Genetic diversity and patterns of population structure in Creole goats from the Americas

Abstract

Biodiversity studies are more efficient when large numbers of breeds belonging to several countries are involved, as they allow for an in-depth analysis of the within- and between-breed components of genetic diversity. A set of 21 microsatellites was used to investigate the genetic composition of 24 Creole goat breeds (910 animals) from 10 countries to estimate levels of genetic variability, infer population structure and understand genetic relationships among populations across the American continent. Three commercial transboundary breeds were included in the analyses to investigate admixture with Creole goats. Overall, the genetic diversity of Creole populations (mean number of alleles = 5.82 ± 1.14, observed heterozygosity = 0.585 ± 0.074) was moderate and slightly lower than what was detected in other studies with breeds from other regions. The Bayesian clustering analysis without prior information on source populations identified 22 breed clusters. Three groups comprised more than one population, namely from Brazil (Azul and Graúna; Moxotó and Repartida) and Argentina (Long and shorthair Chilluda, Pampeana Colorada and Angora-type goat). Substructure was found in Criolla Paraguaya. When prior information on sample origin was considered, 92% of the individuals were assigned to the source population (threshold q ≥ 0.700). Creole breeds are well-differentiated entities (mean coefficient of genetic differentiation = 0.111 ± 0.048, with the exception of isolated island populations). Dilution from admixture with commercial transboundary breeds appears to be negligible. Significant levels of inbreeding were detected (inbreeding coefficient > 0 in most Creole goat populations, P < 0.05). Our results provide a broad perspective on the extant genetic diversity of Creole goats, however further studies are needed to understand whether the observed geographical patterns of population structure may reflect the mode of goat colonization in the Americas.

Dissection of ancestral genetic contributions to Creole goat populations

“…Although several studies have been carried out to characterise the genetic diversity of European, African, and South and Central American goats at the continental level (e.g. Cañón et al, 2006;Naderi et al, 2007;Ginja et al, 2017), a comprehensive joint analysis of breeds from the various continents has not been accomplished so far. Some research on New World goats has relied on mitochondrial DNA sequences (Amills et al, 2009), which reflect only the history of femalemediated gene flow and thus lack the power to track complex histories of introgression and admixture.…”

Local Goat Breeds in the United States

“…The approach of evaluating goats by this external phenotype has been validated by DNA testing, revealing that this phenotype, which occurs throughout the Americas, does reflect an underlying genotypic similarity. This indicates that the history and development of this type of goat traces back to a common foundation centuries ago [5,6].…”

“…Research is now documenting that Spanish goats are generally superior to Boer goats in overall productivity measured on a herd-wide basis, and are on a par with Kiko goats [5,6]. This documentation points to the need to carefully evaluate local resources before replacing them with exotic resources, because local resources may indeed be equal or superior due to environmental adaptation.…”

Genome‐wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds

“…Similarly, a study investigating breed composition of Creole goats from 10 American countries found moderate to high heterozygosity values (Ginja et al . ).…”