespa goats and the phenotypically similar Angora breed (Lopes et al, 2016).…”

Ancestry analysis of locally adapted Crespa goats from southernmost Brazil

“…In Brazil, a few studies have recently addressed the existence of local breeds using either microsatellites or mtDNA, and all have focused on those from the northern region of the country, for example the Canindé, Graúna, Marota, Moxotó, Repartida, and Serrana Azul (Araújo et al, 2006;Menezes et al, 2006;Oliveira et al, 2007Oliveira et al, , 2010. Recently, a next-generation sequencing approach was employed to investigate genetic variation in Brazilian naturalized breeds (Moura et al, 2015).…”

“…Only in the late 19th century were foreign goat breeds recognized as economically important, and therefore managed in Brazil (Oliveira et al, 2007). In RS, however, improvements in goat breeding, including phenotypic selection to increase meat and milk production, started only in the 1980s with the foundation of CAPRISUL (Ponciano V, personal communication).…”