Understanding the morphological and genetic distinctiveness of the Spanish pouter pigeons: the Marchenero Pouter as a case study

Domestic species are excellent examples of the great adaptive potential of animal species under strong selective pressure. Among them, domestic pigeons (Columba livia var domestica) represent one of the first domesticated bird species. Artificial selection through centuries, together with the multipurpose use of this species, has led to an extraordinary phenotypic diversity among breeds. Here, the morphometric and genetic diversity of Marchenero Pouter, one of the oldest and most representative pouter breeds in Spain, was analysed and compared with other Spanish pouter breeds. Nine morphometric variables were measured in four breeds, for which we detected significant differences in the weight, wing length and tail length in the Marchenero Pouter. Genetic analyses were conducted using 10 microsatellite loci. The statistically significant genetic differences found in Marchenero Pouter in comparison with other Spanish pouter breeds in this study provide sufficient evidence to recognize it as an independent pouter breed. In addition, Marchenero Pouter showed low genetic diversity compared with other pigeon breeds from this and previous studies. Our results provide valuable information about the current status of Marchenero Pouter, which could be used to preserve this unique breed.     

Using molecular markers and multivariate methods to study the genetic diversity of local European and Asian chicken breeds

French and Asian subsets of chicken breeds were first analysed using 22 microsatellites and then compared to the AVIANDIV European set using 14 loci. Positive correlations were observed between F _IT or F _ST and typological values or variance of markers using the multivariate analysis mcoa . The first axis of the multivariate representation separated Asian from European breeds, revealing breeds with Asian ancestor. Using all or 14 loci, correct assignation rate was always higher than 93%. The Weitzman index and the aggregate diversity D were calculated using 22 loci within French and Asian breeds. The French breed Coucou de Rennes and the Hua-Tung breed seemed to contribute the most to the global diversity of each subset. This approach on French-only breeds and then on French with AVIANDIV domestic breeds (14 loci) showed that the Marans breed contributed the most. The AVIANDIV framework could be useful to evaluate the genetic diversity of local breeds and to help in connecting national and regional conservation policies.     

Molecular identification of livestock breeds: a tool for modern conservation biology

Global livestock genetic diversity includes all of the species, breeds and strains of domestic animals, and their variations. Although a recent census indicated that there were 40 species and over 8000 breeds of domestic animals; for the purpose of conservation biology the diversity between and within breeds rather than species is regarded to be of crucial importance. This domestic animal genetic diversity has developed through three main evolutionary events, from speciation (about 3 million years ago) through domestication (about 12000 years ago) to specialised breeding (starting about 200 years ago). These events and their impacts on global animal genetic resources have been well documented in the literature. The key importance of global domestic animal resources in terms of economic, scientific and cultural heritage has also been addressed. In spite of their importance, there is a growing number of reports on the alarming erosion of domestic animal genetic resources. This erosion of is happening in spite of several global conservation initiatives designed to mitigate it. Herein we discuss these conservation interventions and highlight their strengths and weaknesses. However, pivotal to the success of these conservation initiatives is the reliability of the genetic assignment of individual members to a target breed. Finally, we discuss the prospect of using improved breed identification methodologies to develop a reliable breed‐specific molecular identification tool that is easily applicable to populations of livestock breeds in various ecosystems. These identification tools, when developed, will not only facilitate the regular monitoring of threatened or endangered breed populations, but also enhance the development of more efficient and sustainable livestock production systems.     

The genetic structure of domestic rabbits

Understanding the genetic structure of domestic species provides a window into the process of domestication and motivates the design of studies aimed at making links between genotype and phenotype. Rabbits exhibit exceptional phenotypic diversity, are of great commercial value, and serve as important animal models in biomedical research. Here, we provide the first comprehensive survey of nucleotide polymorphism and linkage disequilibrium (LD) within and among rabbit breeds. We resequenced 16 genomic regions in population samples of both wild and domestic rabbits and additional 35 fragments in 150 rabbits representing six commonly used breeds. Patterns of genetic variation suggest a single origin of domestication in wild populations from France, supporting historical records that place rabbit domestication in French monasteries. Levels of nucleotide diversity both within and among breeds were ~0.2%, but only 60% of the diversity present in wild populations from France was captured by domestic rabbits. Despite the recent origin of most breeds, levels of population differentiation were high (F(ST) = 17.9%), but the majority of polymorphisms were shared and thus transferable among breeds. Coalescent simulations suggest that domestication began with a small founding population of less than 1,200 individuals. Taking into account the complex demographic history of domestication with two successive bottlenecks, two loci showed deviations that were consistent with artificial selection, including GPC4, which is known to be associated with growth rates in humans. Levels of diversity were not significantly different between autosomal and X-linked loci, providing no evidence for differential contributions of males and females to the domesticated gene pool. The structure of LD differed substantially within and among breeds. Within breeds, LD extends over large genomic distances. Markers separated by 400 kb typically showed r(2) higher than 0.2, and some LD extended up to 3,200 kb. Much less LD was found among breeds. This advantageous LD structure holds great promise for reducing the interval of association in future mapping studies.     

Geographical partitioning of goat diversity in Europe and the Middle East

Thirty microsatellite markers were analysed in 1426 goats from 45 traditional or rare breeds in 15 European and Middle Eastern countries. In all populations inbreeding was indicated by heterozygosity deficiency (mean FIS = 0.10). Genetic differentiation between breeds was moderate with a mean FST value of 0.07, but for most (c. 71%) northern and central European breeds, individuals could be assigned to their breeds with a success rate of more than 80%. Bayesian-based clustering analysis of allele frequencies and multivariate analysis revealed at least four discrete clusters: eastern Mediterranean (Middle East), central Mediterranean, western Mediterranean and central/northern Europe. About 41% of the genetic variability among the breeds could be explained by their geographical origin. A decrease in genetic diversity from the south-east to the north-west was accompanied by an increase in the level of differentiation at the breed level. These observations support the hypothesis that domestic livestock migrated from the Middle East towards western and northern Europe and indicate that breed formation was more systematic in north-central Europe than in the Middle East. We propose that breed differentiation and molecular diversity are independent criteria for conservation.     

Phylogeography and Origin of Sheep Breeds in Northern China

With the establishment of modern sheep production systems in China, various forms of hybridization with Western breeds and between native breeds have been utilized for genetic improvement. At the same time, the progressive destruction or deterioration of sheep habitat has accompanied urbanization in China. Together these factors have accelerated the loss of genetic diversity, or even resulted in the extinction of some indigenous breeds. It is therefore important that efficient strategies for surveillance, evaluation, conservation and utilization of available genetic resources are developed for this species. In this study, a total of 30 microsatellite markers were used to assess genetic diversity for 12 native breeds and one Western sheep breed in Northern China. The high polymorphism information contents at the 30 markers, varying from averages of 0.519 to 0.666 for the 13 breeds, imply the retention of natural variation from source populations in the domestic breeds from different geographic regions in China. Analysis of genetic differentiation revealed substantial divergence among these breeds. Neutrality tests indicated that more than one third of the 30 loci were in departure from neutrality, implying that some evolutionary forces (e.g. selection and migration) had acted on these populations. Phylogenetic and phylogeographic analyses displayed a remarkable degree of consistency between geographic origins, breeding histories and the pattern of genetic differentiation.     

Different levels of human intervention in domestic rabbits: effects on genetic diversity

The effects of human interaction on domestic rabbits were evaluated through the analysis of animals (up to 267) belonging to fancy breeds (22), a commercial breed (1), and selected strains (2). Microsatellite loci and mtDNA polymorphism revealed that the genetic pool of domestic rabbits studied only originated from that available in France. The good conservation of the original diversity was probably ensured through the multiplicity of samplings from wild populations. Selected strains, because of the breeding strategy, keep a fairly high level of diversity compared to other breeds.     

Cross-species amplification of Bovidae microsatellites and low diversity of the endangered Korean goral

The Korean goral (Nemorhaedus caudatus) is an endangered species of wild goat. The conservation and management of this species could benefit from a better understanding of its genetic diversity and structure. Cross-species amplification of 34 Bovidae microsatellite loci was tested on a panel of 6 Korean gorals and 10 domestic goats. After polymerase chain reaction (PCR) optimization, 29 (85.3%) microsatellite loci amplified successfully for the Korean gorals and 27 (79.4%) for the domestic goats. Of the amplified products, 16 (55.2%) were polymorphic in the Korean goral and 22 (81.5%) in domestic goats. Nei's unbiased mean heterozygosity and mean allele number per locus were, respectively, 0.356 and 2.6 in the Korean goral and 0.636 and 4.8 in domestic goats. Low genetic diversity in the Korean gorals observed in this preliminary microsatellite survey suggests an urgent need for further detailed study of genetic diversity in Korean goral populations and a population management strategy based on these studies. Current results of cross-species amplification of domestic Bovidae microsatellites could be employed for the necessary population genetic studies on the Korean goral and other endangered Caprinae species.     

Evaluation of genetic diversity in Chinese indigenous chicken breeds using microsatellite markers

China is rich in chicken genetic resources, and many indigenous breeds can be found throughout the country. Due to poor productive ability, some of them are threatened by the commercial varieties from domestic and foreign breeding companies. In a large-scale investigation into the current status of Chinese poultry genetic resources, 78 indigenous chicken breeds were surveyed and their blood samples collected. The genomes of these chickens were screened using microsatellite analysis. A total of 2740 individuals were genotyped for 27 microsatellite markers on 13 chromosomes. The number of alleles of the 27 markers ranged from 6 to 51 per locus with a mean of 18.74. Heterozygosity (H) values of the 78 chicken breeds were all more than 0.5. The average H value (0.622) and polymorphism information content (PIC, 0.573) of these breeds suggested that the Chinese indigenous chickens possessed more genetic diversity than that reported in many other countries. The fixation coefficients of subpopulations within the total population (F _ST) for the 27 loci varied from 0.065 (LEI0166) to 0.209 (MCW0078), with a mean of 0.106. For all detected microsatellite loci, only one (LEI0194) deviated from Hardy-Weinberg equilibrium (HWE) across all the populations. As genetic drift or non-random mating can occur in small populations, breeds kept on conservation farms such as Langshan chicken generally had lower H values, while those kept on large populations within conservation regions possessed higher polymorphisms. The high genetic diversity in Chinese indigenous breeds is in agreement with great phenotypic variation of these breeds. Using Nei’s genetic distance and the Neighbor-Joining method, the indigenous Chinese chickens were classified into six categories that were generally consistent with their geographic distributions. The molecular information of genetic diversity will play an important role in conservation, supervision, and utilization of the chicken resources.     

Evaluation of genetic diversity in Chinese indigenous chicken breeds using microsatellite markers

China is regarded as one of the domestication cen-ters for chickens and archaeological studies provided evidence of chicken domestication in northern Chinaas early as 6000 BC[1]. At present, China has the larg-est chicken population in the world, represen…     

Genetic structure in Red Junglefowl (Gallus gallus) populations: Strong spatial patterns in the wild ancestors of domestic chickens in a core distribution range

Red Junglefowl (Gallus gallus) are among the few remaining ancestors of an extant domesticated livestock species, the domestic chicken, that still occur in the wild. Little is known about genetic diversity, population structure, and demography of wild Red Junglefowl in their natural habitats. Extinction threats from habitat loss or genetic alteration from domestic introgression exacerbate further the conservation status of this progenitor species. In a previous study, we reported extraordinary adaptive genetic variation in the MHC B‐locus in wild Red Junglefowl and no evidence of allelic introgression between wild and domestic chickens was observed. In this study, we characterized spatial genetic variation and population structure in naturally occurring populations of Red Junglefowl in their core distribution range in South Central Vietnam. A sample of 212 Red Junglefowl was obtained from geographically and ecologically diverse habitats across an area of 250 × 350 km. We used amplified fragment‐length polymorphism markers obtained from 431 loci to determine whether genetic diversity and population structure varies. We found that Red Junglefowl are widely distributed but form small and isolated populations. Strong spatial genetic patterns occur at both local and regional scales. At local scale, population stratification can be identified to approximately 5 km. At regional scale, we identified distinct populations of Red Junglefowl in the southern lowlands, northern highlands, and eastern coastal portions of the study area. Both local and long‐distance genetic patterns observed in wild Red Junglefowl may reflect the species’ ground‐dwelling and territorial characteristics, including dispersal barriers imposed by the Annamite Mountain Range. Spatially explicit analyses with neutral genetic markers can be highly informative and here elevates the conservation profile of the wild ancestors of domesticated chickens.     

Genetic variability in the Skyros pony and its relationship with other Greek and foreign horse breeds

In Greece, seven native horse breeds have been identified so far. Among these, the Skyros pony is outstanding through having a distinct phenotype. In the present study, the aim was to assess genetic diversity in this breed, by using different types of genetic loci and available genealogical information. Its relationships with the other Greek, as well as foreign, domestic breeds were also investigated. Through microsatellite and pedigree analysis it appeared that the Skyros presented a similar level of genetic diversity to the other European breeds. Nevertheless, comparisons between DNA-based and pedigree-based results revealed that a loss of genetic diversity had probably already occurred before the beginning of breed registration. Tests indicated the possible existence of a recent bottleneck in two of the three main herds of Skyros pony. Nonetheless, relatively high levels of heterozygosity and Polymorphism Information Content indicated sufficient residual genetic variability, probably useful in planning future strategies for breed conservation. Three other Greek breeds were also analyzed. A comparison of these with domestic breeds elsewhere, revealed the closest relationships to be with the Middle Eastern types, whereas the Skyros itself remained isolated, without any close relationship, whatsoever.     

Inference of hazel grouse population structure using multilocus data: a landscape genetic approach

In conservation and management of species it is important to make inferences about gene flow, dispersal and population structure. In this study, we used 613 georeferenced tissue samples from hazel grouse (Bonasa bonasia) where each individual was genotyped at 12 microsatellite loci to make inference on population genetic structure, gene flow and dispersal in northern Sweden. Observed levels of genetic diversity suggest that Swedish hazel grouse do not suffer loss of genetic diversity compared with other grouse species. We found significant F(IS) (deviation from Hardy-Weinberg expectations) over the entire sample using jack-knifed estimators over loci, which is most likely explained by a Wahlund effect. With the use of spatial autocorrelation methods, we detected significant isolation by distance among individuals. Neighbourhood size was estimated in the order of 62-158 individuals corresponding to a dispersal distance of 950-1500 m. Using a spatial statistical model for landscape genetics to infer the number of populations and the spatial location of genetic discontinuities between these populations we found indications that Swedish hazel grouse are divided into a northern and a southern population. We could not find a sharp border between these two populations and none of the observed borders appeared to coincide with any potential geographical barriers.These results imply that gene flow appears somewhat unrestricted in the boreal taiga forests of northern Sweden and that the two populations of hazel grouse in Sweden may be explained by the post-glacial reinvasion history of the Scandinavian Peninsula.     

Isolation and characterization of 15 microsatellite loci in the Korean goral (Nemorhaedus caudatus)

Microsatellites have been applied in a variety of fields, including conservation genetics. Species‐specific microsatellites are considered as more powerful genetic markers to generate an accurate genetic composition of a species itself. Accordingly, we characterized 15 polymorphic microsatellite loci from Korean goral, Nemorhaedus caudatus, one of the most endangered species in South Korea. The new markers should benefit future studies of the endangered species of other Asian gorals and their relatives for the study of genetic diversity and potential conservation management.     

Genetic structure,relationships and admixture with wild relatives in native pig breeds from Iberia and its islands

Background

Native pig breeds in the Iberian Peninsula are broadly classified as belonging to either the Celtic or the Mediterranean breed groups, but there are other local populations that do not fit into any of these groups. Most of the native pig breeds in Iberia are in danger of extinction, and the assessment of their genetic diversity and population structure, relationships and possible admixture between breeds, and the appraisal of conservation alternatives are crucial to adopt appropriate management strategies.

Methods

A panel of 24 microsatellite markers was used to genotype 844 animals representing the 17 most important native swine breeds and wild populations existing in Portugal and Spain and various statistical tools were applied to analyze the results.

Results

Genetic diversity was high in the breeds studied, with an overall mean of 13.6 alleles per locus and an average expected heterozygosity of 0.80. Signs of genetic bottlenecks were observed in breeds with a small census size, and population substructure was present in some of the breeds with larger census sizes. Variability among breeds accounted for about 20% of the total genetic diversity, and was explained mostly by differences among the Celtic, Mediterranean and Basque breed groups, rather than by differences between domestic and wild pigs. Breeds clustered closely according to group, and proximity was detected between wild pigs and the Mediterranean cluster of breeds. Most breeds had their own structure and identity, with very little evidence of admixture, except for the Retinto and Entrepelado varieties of the Mediterranean group, which are very similar. Genetic influence of the identified breed clusters extends beyond the specific geographical areas across borders throughout the Iberian Peninsula, with a very sharp transition from one breed group to another. Analysis of conservation priorities confirms that the ranking of a breed for conservation depends on the emphasis placed on its contribution to the between- and within-breed components of genetic diversity.

Conclusions

Native pig breeds in Iberia reveal high levels of genetic diversity, a solid breed structure and a clear organization in well-defined clusters.     

Evaluation of genetic diversity and population structure of west‐central Indian cattle breeds

Evaluations of genetic diversity in domestic livestock populations are necessary to implement region‐specific conservation measures. We determined the genetic diversity and evolutionary relationships among eight geographically and phenotypically diverse cattle breeds indigenous to west‐central India by genotyping these animals for 22 microsatellite loci. A total of 326 alleles were detected, and the expected heterozygosity ranged from 0.614 (Kenkatha) to 0.701 (Dangi). The mean number of alleles among the cattle breeds ranged from 7.182 (Khillar) to 9.409 (Gaolao). There were abundant genetic variations displayed within breeds, and the genetic differentiation was also high between the Indian cattle breeds, which displayed 15.9% of the total genetic differentiation among the different breeds. The genetic differentiation (pairwise F_ST) among the eight Indian breeds varied from 0.0126 for the Kankrej–Malvi pair to 0.2667 for Khillar–Kenkatha pair. The phylogeny, principal components analysis, and structure analysis further supported close grouping of Kankrej, Malvi, Nimari and Gir; Gaolao and Kenkatha, whereas Dangi and Khillar remained at distance from other breeds.     

Genetic characterisation of a domestic dog<Emphasis Type="Italic">Canis familiaris</Emphasis> breed endemic to South African rural areas

Allozyme electrophoresis (horizontal starch gel and PAGE) and histochemical staining techniques were used to study the genetic composition of an endemic southern African domestic dogCanis familiaris Linnaeus, 1758, the Africanis breed. Genetic differentiation was analysed at 21 protein-coding loci. The results were compared to those for three other populations/breeds: representatives of established Western breeds, crossbred dogs of Western descent from rural areas in South Africa, and indigenous Saluki dogs from the Middle East. Nine polymorphic loci were found (Ak-1,-2, Ck, Per, Hb, Po-A-1 to-3 andPo-Tf). Two unique alleles at theCk andPo-A-2 loci separated the Africanis breed from the other groups. There were also significant differences between Africanis and the other breeds in pair-wise comparisons of allelic frequencies at polymorphic loci. An assignment test, fixation index values, gene flow and genetic distance values indicated a closer genetic association between the Africanis and Saluki breeds than with dogs of Western origin. This finding supports archaeological evidence that the endemic Africanis breed was introduced from the Middle East into Africa thousands of years ago, and not through later western influences. The average heterozygosity ranged from 0.106–0.15, with least heterozygosity in the Africanis and most in the rural crossbred group. The percentage of polymorphic loci, the mean number of alleles per locus (biologically more significant than heterozygosity), and conformation of genotypes to Hardy-Weinberg proportions showed no evidence of recent loss of genetic diversity in Africanis. Genetic differentiation and support of archaeological evidence by genetics indicate that the endemic southern African domestic dog breed is unique.     

Characterization of the genetic diversity, structure and admixture of British chicken breeds

The characterization of livestock genetic diversity can inform breed conservation initiatives. The genetic diversity and genetic structure were assessed in 685 individual genotypes sampled from 24 British chicken breeds. A total of 239 alleles were found across 30 microsatellite loci with a mean number of 7.97 alleles per locus. The breeds were highly differentiated, with an average F(ST) of 0.25, similar to that of European chicken breeds. The genetic diversity in British chicken breeds was comparable to that found in European chicken breeds, with an average number of alleles per locus of 3.59, ranging from 2.00 in Spanish to 4.40 in Maran, and an average expected heterozygosity of 0.49, ranging from 0.20 in Spanish to 0.62 in Araucana. However, the majority of breeds were not in Hardy-Weinberg Equilibrium, as indicated by heterozygote deficiency in the majority of breeds (average F(IS) of 0.20), with an average observed heterozygote frequency of 0.39, ranging from 0.15 in Spanish to 0.49 in Cochin. Individual-based clustering analyses revealed that most individuals clustered to breed origin. However, genetic subdivisions occurred in several breeds, and this was predominantly associated with flock supplier and occasionally by morphological type. The deficit of heterozygotes was likely owing to a Wahlund effect caused by sampling from different flocks, implying structure within breeds. It is proposed that gene flow amongst flocks within breeds should be enhanced to maintain the current levels of genetic diversity. Additionally, certain breeds had low levels of both genetic diversity and uniqueness. Consideration is required for the conservation and preservation of these potentially vulnerable breeds.     

Unfolding of population structure in Baltic sheep breeds using microsatellite analysis

Studies of domestic animals are performed on breeds, but a breed does not necessarily equate to a genetically defined population. The division of sheep from three native and four modern Baltic sheep breeds was studied using 21 microsatellite loci and applying a Bayesian clustering method. A traditional breed-wise approach was compared to that relying on the pattern of molecular diversity. In this study, a breed was found to be inconsistent with a distinct genetic population for three reasons: (i) a lack of differentiation between modern Baltic breeds, since the majority of the studied sheep formed a single population; (ii) the presence of individuals of foreign ancestry within the breed; and (iii) an undefined local Saaremaa sheep was referred to as a breed, but was shown to consist of separate populations. In the breed-wise approach, only the clearly distinct Ruhnu sheep demonstrated low within-breed variation, although the newly identified Saaremaa populations also have low variability. Providing adequate management recommendations for the Saaremaa sheep is not possible without further studies, but the potential harmful effects of inbreeding in the Ruhnu sheep could be reduced through the use of two genetically related Saaremaa populations. In other breeds, excessive crossing appears to be a larger concern than inbreeding. Assigning individuals into populations based on the pattern of genetic diversity offers potentially unbiased means of elucidating the genetic population structure of species. Combining these genetic populations with phenotypic and aetiological data will enable formulation of the most informed recommendations for gene resource management.     

Genetic variation in Przewalski's horses, with special focus on the last wild caught mare, 231 Orlitza III

In our continuing efforts to document genetic diversity in Przewalski's horses and relatedness with domestic horses, we report genetic variation at 22 loci of blood group and protein polymorphisms and 29 loci of DNA (microsatellite) polymorphisms. The loci have been assigned by linkage or synteny mapping to 20 autosomes and the X chromosome of the domestic horse (plus four loci unassigned to a chromosome). With cumulative data from tests of 568 Przewalski's horses using blood, hair or tooth samples, no species-defining markers were identified, however a few markers were present in the wild species but not in domestic horses. Inheritance patterns and linkage relationships reported in domestic horses appeared to be conserved in Przewalski's horses. A derived type for the last wild caught mare 231 Orlitza III provided evidence for markers apparently not found in (or not currently available by descent from) the other species founders that were captured at the end of the nineteenth century. This information has been critical to the development of parentage analyses in the studbook population of Przewalski's horses at Askania Nova, at one time the largest herd of captive animals and the source of stock for reintroduction efforts. Some horses in the study showed genetic incompatibilities with their sire or dam, contradicting published studbook information. In many cases alternative parentage could be assigned from living animals. To assist in identification of correct parentage, DNA marker types for deceased horses were established from archived materials (teeth) or derived from offspring. Genetic markers were present in pedigreed animals whose origin could not be accounted for from founders. Genetic distance analysis of erythrocyte protein, electrophoretic and microsatellite markers in Przewlaski's horses and ten breeds of domestic horse place the Przewalski's horse as an outgroup to domestic horses, introgression events from domestic horses not withstanding.