Drift across the Atlantic: genetic differentiation and population structure in Brazilian and Portuguese native goat breeds

The Portuguese Serrana goat breed: a review

Goats were among the first animals to be domesticated over 10,000 years ago and are part of human societies since the beginning of agriculture. Goats play a major role both in commercial farming systems and in subsistence agriculture systems, particularly in tropical, subtropical and Mediterranean regions where they are crucial for the supply of meat, milk, fibre and dung. This review concerns the Serrana breed, the most important and numerous indigenous goat breed from Portugal that was furthermore exported to other regions of the world, notably South America during the Portuguese colonization. Herein, we describe the origin and history of the breed as well as the productive performance and most common production systems. Finally, we address the local and traditional PDO (protected denomination of origin) and PGI (protected geographical indication) that are produced from these animals.

Diversity Analysis and Genetic Relationships among Local Brazilian Goat Breeds Using SSR Markers

Simple Summary

This study aimed to evaluate the genetic diversity of six groups of native Brazilian goats using a panel of single sequence repeats (SSRs). Results indicated a definite genetic differentiation among the Brazilian goat herd, which indicates the existence of at least four breeds according to the international concepts (Moxotó and Repartida; the Grauna and Serrana Azul; Canindé and Marota breeds).

Abstract

The genetic diversity of six Brazilian native goats was reported using molecular markers. Hair samples of 332 animals were collected from different goat breeds (Moxotó, Canindé, Serrana Azul, Marota, Repartida, and Graúna) from five states of Northeast Brazil (Paraíba, Pernambuco, Rio Grande do Norte, Bahia, and Piauí). A panel of 27 microsatellites or single sequence repeats (SSRs) were selected and amplified using a polymerase chain reaction (PCR) technique. All populations showed an average allele number of over six. The mean observed heterozygosity for Brazilian breeds was superior to 0.50. These results demonstrated the high genetic diversity in the studied populations with values ranging from 0.53 (Serrana Azul) to 0.62 (Repartida). The expected average heterozygosity followed the same trend ranging from 0.58 (Serrana Azul) to 0.65 (Repartida), and the values obtained are very similar for all six breeds. The fixation index (Fis) had values under 10% except for the Moxotó breed (13%). The mean expected heterozygosity of all Brazilian populations was over 0.50. Results indicated a within-breed genetic variability in the Brazilian breeds based on the average number of alleles and the average observed heterozygosity. The interbreed genetic diversity values showed proper genetic differentiation among local Brazilian goat breeds.

Population structure of indigenous southern African goats based on the Illumina Goat50K SNP panel

In this study, the genetic structure of indigenous Tswana and Swazi goats using the Illumina Goat50K SNP array was investigated. Two South African commercial goat breeds were included to investigate admixture with the indigenous populations in southern Africa. A total of 144 DNA samples including Boer goats (n = 24), Kalahari Red (n = 24), Swazi (n = 48), and Tswana goats (n = 48) were genotyped. Statistical analysis was performed using PLINK version 1.07. Genetic diversity, measured as expected heterozygosity, was estimated at 0.390, 0.398, 0.413, and 0.387 for Boer, Kalahari Red, Tswana, and Swazi goats, respectively. The individual inbreeding coefficient varied from 0.019 ± 0.05 to 0.011 ± 0.06 for the Tswana and Swazi goats, respectively. The Principal component analysis clustered the populations according to geographical origin and breed type. Linkage disequilibrium (LD) for shorter intervals (0-10 kb) ranged from 0.44 to 0.56 and commercial breeds had higher values. Effective population sizes decreased with generations and at the 13th generation ranged between 87 for Boer to 266 for Tswana goats. The Tswana population exhibited the highest level of genetic variation and effective population size, which holds potential for improved production in marginal regions. A national strategy is required to maintain genetic diversity in communal goat production systems through well-structured breeding and conservation programs.

Organization and Management of Conservation Programs and Research in Domestic Animal Genetic Resources

Creating national committees for domestic animal genetic resources within genetic resource national commissions is recommended to organize in situ and ex situ conservation initiatives. In situ conservation is a high priority because it retains traditional zootechnical contexts and locations to ensure the long-term survival of breeds. In situ actions can be based on subsidies, technical support, structure creation, or trademark definition. Provisional or permanent relocation of breeds may prevent immediate extinction when catastrophes, epizootics, or social conflicts compromise in situ conservation. Ex situ in vivo (animal preservation in rescue or quarantine centers) and in vitro methods (germplasm, tissues/cells, DNA/genes storage) are also potential options. Alert systems must detect emergencies and summon the national committee to implement appropriate procedures. Ex situ coordinated centers must be prepared to permanently or provisionally receive extremely endangered collections. National germplasm banks must maintain sufficient samples of national breeds (duplicated) in their collections to restore extinct populations at levels that guarantee the survival of biodiversity. A conservation management survey, describing national and international governmental and non-governmental structures, was developed. Conservation research initiatives for international domestic animal genetic resources from consortia centralize the efforts of studies on molecular, genomic or geo-evolutionary breed characterization, breed distinction, and functional gene identification. Several consortia also consider ex situ conservation relying on socioeconomic or cultural aspects. The CONBIAND network (Conservation for the Biodiversity of Local Domestic Animals for Sustainable Rural Development) exemplifies conservation efficiency maximization in a low-funding setting, integrating several Latin American consortia with international cooperation where limited human, material, and economic resources are available.

Dissection of ancestral genetic contributions to Creole goat populations

Goats have played a key role as source of nourishment for humans in their expansion all over the world in long land and sea trips. This has guaranteed a place for this species in the important and rapid episode of livestock expansion triggered by Columbus' arrival in the Americas in the late 1400s. The aims of this study are to provide a comprehensive perspective on genetic diversity in American goat populations and to assess their origins and evolutionary trajectories. This was achieved by combining data from autosomal neutral genetic markers obtained in more than two thousand samples that encompass a wide range of Iberian, African and Creole goat breeds. In general, even though Creole populations differ clearly from each other, they lack a strong geographical pattern of differentiation, such that populations of different admixed ancestry share relatively close locations throughout the large geographical range included in this study. Important Iberian signatures were detected in most Creole populations studied, and many of them, particularly the Cuban Creole, also revealed an important contribution of African breeds. On the other hand, the Brazilian breeds showed a particular genetic structure and were clearly separated from the other Creole populations, with some influence from Cape Verde goats. These results provide a comprehensive characterisation of the present structure of goat genetic diversity, and a dissection of the Iberian and African influences that gave origin to different Creole caprine breeds, disentangling an important part of their evolutionary history. Creole breeds constitute an important reservoir of genetic diversity that justifies the development of appropriate management systems aimed at improving performance without loss of genomic diversity.

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

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.

The Southwestern fringe of Europe as an important reservoir of caprine biodiversity

Background

Portugal and Spain, with six and 22 officially recognized caprine breeds, encompass 25 % of the European Union goat census. Many of these populations have suffered strong demographic declines because of competition with exotic breeds and the phasing-out of low income rural activities. In this study, we have investigated the consequences of these and other demographic processes on the genetic diversity, population structure and inbreeding levels of Iberian and Atlantic goats.

Methods

A sample of 975 individuals representing 25 officially recognized breeds from Portugal and Spain, two small populations not officially recognized (Formentera and Ajuí goats) and two ecotypes of the Tinerfeña and Blanca Celtibérica breeds were genotyped with a panel of 20 microsatellite markers. A wide array of population genetics methods was applied to make inferences about the genetic relationships and demography of these caprine populations.

Results

Genetic differentiation among Portuguese and Spanish breeds was weak but significant (F_ST = 0.07; P < 0.001), which is probably the consequence of their short splitting times and extensive gene flow due to transhumance. In contrast, Canarian goats were strongly differentiated because of prolonged geographic isolation. Most populations displayed considerable levels of diversity (mean H_e = 0.65).

Conclusions

High diversity levels and weak population structures are distinctive features of Portuguese and Spanish breeds. In general, these local breeds have a reduced census, but are still important reservoirs of genetic diversity. These findings reinforce the need for the implementation of management and breeding programs based on genetic data in order to minimize inbreeding, maintain overall genetic and allelic diversities and breed identities, while at the same time taking into account the within-breed genetic structure.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-015-0167-8) contains supplementary material, which is available to authorized users.

Potential benefits of genomic selection on genetic gain of small ruminant breeding programs

In conventional small ruminant breeding programs, only pedigree and phenotype records are used to make selection decisions but prospects of including genomic information are now under consideration. The objective of this study was to assess the potential benefits of genomic selection on the genetic gain in French sheep and goat breeding designs of today. Traditional and genomic scenarios were modeled with deterministic methods for 3 breeding programs. The models included decisional variables related to male selection candidates, progeny testing capacity, and economic weights that were optimized to maximize annual genetic gain (AGG) of i) a meat sheep breeding program that improved a meat trait of heritability (h(2)) = 0.30 and a maternal trait of h(2) = 0.09 and ii) dairy sheep and goat breeding programs that improved a milk trait of h(2) = 0.30. Values of ±0.20 of genetic correlation between meat and maternal traits were considered to study their effects on AGG. The Bulmer effect was accounted for and the results presented here are the averages of AGG after 10 generations of selection. Results showed that current traditional breeding programs provide an AGG of 0.095 genetic standard deviation (σa) for meat and 0.061 σa for maternal trait in meat breed and 0.147 σa and 0.120 σa in sheep and goat dairy breeds, respectively. By optimizing decisional variables, the AGG with traditional selection methods increased to 0.139 σa for meat and 0.096 σa for maternal traits in meat breeding programs and to 0.174 σa and 0.183 σa in dairy sheep and goat breeding programs, respectively. With a medium-sized reference population (nref) of 2,000 individuals, the best genomic scenarios gave an AGG that was 17.9% greater than with traditional selection methods with optimized values of decisional variables for combined meat and maternal traits in meat sheep, 51.7% in dairy sheep, and 26.2% in dairy goats. The superiority of genomic schemes increased with the size of the reference population and genomic selection gave the best results when nref > 1,000 individuals for dairy breeds and nref > 2,000 individuals for meat breed. Genetic correlation between meat and maternal traits had a large impact on the genetic gain of both traits. Changes in AGG due to correlation were greatest for low heritable maternal traits. As a general rule, AGG was increased both by optimizing selection designs and including genomic information.