Genetic relationships among Spanish sheep using microsatellites

Five indigenous Spanish breeds of sheep, Churra, Latxa, Manchega, Rasa–Aragonesa and Merino, with Awassi sheep as a reference breed were genotyped for 19 DNA microsatellites. Allele frequencies and mean heterozygosities revealed the greatest genetic variation in Merino sheep and the lowest in Awassis. Differences in variability were not great in the other breeds studied. The dendrograms obtained based on genetic distances showed a large differentiation between Awassi sheep and the Spanish breeds, as was to be expected from their distinct genetic origin. Merinos appeared separated from the other four breeds, of which, according to a classification based on the fleece characteristics, Churra and Latxa belong to the churro type and Manchega and Rasa–Aragonesa to the so called entrefino type, though no clear separation was evident between the two types. These results suggest that morphological data alone are insufficient for determining relationships between breeds and that studies involving genetic markers may be of great assistance.     

Genetic diversity and subdivision of 57 European and Middle-Eastern sheep breeds

The population structure and genetic diversity of 57 European and Middle Eastern marginal and cosmopolitan sheep breeds from 15 countries were analysed by typing 31 microsatellite markers. Mean unbiased expected heterozygosities ranged from 0.63 in British Exmoor Horn to 0.77 in Albanian Ruda. South-eastern European and Middle-Eastern sheep breeds were significantly more variable than northwestern and western European breeds. An overall heterozygote deficiency (f) across all loci was observed (P < 0.001), while genetic differentiation (theta) was 5.7%. Principal component analysis and Bayesian model-based clustering indicate a south-east to north-west cline, but also revealed distinct groups of Middle-Eastern fat-tailed sheep, south-eastern European sheep and north-western/western European sheep. Within the last group, two less-distinct clusters comprised the Merino-type and Alpine breeds respectively. The incomplete demarcations of most clusters probably reflects cross-breeding and/or upgrading.     

Genetic relationships among Turkish sheep

Genetic relationships among Turkish sheep breeds were analysed on the basis of 30 microsatellite markers. Phylogenetic analyses based on the estimation of genetic distances revealed the closest relationships for the Akkaraman, Morkaraman and Tuj breeds, which were clearly differentiated from the others in the dendrogram. Our pattern was completely confirmed by results from the Factorial Correspondence Analysis. All the results described analysing either population parameters or individuals revealed a clear separation between the fat-tailed group and the others. These results, based on nuclear DNA, are discussed along with those already reported for these breeds through the investigation of mitochondrial DNA, which had revealed the invaluable significance of the genetic background of these Turkish sheep.     

Microsatellite analysis to estimate genetic relationships among five bulgarian sheep breeds

Herein, genetic relationships among five breeds of Bulgarian sheep were estimated using microsatellite markers. The total number of alleles identified was 226 at the 16 loci examined. D(A) distance values were used for phylogenetic tree construction with the UPGMA algorithm. The two Tsigai and two Maritza populations were found to be geneticallvery closely related to each other y (0.198, and 0.258 respectively). The Pleven Black Head population was distinct from the other four. These results could be useful for preserving genes in these breeds, thereby ensuring their preservation in Bulgaria.     

Genetic diversity analysis of six Spanish native cattle breeds using microsatellites

Six native Spanish cattle breeds have been characterized by using 30 microsatellite markers. The studied populations can be divided into three groups: Brown orthoid (Asturian Mountain, Asturian Lowland and the Nord-west Brown Group), Red convex (Pyrenean and Menorquina) and the Iberian bovine (Fighting bull). Allele frequencies were calculated and used for the characterization of the breeds and the study of their genetic relationships. Different genetic distance measures were calculated and used for dendogram construction. The closest populations were those representing Asturian breeds, the most divergent being Menorquina and Fighting Bull. The latter also showed the lowest diversity values (mean number of alleles per locus and heterozygosity). Genetic distances obtained between the other populations under analysis were similar to those reported for different European cattle breeds. This work analyzes the recent origin of these populations and contributes to the knowledge and genetic characterization of European native breeds.     

Genetic variability and individual assignment of Chinese indigenous sheep populations (Ovis aries) using microsatellites

The purpose of this study was to assess the genetic characteristics of six breeds of Chinese local sheep using 19 microsatellite loci and to effectively validate statistical methods for individual assignment based on informative microsatellites. All the six breeds deviated from Hardy–Weinberg equilibrium expectations, while the majority of markers complied. The polymorphism information content (PIC) of overall loci for the six populations ranged from 0.283 (SRCRSP5) to 0.852 (OarVH72). Tibetan sheep were the most diverse population with the highest mean allelic richness (6.895), while Ujmuqin (UQ) harboured the lowest allelic richness (6.000). The F‐statistics for the six populations were F_IS = ?0.172, F_IT = ?0.082 and F_ST = 0.077, respectively. Furthermore, the pair‐wise F_IS revealed a moderate genetic differentiation among populations (P < 0.01), indicating that all breeds can be considered genetically independent entities. The lowest genetic differentiation was between Tengchong (TC) and UQ (F_ST = 0.041), and the highest one was between TC and Fat‐tailed Han (F_ST = 0.111). In comparing the three statistical models, we note that the seven microsatellite loci (MAF65, OarJMP58, SRCRSP9, MCM140, OarAE129, BM8125 and SRCRSP5) commonly used for individual assignment will ensure a powerful detection of individual origin, with accuracy up to 91.87%, when the likelihood‐based method is used. Overall, these findings shed light onto the genetic characteristics of Chinese indigenous sheep and offer a set of microsatellite loci that is simple, economic and highly informative for individual assignment of Chinese sheep.     

Genetic differentiation in pointing dog breeds inferred from microsatellites and mitochondrial DNA sequence

Recent studies presenting genetic analysis of dog breeds do not focus specifically on genetic relationships among pointing dog breeds, although hunting was among the first traits of interest when dogs were domesticated. This report compares histories with genetic relationships among five modern breeds of pointing dogs (English Setter, English Pointer, Epagneul Breton, Deutsch Drahthaar and German Shorthaired Pointer) collected in Spain using mitochondrial, autosomal and Y-chromosome information. We identified 236 alleles in autosomal microsatellites, four Y-chromosome haplotypes and 18 mitochondrial haplotypes. Average F _ST values were 11.2, 14.4 and 13.1 for autosomal, Y-chromosome microsatellite markers and mtDNA sequence respectively, reflecting relatively high genetic differentiation among breeds. The high gene diversity observed in the pointing breeds (61.7–68.2) suggests contributions from genetically different individuals, but that these individuals originated from the same ancestors. The modern English Setter, thought to have arisen from the Old Spanish Pointer, was the first breed to cluster independently when using autosomal markers and seems to share a common maternal origin with the English Pointer and German Shorthaired Pointer, either via common domestic breed females in the British Isles or through the Old Spanish Pointer females taken to the British Isles in the 14th and 16th centuries. Analysis of mitochondrial DNA sequence indicates the isolation of the Epagneul Breton, which has been formally documented, and shows Deutsch Drahthaar as the result of crossing the German Shorthaired Pointer with other breeds. Our molecular data are consistent with historical documents.     

Accuracy of genotype imputation in sheep breeds

Although genomic selection offers the prospect of improving the rate of genetic gain in meat, wool and dairy sheep breeding programs, the key constraint is likely to be the cost of genotyping. Potentially, this constraint can be overcome by genotyping selection candidates for a low density (low cost) panel of SNPs with sparse genotype coverage, imputing a much higher density of SNP genotypes using a densely genotyped reference population. These imputed genotypes would then be used with a prediction equation to produce genomic estimated breeding values. In the future, it may also be desirable to impute very dense marker genotypes or even whole genome re‐sequence data from moderate density SNP panels. Such a strategy could lead to an accurate prediction of genomic estimated breeding values across breeds, for example. We used genotypes from 48 640 (50K) SNPs genotyped in four sheep breeds to investigate both the accuracy of imputation of the 50K SNPs from low density SNP panels, as well as prospects for imputing very dense or whole genome re‐sequence data from the 50K SNPs (by leaving out a small number of the 50K SNPs at random). Accuracy of imputation was low if the sparse panel had less than 5000 (5K) markers. Across breeds, it was clear that the accuracy of imputing from sparse marker panels to 50K was higher if the genetic diversity within a breed was lower, such that relationships among animals in that breed were higher. The accuracy of imputation from sparse genotypes to 50K genotypes was higher when the imputation was performed within breed rather than when pooling all the data, despite the fact that the pooled reference set was much larger. For Border Leicesters, Poll Dorsets and White Suffolks, 5K sparse genotypes were sufficient to impute 50K with 80% accuracy. For Merinos, the accuracy of imputing 50K from 5K was lower at 71%, despite a large number of animals with full genotypes (2215) being used as a reference. For all breeds, the relationship of individuals to the reference explained up to 64% of the variation in accuracy of imputation, demonstrating that accuracy of imputation can be increased if sires and other ancestors of the individuals to be imputed are included in the reference population. The accuracy of imputation could also be increased if pedigree information was available and was used in tracking inheritance of large chromosome segments within families. In our study, we only considered methods of imputation based on population‐wide linkage disequilibrium (largely because the pedigree for some of the populations was incomplete). Finally, in the scenarios designed to mimic imputation of high density or whole genome re‐sequence data from the 50K panel, the accuracy of imputation was much higher (86–96%). This is promising, suggesting that in silico genome re‐sequencing is possible in sheep if a suitable pool of key ancestors is sequenced for each breed.     

Phylogenetic relationships among Spanish goats breeds

We partially sequenced the mitochondrial hypervariable region 1 (HVR1) in 60 goats belonging to six Spanish breeds. The analysis of these and previously published sequences reveals a weak phylogeographical structure in the Iberian Peninsula breeds. Individuals from a single breed did not group into a single cluster. Furthermore, individuals from different breeds often shared single phylogenetic tree branches after UPGMA analysis. This could reflect the non-existence of breed isolation because of traditional seasonal pastoralism and annual long-distance migrations. Three goats belonging to the C maternal lineage were found, demonstrating a wider than previously thought distribution for this lineage.     

Evaluation of factors affecting individual assignment precision using microsatellite data from horse breeds and simulated breed crosses

Assignment tests have been utilized to investigate population classification, measure genetic diversity and to solve forensic questions. Using microsatellite data from 26 loci genotyped in eight horse breeds we examined how population differentiation, number of scored loci, number of scored animals per breed and loci variability affected individual assignment precision applying log likelihood methods. We found that both genetic differentiation and number of scored loci were highly important for recognizing the breed of origin. When comparing two and two breeds, a proportion of 95% of the most differentiated breeds (0.200 < or = FST < or = 0.259) could be identified scoring only three loci, while the corresponding number was six for the least differentiated breeds (0.080 < or = FST < or = 0.139). An identical proportion of simulated breed crosses, differentiated from their parental breeds by FST estimates in the range 0.050-0.069, was identified when scoring 12 loci. This level of source identification was not obtained for the less differentiated breed crosses. The current data further suggested that population sample size and locus variability were not critical for the assignment precision as long as moderately large sample sizes (> or = 20 animals per population) and fairly variable loci were used.     

Assessing genetic diversity of Vietnamese local chicken breeds using microsatellites

This study aimed to assess genetic diversity within and between nine Vietnamese local chicken breeds and two Chinese breeds included for comparison. Genotyping 29 microsatellites revealed high diversity of both Vietnamese and Chinese breeds. Cluster analysis using the structure software suggested six clusters as the most likely grouping of the 11 breeds studied. These groups encompassed four homogeneous clusters, one formed by the two Chinese breeds and the other three representing a single breed each: the Mekong Delta breed Ac, the South Central Coast breed Choi, and the Red River Delta breed Dong Tao. The six remaining breeds formed two additional admixed clusters.     

Molecular structure in peripheral dog breeds: Portuguese native breeds as a case study

Genetic variability in purebred dogs is known to be highly structured, with differences among breeds accounting for ∼30% of the genetic variation. However, analysis of the genetic structure in non-cosmopolitan breeds and local populations is still limited. Nine Portuguese native dog breeds, and other peripheral dog populations (five) with regional affinities, were characterized using 16 microsatellites and 225 amplified fragment length polymorphism (AFLP) markers, and the pattern of genetic differentiation was investigated. Although the level of breed differentiation detected is below that of other dog breeds, there is in most cases a correlation between breed affiliation and molecular structure. AFLP markers and Bayesian clustering methods allowed an average of 73.1% of individuals to be correctly assigned to source populations, providing robust genotypic assessment of breed affiliation. A geographical genetic structure was also detected, which suggests a limited influence of African dogs on the Iberian breeds. The sampling effect on the estimation of population structure was evaluated and there was a 2.2% decrease in genetic differentiation among breeds when working animals were included. Genetic diversity of stray dogs was also assessed and there is no evidence that they pose a threat to the preservation of the gene pool of native dog breeds.     

Pronounced differences in the frequency of TaqI βA-inhibin alleles between sheep breeds with different reproductive performance

A total of 419 individuals of four breeds with differing fecundity (Rhoenschaf, Merinolandschaf, East Friesian Milksheep, Romanov) and several wild sheep of the Ovis musimon, O. orientalis, O. vignei and O. ammon groups were screened for genetic variation at the βA-inhibin (INHBA) locus with up to 11 enzymes. The four breeds differed significantly (P< 0.001) in TaqI allele frequencies. The frequency of the TaqI A allele coincided with the average litter size in each breed.     

Genetic variations in blood proteins within and between Spanish dairy sheep breeds

Eleven flocks of three Spanish sheep breeds have been studied: four Churra, four Lacha and three Manchega. Genetic variations between flocks of the same and different breeds have been analysed, using eight genetic blood systems and a wide range of statistical methods. The results show that the Churra, Lacha and Manchega breeds present significant differences between each other. Significant intraracial variations have been observed in Churras and Lachas, although they were almost non-existent in Manchegas. In some cases the genetic distances between flocks of the same breed were greater than the distances between flocks of different breeds. The data indicate that the closest breeds genetically are Lacha and Manchega.     

Genetic diversity among Angus, American Brahman, Senepol and Romosinuano cattle breeds

The objective of this study was to quantify the genetic diversity among breeds under evaluation for tropical adaptability traits that affect the performance of beef cattle at the USDA/ARS SubTropical Agricultural Research Station (STARS) near Brooksville, FL, USA. Twenty-six microsatellite loci were used to estimate parameters of genetic diversity among the breeds American Brahman, Angus, Senepol and Romosinuano; the latter was comprised of two distinct bloodlines (Costa Rican and Venezuelan). Genotypes of 47 animals from each of these STARS herds were analysed for genetic diversity and genetic distance. Using two methods, the greatest genetic distance was detected between the Costa Rican line of Romosinuano and the Senepol. Gene diversity ranged between 0.64 (Costa Rican line of Romosinuano) and 0.75 (American Brahman). The breed relationship inferences, which are based on genetic distance, provide additional tools for consideration in future crossbreeding studies and for testing the relationship between quantified breed diversity and observed heterosis.     

Tracing genetic differentiation of Chinese Mongolian sheep using microsatellites

The genetic consequences of population differentiation and isolation have been the subject of conservation biology. In this study, we analysed the genetic diversity and structure of Mongolian sheep in China. These animals belong to a traditional local breed with high production, extensive adaption, early maturity and roughage resistance. For this purpose, 26 microsatellites were genotyped for five Mongolian sheep populations. The Bayesian clustering indicated five clusters as the most probable genetic structure of the populations investigated. In addition, a clear genetic structure was revealed in three populations distributed at large geographical scales, while the other cluster encompassed UQ and HLBR sheep that displayed no clear differentiation, probably due to their close and small geographical distributions. Overall, our results are helpful in understanding the interplay of population dynamics in these close genetic lineages of Mongolian sheep.     

Pedigree analysis of eight Spanish beef cattle breeds

The genetic structure of eight Spanish autochthonous populations (breeds) of beef cattle were studied from pedigree records. The populations studied were: Alistana and Sayaguesa (minority breeds), Avileña – Negra Ibérica and Morucha ("dehesa" breeds, with a scarce incidence of artificial insemination), and mountain breeds, including Asturiana de los Valles, Asturiana de la Montaña and Pirenaica, with extensive use of AI. The Bruna dels Pirineus breed possesses characteristics which make its classification into one of the former groups difficult. There was a large variation between breeds both in the census and the number of herds. Generation intervals ranged from 3.7 to 5.5 years, tending to be longer as the population size was larger. The effective numbers of herds suggest that a small number of herds behaves as a selection nucleus for the rest of the breed. The complete generation equivalent has also been greatly variable, although in general scarce, with the exception of the Pirenaica breed, with a mean of 3.8. Inbreeding effective population sizes were actually small (21 to 127), especially in the mountain-type breeds. However, the average relatedness computed for these breeds suggests that a slight exchange of animals between herds will lead to a much more favourable evolution of inbreeding. The effective number of founders and ancestors were also variable among breeds, although in general the breeds behaved as if they were founded by a small number of animals (25 to 163).     

Genetic relationships between seven Spanish native breeds of cattle

Summary. Ten genetic markers were studied in seven Spanish native cattle breeds, using a total of 725 animals. Of the ten, two were found to be monomorphic in all seven breeds. The genetic relationships of the seven breeds are estimated by three different genetic-statistical methods (genetic distances, main coordinate analysis and cluster analysis), which indicate three clearly distinct groups of populations: one where the Cárdena Andaluza and Alistana Sanabresa are very closely related, one comprising Sayaguesa, Morucha, Asturiana de los Valles and Asturiana de la Montaña cattle, and a third, genetically distant from the other two, comprising only Blanca Cacereña. The dendrogram drawn from the genetic distances matrix would seem to imply that the seven breeds are descended from different ancestors.     

Genetic diversity and variability in Alpine sheep breeds

The aim of this study was to analyze, through the use of microsatellite molecular markers, the genetic diversity and variability of nine Alpine sheep breeds reared in Italy (Bergamasca, Biellese, Schwarzbraunes Bergschaf, Tiroler Bergschaf, and Schnalserschaf), Germany (Brillenschaf and Weisses Bergschaf) and Slovenia (Bovška and Jezerzkǒ-Solčavska), and one Italian crossbreed population. Allelic richness was rather high in each breed highlighting a considerable genetic diversity. However, the study evidenced a significant departure from Hardy–Weinberg equilibrium in all analyzed breeds caused by a heterozygote deficiency. Such lack seems to be caused both to the presence of population substructure within breed and to a rather high level of inbreeding. The genetic differentiation among breed was rather low (F_ST = 0.057) but significant. The clustering analysis performed with STRUCTURE detected the presence of eight clusters; Schwarzbraunes Bergschaf and Tiroler Bergschaf were grouped together and Biellese and Bergamasca as well, evidencing a high similarity of their genetic make up. Reynolds’ genetic distance estimates confirmed the close relationship between these pairs of breeds. Moreover, Bovška, Jezerzkǒ-Solčavska and Brillenschaf resulted rather similar as expected according to their region of origin and to their common ancestors. Molecular coancestry confirmed as well such findings, suggesting that the studied breeds had origin from different ancestral populations. Concluding, microsatellite resulted a useful tool to investigate breed variability and to characterize Alpine sheep breeds. Obtained findings suggest the need to set up a conservation plan aiming to safeguard and increase the genetic variability of the studied breeds compromised by the high level of inbreeding. Microsatellites genotyping could help to monitor breed variability and to organize matings.