Genetic diversity and population structure in Portuguese goat breeds

Analysis of the population genetic structure using microsatellite markers in goat populations in Taiwan

Due to the poor growth rate of the Taiwan black (TB) goat in Taiwan, many exotic breeds were brought into breeding schemes to improve TB goat. However, the excessive cross-breeding of alien species with TB goat has decreased its population numbers, genetic variation and biodiversity. Therefore, TB goat population considered an endemic species in Taiwan that needed to be conservation. The objective of the present study was to analyze the genetic structure and TB goat using genetic markers for genetic improvement and to sustain germplasm conservation and utilization. 15 microsatellite markers, divided into three sets, were used to analyze 690 goats sampled from 10 goat populations. The average number of alleles (Na) and effective alleles (Ne) was 11.87 ± 3.93 and 5.093 ± 1.768, respectively. The average expected heterozygosity (HE) and observed heterozygosity (HO) was 0.780 ± 0.084 and 0.602 ± 0.116, respectively. The average polymorphic information content (PIC) was 0.747 ± 0.103; FIS was 0.058 ± 0.075. All 15 microsatellite markers were highly polymorphic. The genetic distances between individuals were estimated to construct a phylogenetic tree. In present study, the 690 goat samples were divided into 8 clusters. The results indicated that these 15 microsatellite markers successfully clustered goat populations in Taiwan and could assist in the preservation of TB goats.

Genetic Differentiation among Livestock Breeds—Values for Fst

Simple Summary

The degree of relationship among livestock breeds can be quantified by the F_st statistic, which measures the extent of genetic differentiation between them. An F_st value of 0.1 has often been taken as indicating that two breeds are indeed genetically distinct, but this concept has not been evaluated critically. Here, F_st values have been collated for the six major livestock species: cattle, sheep, goats, pigs, horses, and chickens. These values are remarkably variable both within and between species, demonstrating that F_st > 0.1 is not a reliable criterion for breed distinctiveness. However, the large body of F_st data accumulated in the last 20–30 years represents an untapped database that could contribute to the development of interdisciplinary research involving livestock breeds.

Abstract

(1) Background: The F_st statistic is widely used to characterize between-breed relationships. F_st = 0.1 has frequently been taken as indicating genetic distinctiveness between breeds. This study investigates whether this is justified. (2) Methods: A database was created of 35,080 breed pairs and their corresponding F_st values, deduced from microsatellite and SNP studies covering cattle, sheep, goats, pigs, horses, and chickens. Overall, 6560 (19%) of breed pairs were between breeds located in the same country, 7395 (21%) between breeds of different countries within the same region, 20,563 (59%) between breeds located far apart, and 562 (1%) between a breed and the supposed wild ancestor of the species. (3) Results: General values for between-breed F_st were as follows, cattle: microsatellite 0.06–0.12, SNP 0.08–0.15; sheep: microsatellite 0.06–0.10, SNP 0.06–0.17; horses: microsatellite 0.04–0.11, SNP 0.08–0.12; goats: microsatellite 0.04–0.14, SNP 0.08–0.16; pigs: microsatellite 0.06–0.27, SNP 0.15–0.22; chickens: microsatellite 0.05–0.28, SNP 0.08–0.26. (4) Conclusions: (1) Large amounts of F_st data are available for a substantial proportion of the world’s livestock breeds, (2) the value for between-breed F_st of 0.1 is not appropriate owing to its considerable variability, and (3) accumulated F_st data may have value for interdisciplinary research.

An Overview of the Use of Genotyping Techniques for Assessing Genetic Diversity in Local Farm Animal Breeds

Simple Summary

The number of local farm animal breeds is declining worldwide. However, these breeds have different degrees of genetic diversity. Measuring genetic diversity is important for the development of conservation strategies and, therefore, various genomic analysis techniques are available. The aim of the present work was to shed light on the use of these techniques in diversity studies of local breeds. In summary, a total of 133 worldwide studies that examined genetic diversity in local cattle, sheep, goat, chicken and pig breeds were reviewed. The results show that over time, almost all available genomic techniques were used and various diversity parameters were calculated. Therefore, the present results provide a comprehensive overview of the application of these techniques in the field of local breeds. This can provide helpful insights into the advancement of the conservation of breeds with high genetic diversity.

Abstract

Globally, many local farm animal breeds are threatened with extinction. However, these breeds contribute to the high amount of genetic diversity required to combat unforeseen future challenges of livestock production systems. To assess genetic diversity, various genotyping techniques have been developed. Based on the respective genomic information, different parameters, e.g., heterozygosity, allele frequencies and inbreeding coefficient, can be measured in order to reveal genetic diversity between and within breeds. The aim of the present work was to shed light on the use of genotyping techniques in the field of local farm animal breeds. Therefore, a total of 133 studies across the world that examined genetic diversity in local cattle, sheep, goat, chicken and pig breeds were reviewed. The results show that diversity of cattle was most often investigated with microsatellite use as the main technique. Furthermore, a large variety of diversity parameters that were calculated with different programs were identified. For 15% of the included studies, the used genotypes are publicly available, and, in 6%, phenotypes were recorded. In conclusion, the present results provide a comprehensive overview of the application of genotyping techniques in the field of local breeds. This can provide helpful insights to advance the conservation of breeds.

Exploring genetic diversity and population structure of Punjab goat breeds using Illumina 50 K SNP bead chip

Pakistan has 35 goat breeds. Moreover, the province of Punjab has highest goat population constituting 37% of country's total population with seven goat breeds including Beetal, Daira Deen Panah, Nachi, Barbari, Teddi, Pahari, and Pothwari. The diversity study of breeds warrants the documentation of breeds particularly using genome wide panel of markers, i.e., SNP chip. The objective of the current study was to fill this gap of information. Therefore, in current study we collected total of 879 unrelated goat blood samples along with data on body weight measurements; genomic DNA was extracted, and genotyping was carried out using 50 K SNP bead chip. Quality control measures were performed in Plink 1.07. Genetic diversity was observed among studied populations using heterozygosity and pairwise F_ST estimates, principal component analysis, admixture analysis in Plink software with visualization in Clumpak, and constructing phylogenetic tree in Mega 7 software. Moderate to high level of heterozygosity was observed among the studied populations. Coefficient of inbreeding varied from 0.0186 ± 0.0327 in Pahari to 0.183 ± 0.0715 in Barbari. Barbari and Daira Deen Panah had quite higher level of inbreeding coefficient as compared to all other breeds with value of 0.183 ± 0.0715 and 0.1378 ± 0.0741, respectively. PCA identified three steps of subdividing the seven goat breeds at various levels of K. All the seven breeds made independent clusters at various levels of PCA. Admixture analysis revealed the distinctness of Teddi and Barbari breeds. Genetic sub-structuring was observed in the admixture patterns of Beetal breed. Moreover, high level of genetic admixture was observed in Nachi, Pahari, Pothwari, and Daira Deen Panah breeds. Admixture results were further interpreted by calculating pairwise F_ST values. Our results provided first insights about genetic diversity of Pakistani goat breeds based on genomic data. To conclude, the enriched goat breed diversity in Pakistan could provide valuable genetic reservoir for national breeding schemes.

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.

Molecular Identification of the "Facciuta Della Valnerina" Local Goat Population Reared in the Umbria Region, Italy

Italy holds important genetic resources of small ruminant breeds. By distinguishing goat breeds at the DNA level, certification of products from specific breeds can be valorized. The aim of this study was to establish the genetic identity of Facciuta della Valnerina, a local goat population of Italy, compared with the cosmopolitan breeds, Saanen and Camosciata delle Alpi, reared in the same geographic area. A total of 116 microsatellite alleles ranging from 4 to 13 were detected at 16 loci in the three goat populations/breeds. A total of 23 private alleles with frequencies lower than 0.3 were detected in the Facciuta della Valnerina population. The mean numbers of alleles were 6.67, 4.58, and 4.92 in Facciuta della Valnerina, Camosciata delle Alpi, and Saanen, respectively. The expected heterozygosity ranged from 0.20 to 0.86. Most loci were highly polymorphic and informative (polymorphic information content ≥0.50). Factorial correspondence analysis and principal components analysis revealed very clear separation between Facciuta della Valnerina and the two reference goat breeds. Reducing the number of markers from 16 to 12 (on the basis of polymorphic information content and the number of alleles) still allowed us to distinguish the local population, indicating that microsatellite markers are capable of discriminating local livestock breeds at a low cost.

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.

Microsatellite based phylogeny and bottleneck studies of Iranian indigenous goat populations

Genetic analyses, structure, and bottlenecks were examined in six populations of Iranian indigenous goat using 13 microsatellite loci. The overall heterozygosity, polymorphism information content (PIC), and Shannon index values were 0.80, 0.74, and 2.14, respectively, indicating high genetic diversity. Both a phylogenetic tree and factorial correspondence analysis grouped the populations into two major clusters. Signatures for bottleneck events in the populations were examined by two methods, which suggested that bottlenecks had occurred in two Tali and Markhoz populations, whereas other populations (Raeini, Korki jonobe Khorasan, Lori, and Najdi) showed no signature of a genetic bottleneck in the recent past. The results showed that Iranian goats have high genetic diversity and may be of value to alternative breeding and conservation programs.

Analysis of Geographic and Pairwise Distances among Chinese Cashmere Goat Populations

This study investigated the geographic and pairwise distances of nine Chinese local Cashmere goat populations through the analysis of 20 microsatellite DNA markers. Fluorescence PCR was used to identify the markers, which were selected based on their significance as identified by the Food and Agriculture Organization of the United Nations (FAO) and the International Society for Animal Genetics (ISAG). In total, 206 alleles were detected; the average allele number was 10.30; the polymorphism information content of loci ranged from 0.5213 to 0.7582; the number of effective alleles ranged from 4.0484 to 4.6178; the observed heterozygosity was from 0.5023 to 0.5602 for the practical sample; the expected heterozygosity ranged from 0.5783 to 0.6464; and Allelic richness ranged from 4.7551 to 8.0693. These results indicated that Chinese Cashmere goat populations exhibited rich genetic diversity. Further, the Wright’s F-statistics of subpopulation within total (FST) was 0.1184; the genetic differentiation coefficient (GST) was 0.0940; and the average gene flow (Nm) was 2.0415. All pairwise FST values among the populations were highly significant (p<0.01 or p<0.001), suggesting that the populations studied should all be considered to be separate breeds. Finally, the clustering analysis divided the Chinese Cashmere goat populations into at least four clusters, with the Hexi and Yashan goat populations alone in one cluster. These results have provided useful, practical, and important information for the future of Chinese Cashmere goat breeding.

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

Brazilian goat breeds are believed to derive mainly from animals brought by Portuguese settlers since the 16th century. We used microsatellite markers in a sample of 436 animals to study genetic variability and differentiation of the six Portuguese (PT) and six Brazilian (BR) goat breeds currently recognized in the two countries. These breeds were also compared with an outgroup represented by a sample of Alpine (ALP) goats. The effective number of alleles and allelic richness were slightly higher in PT than in BR breeds. The global F(ST) was nearly 0.11 when PT and BR breeds were considered, with a mean pairwise F(ST) of about 0.03 among PT breeds, 0.07 among BR breeds and 0.15 between PT and BR breeds. The dendrogram illustrating relationships between populations and the correspondence analysis indicate the existence of two very distinct clusters, corresponding to the countries of origin of the breeds studied, which are nearly equidistant from the Alpine outgroup. The analysis with structure confirmed the separation between PT and BR breeds but suggests that some BR breeds, especially Graúna and Canindé, may share a common ancestry with PT breeds. The divergence observed between PT and BR breeds may result from founder effects and genetic drift but could also reflect the introduction in Brazil of goats originating from other regions, e.g., West Africa.