Evaluation of genetic differentiation in Bos indicus cattle breeds from Marathwada region of India using microsatellite polymorphism

Elucidation of genetic variability and genetic relationship among breeds has direct relevance with the issues of sustainable use of domestic animal genetic resources. In the present study, genetic polymorphism was evaluated using 22 microsatellite loci in unrelated samples of Red Kandhari and Deoni cattle breeds inhabiting the same geographical area of Marathwada region in Maharashtra state (western India). This work was mainly aimed at assessing the current genetic diversity to understand whether the two zebu populations in question are genetically differentiated. A total of 164 alleles were detected with an average of 5.82 and 5.86 alleles per locus (MNA) in Red Kandhari and Deoni breeds, respectively. The estimated mean observed (Ho) and expected (He) heterozygosity were 0.47 and 0.64 in Red Kandhari vs. 0.57 and 0.69 in Deoni cattle, respectively, demonstrating considerable level of genetic variation in both the populations. Mean estimates of F statistics were: F (FIT) = 0.315 +/- 0.035, f(FIS) = 0.231 +/- 0.031, theta(FST) = 0.110 +/- 0.022, with both the breeds exhibiting significant deficit of heterozygotes (FIS = 0.179 in Deoni; 0.278 in Red Kandhari). The multilocus FST values implied that 11.0% of the total genetic variation corresponds to breed and were statistically greater than zero for the two populations, suggesting population division. The evaluation of exact test also indicated that allele frequencies across all the loci differed significantly (P < 0.001) between two zebu breeds, further supporting population differentiation. Different genetic distance measures showed considerable levels of distances between the two cattle breeds (0.318 = Nei's standard DS; 0.250 = Nei's DA; 0.416 = Cavalli-Sforza and Edwards's Dc; 0.164 = Reynold's, and 2.64 = Delta mu square (dmicro)2. Bayesian statistical approach to assign each individual to the population also supported considerable differentiation between the two cattle breeds, possibly reflecting the limited gene flow between the two Marthwada cattle populations. The existence of cohesive breeding structure of both the breeds was further substantiated by allele-sharing distance measures (DAS) among individual animals. The results of this study thus revealed that the two Bos indicus breeds sharing the common breeding tracts are genetically differentiated enough as separate breeds.     

Evaluation of Genetic Differentiation in Bos indicus Cattle Breeds from Marathwada Region of India Using Microsatellite Polymorphism

Elucidation of genetic variability and genetic relationship among breeds has direct relevance with the issues of sustainable use of domestic animal genetic resources. In the present study, genetic polymorphism was evaluated using 22 microsatellite loci in unrelated samples of Red Kandhari and Deoni cattle breeds inhabiting the same geographical area of Marathwada region in Maharashtra state (western India). This work was mainly aimed at assessing the current genetic diversity to understand whether the two zebu populations in question are genetically differentiated. A total of 164 alleles were detected with an average of 5.82 and 5.86 alleles per locus (MNA) in Red Kandhari and Deoni breeds, respectively. The estimated mean observed (Ho) and expected (He) heterozygosity were 0.47 and 0.64 in Red Kandhari vs. 0.57 and 0.69 in Deoni cattle, respectively, demonstrating considerable level of genetic variation in both the populations. Mean estimates of F statistics were: F (FIT) = 0.315±0.035, f(FIS) = 0.231±0.031, θ(FST) = 0.110±0.022, with both the breeds exhibiting significant deficit of heterozygotes (FIS = 0.179 in Deoni; 0.278 in Red Kandhari). The multilocus FST values implied that 11.0% of the total genetic variation corresponds to breed and were statistically greater than zero for the two populations, suggesting population division. The evaluation of exact test also indicated that allele frequencies across all the loci differed significantly (P < 0.001) between two zebu breeds, further supporting population differentiation. Different genetic distance measures showed considerable levels of distances between the two cattle breeds (0.318 = Nei's standard DS; 0.250 = Nei's DA; 0.416 = Cavalli-Sforza and Edwards's DC; 0.164 = Reynold's, and 2.64 = Delta mu square (dμ)2. Bayesian statistical approach to assign each individual to the population also supported considerable differentiation between the two cattle breeds, possibly reflecting the limited gene flow between the two Marthwada cattle populations. The existence of cohesive breeding structure of both the breeds was further substantiated by allele-sharing distance measures (DAS) among individual animals. The results of this study thus revealed that the two Bos indicus breeds sharing the common breeding tracts are genetically differentiated enough as separate breeds.     

Use of linked loci as individuals or haplotypes for marker-assisted breed assignment

The objective of this study was to use simulation to evaluate the benefits of considering haplotypes of loci when linked single nucleotide polymorphisms are used for breed assignment. Three breeds of 10 000 females each were simulated under eight scenarios that differed according to the number of generations separating the breeds, size of breed founder populations and recombination rate between linked loci. Molecular genotypes consisted of 20 groups of three linked loci each. Breed assignment was performed in the final generation and was based on the frequency method. Haplotypes were reconstructed using the expectation–maximization algorithm. Accuracy of breed assignment was based on the frequency of correct breed assignment. Assignment accuracy increased as more genotypes (loci or haplotypes) were considered and more animals were used to estimate genotypic frequencies within breed. For most scenarios, use of haplotypes yielded equal or greater accuracies than when loci were considered independent. The advantage of haplotypes tended to increase as linkage disequilibrium between adjacent loci increased. The greatest advantage for using haplotypes was observed when recombination rate was low (0.001), breeds were separated by few generations (100), and a relatively large number of founder animals (110) was used to form new breeds. In this situation, 90% accuracy of breed assignment was achieved using nine to 14 haplotypes (i.e. 27–42 loci) depending on breed, vs. 39–57 individual loci.     

Differentiation among Spanish sheep breeds using microsatellites

Genetic variability at 18 microsatellites was analysed on the basis of individual genotypes in five Spanish breeds of sheep – Churra, Latxa, Castellana, Rasa-Aragonesa and Merino -, with Awassi also being studied as a reference breed. The degree of population subdivision calculated between Spanish breeds from F_ST diversity indices was around 7% of total variability. A high degree of reliability was obtained for individual-breed assignment from the 18 loci by using different approaches among which the Bayesian method provided to be the most efficient, with an accuracy for nine microsatellites of over 99%. Analysis of the Bayesian assignment criterion illustrated the divergence between any one breed and the others, which was highest for Awassi sheep, while no great differences were evident among the Spanish breeds. Relationships between individuals were analysed from the proportion of shared alleles. The resulting dendrogram showed a remarkable breed structure, with the highest level of clustering among members of the Spanish breeds in Latxa and the lowest in Merino sheep, the latter breed exhibiting a peculiar pattern of clustering, with animals grouped into several closely set nodes. Analysis of individual genotypes provided valuable information for understanding intra- and inter-population genetic differences and allowed for a discussion with previously reported results using populations as taxonomic units.     

Genetic diversity among horse populations with a special focus on the Franches-Montagnes breed

Genetic characterization helps to assure breed integrity and to assign individuals to defined populations. The objective of this study was to characterize genetic diversity in six horse breeds and to analyse the population structure of the Franches-Montagnes breed, especially with regard to the degree of introgression with Warmblood. A total of 402 alleles from 50 microsatellite loci were used. The average number of alleles per locus was significantly lower in Thoroughbreds and Arabians. Average heterozygosities between breeds ranged from 0.61 to 0.72. The overall average of the coefficient of gene differentiation because of breed differences was 0.100, with a range of 0.036-0.263. No significant correlation was found between this parameter and the number of alleles per locus. An increase in the number of homozygous loci with increasing inbreeding could not be shown for the Franches-Montagnes horses. The proportion of shared alleles, combined with the neighbour-joining method, defined clusters for Icelandic Horse, Comtois, Arabians and Franches-Montagnes. A more disparate clustering could be seen for European Warmbloods and Thoroughbreds, presumably from frequent grading-up of Warmbloods with Thoroughbreds. Grading-up effects were also observed when Bayesian and Monte Carlo resampling approaches were used for individual assignment to a given population. Individual breed assignments to defined reference populations will be very difficult when introgression has occurred. The Bayesian approach within the Franches-Montagnes breed differentiated individuals with varied proportions of Warmblood.     

Comparative F statistics analysis of the genetic structure of ten Spanish dog breeds.

The genetic structure and relationships among 10 Spanish dog breeds have been studied by using F statistics. Data came from 21 structural genic loci that codify for blood-soluble proteins and enzymes detected by electrophoresis. Of the 21 loci, 11 were found to be polymorphic. The study was done at three levels of hierarchical differentiation: ancestral trunks, breeds, and subpopulations. The deficit of heterozygotes was estimated at the subpopulation, breed, and ancestral trunk levels, with values of 4.0%, 6.5%, and 11.2%, respectively. In the whole population, the deficit of heterozygotes was about 17%. The proportion of genetic variability attributable to differences between subpopulations, breeds, and ancestral trunks was estimated to be 14.2%, 9.9%, and 6.9%, respectively. The dendrogram, obtained by using values of genic differentiation (FST) as a measure of the genetic distance among populations, is topologically identical to the one obtained using Nei's index of distance, which indicates a high correlation (r = .99) between both distances. These racial groupings, however, differ from the grouping obtained from historical, archeological, and morphological data.     

Genetic diversity and relationships of indigenous Kenyan camel (Camelus dromedarius) populations: implications for their classification

The genetic diversity and relationships amongst the dromedary (Camelus dromedarius) populations are poorly documented. Four recognized Kenyan dromedary breeds (Somali, Turkana, Rendille, Gabbra) and dromedary from Pakistan and the Arabian Peninsula (Saudi Arabia, United Arab Emirates) were studied using 14 microsatellite loci. Phylogenetic analysis showed that Kenyan dromedaries are distinct from Arabian and Pakistani populations. Expected heterozygosity and allelic diversity values indicate that Kenyan dromedaries are less diverse than non-Kenyan populations. With the exception of the Somali population, the Kenyan dromedaries are poorly differentiated (average FST=0.009), with only one to two loci separating the Gabbra, Rendille and Turkana populations studied (P < 0.05). Individual assignments were performed using the maximum likelihood method. A correct breed assignment of only 39-48% was observed for the Kenyan dromedaries, using an allocation stringency of a log of the odds ratio >2. Our results do not support the present classification of the indigenous Kenyan dromedary into four distinct breeds based on socio-geographical criteria. Instead, our results point to just two separate genetic entities, the Somali and a group including the Gabbra, Rendille and Turkana populations.     

Individual assignment using microsatellite DNA reveals unambiguous breed identification in the domestic dog

Modern individual clustering methods utilising hypervariable nuclear microsatellite DNA polymorphisms are being increasingly applied in the field of population genetics. This study explores the efficiency of the clustering methods in identifying the breeds of origin of 250 domestic dog (Canis familiaris) individuals based on 10 microsatellite loci. An allele sharing distance (DAS) matrix and the corresponding neighbour-joining tree of individuals revealed monophyletic assemblages that corresponded perfectly with the breeds of origin of the dogs. Individual assignment tests using a Bayesian statistical approach, an allele frequency based method, and a DCE genetic distance based method were all extremely powerful. Most strikingly, the Bayesian method provided 100% assignment success of individuals into their correct breeds of origin and 100% exclusion success of individuals from all alternate reference populations with a high level of statistical confidence (P < 0.0001). A Bayesian Markov Chain Monte Carlo clustering approach revealed clear distinction of individuals into groups according to their breeds of origin, with a near-zero level of 'genetic admixture' among breeds. The results demonstrate that an FST of 0.18, mean expected gene diversity of 0.6 across 10 loci, and approximately 50 individuals per reference population suffice to provide maximum individual assignment success in C. familiaris. This refutes the traditional view that DNA based dog breed identification is not feasible at the individual level of resolution.     

Genetic diversity and population structure of Sicilian sheep breeds using microsatellite markers

Genetic diversity studies in domestic animals aim at evaluating genetic variation within and across breeds mainly for conservation purposes. In Sicily, dairy sheep production represents an important resource for hilly and mountain areas economy. Their milk is used for the production of traditional raw milk cheeses, sometimes protected designation of origin (PDO) cheeses. In some cases, the quality of these products is linked to a specific breed, i.e. mono-breed labelled cheeses and it is therefore important to be able to distinguish the milk of a breed from that of others, in order to guarantee both the consumer and the breed itself. In order to investigate the genetic structure and to perform an assignment test, a total of 331 individuals (Barbaresca, BAR n = 57, Comisana, COM n = 65, Pinzirita, PIN n = 75, Sarda, SAR n = 64, and Valle del Belice, VDB n = 70) were analysed using a panel of 20 microsatellite markers. A total of 259 alleles were observed with average polymorphic information content equal to 0.76, showing that the microsatellites panel used was highly informative. Estimates of observed heterozygosity ranged from 0.65 in the BAR breed to 0.75 in the COM breed. The low value of genetic differentiation among breeds (F_st = 0.049) may indicate that these breeds are little differentiated probably due to common history and breeding practices. The low F_is and F_it values indicated low level of inbreeding within and among breeds. The unrooted neighbor-joining dendrogram obtained from the Reynold's genetic distances, and factorial correspondence analysis revealed a separation between BAR and the other sheep breeds. Recent migration rates were estimated, showing that four out of the five breeds have not received a significant proportion of migrants. Only for the PIN breed a recent introgression rate from the VDB breed (7.2%) was observed. The Bayesian assignment test showed that BAR and SAR breeds had a more definite genetic structure (proportion of assignment of 92% and 86.6%, respectively), whereas the lowest assignment value was found in the PIN breed (67.1%). Our results indicated high genetic variability, low inbreeding and low genetic differentiation, except for BAR breed, and were in accordance with geographical location, history, and breeding practices. The low robustness of the assignment test makes it unfeasible for traceability purposes, due to the high level of admixture, in particular for COM, PIN and VDB.     

The genetic structure of Spanish Celtic horse breeds inferred from microsatellite data

Partition of the genetic variability, genetic structure and relationships among seven Spanish Celtic horse breeds were studied using PCR amplification of 13 microsatellites on 481 random individuals. In addition, 60 thoroughbred horses were included. The average observed heterozygosity and the mean number of alleles were higher for the Atlantic horse breeds than for the Balearic Islands breeds. Only eight percentage of the total genetic variability could be attributed to differences among breeds (mean FST approximately 0.08; P < 0.01). Atlantic breeds clearly form a separate cluster from the Balearic Islands breeds and among the former only two form a clear clustering, while the rest of Atlantic breeds (Jaca Navarra, Caballo Gallego and Pottoka) are not consistently differentiated. Multivariate analysis showed that Asturcon populations, Losina and Balearic Islands breeds are clearly separated from each other and from the rest of the breeds. In addition to this, the use of the microsatellites proved to be useful for breed assignment.     

Genetic structure of seven European cattle breeds assessed using 20 microsatellite markers

Genotype data from 20 microsatellites typed in 253 animals is used here to assess the genetic structure of seven European pedigree cattle breeds. Estimation of genetic subdivision using classical drift-based measures shows that the average proportion of genetic variation among breeds varies between 10 and 11% of the total, depending on the estimator used. We demonstrate that a simple allele-sharing genetic distance parameter can be used to construct a dendrogram of relationships among animals. This phylogenetic tree displays a remarkable degree of breed clustering and reflects an extensive underlying kinship structure, particularly for the Swiss Simmental breed and four breeds originating from the British Isles. Condensation of allele frequencies and individual genotypic compositions using principal component analysis is also used to investigate genetic structure among breeds and individual animals. In addition, the underlying genetic demarcation of European cattle breeds is emphasized in simulations of breed assignment using allele frequency distributions from samples of microsatellite loci. Correct breed designation can be inferred with accuracies approaching 100% using data from a panel of 10 microsatellite loci.     

Breed demarcation and potential for breed allocation of horses assessed by microsatellite markers

Population demarcation of eight horse breeds was investigated using genotype information of 306 horses from 26 microsatellite loci. The breeds include the indigenous Norwegian breeds Fjord Horse, Nordland/Lyngen Horse, Døle Horse and Coldblooded Trotter together with Icelandic Horse, Shetland Pony, Standardbred and Thoroughbred. Both phylogenetic analysis and a maximum likelihood method were applied to examine the potential for breed allocation of individual animals. The phylogenetic analysis utilizing simple allele sharing statistics revealed clear demarcation among the breeds; 95% of the individuals clustered together with animals of the same breed in the phylogenetic tree. Even breeds with a short history of divergence like Døle Horse and Coldblooded Trotter formed distinct clusters. Implementing the maximum likelihood method allocated 96% of the individuals to their source population, applying an assignment stringency of a log of the odds ratio larger than 2. Lower allocation stringency assigned nearly all the horses. Only three individuals were wrongly allocated a breed by both methods. In conclusion, the study demonstrates clear distinction among horse breeds, and by combining the two assignment methods breed allocation could be determined for more than 99% of the individuals.     

Genetic characterization and founder effect analysis of recently introduced Salers cattle breed population

Salers are a native French breed used for beef and dairy production that has expanded to all the continents. The Salers breed was introduced to the north of Spain in 1985 with only 15 individuals from France and has successfully increased to over 20 000 animals. Although over time new animals have been imported from France for breeding, it is possible that the limiting number of founder animals could have resulted in a reduction of the genetic diversity found in Spanish Salers. Thus, the purpose of the present study has been to characterize the genetic diversity of Salers breed in Spain and evaluate a possible founder effect due to reduced number of the first reproducers. A total of 403 individuals from 12 Salers herds were analyzed using 12 microsatellite markers and compared with phylogenetically and geographically close related Blonde d’Aquitaine, Limousin and Charolais French breeds but also other 16 European breeds. Microsatellites in Salers were polymorphic, with a mean allelic richness of 5.129 and an expected heterozygosity of 0.621 across loci (0.576 to 0.736 among all breeds). Average observed heterozygosity was 0.618. All the loci fit the Hardy–Weinberg (HW) equilibrium except TGLA227 locus due to a significant deficit of heterozygotes in only one of the herds, probably attributable to a sampling effect. When all loci were combined, Salers inbreeding coefficient did not differ statistically from 0 (F_IS=0.005), indicating not significant excess or deficit of heterozygotes (P=0.309). Based in allelic distribution, Salers revealed a frequency of 0.488 in BM2113-131 and 0.064 in BM2113-143 diagnostic alleles, which are specific to the African zebu. These zebu alleles are also found in some French breeds, supported by STR data previously postulated hypothesis of a migration route through Mediterranean route by which North African cattle may have left a genetic signature in southern Europe. Phylogenetic tree and population structure analyses could unambiguously differentiate Salers cattle from the other populations and 10% of the total genetic variability could be attributed to differences among breeds (mean R_ST=0.105; P<0.01). Mutation-drift equilibrium tests (sign test and Wilcoxon’s sign rank test) were in correspondence to the absence of founder effect when Bonferroni was applied. Gene diversity previously reported in French Salers was comparable with the observed in our population. Thus, high genetic diversity in Spanish Salers highlights the resources of this population, which looks toward future breeding and selection programs.     

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.     

Population structure and breed composition prediction in a multi-breed sheep population using genome-wide single nucleotide polymorphism genotypes

Knowledge of population structure and breed composition of a population can be advantageous for a number of reasons; these include designing optimal (cross)breeding strategies in order to maximise non-additive genetic effects, maintaining flockbook integrity by authenticating animals being registered and as a quality control measure in the genotyping process. The objectives of the present study were to 1) describe the population structure of 24 sheep breeds, 2) quantify the breed composition of both flockbook-recorded and crossbred animals using single nucleotide polymorphism BLUP (SNP-BLUP), and 3) quantify the accuracy of breed composition prediction from low-density genotype panels containing between 2000 and 6000 SNPs. In total, 9334 autosomal SNPs on 11 144 flockbook-recorded animals and 1172 crossbred animals were used. The population structure of all breeds was characterised by principal component analysis (PCA) as well as the pairwise breed fixation index (F_st). The total number of animals, all of which were purebred, included in the calibration population for SNP-BLUP was 2579 with the number of animals per breed ranging from 9 to 500. The remaining 9559 flockbook-recorded animals, composite breeds and crossbred animals represented the test population; three breeds were excluded from breed composition prediction. The breed composition predicted using SNP-BLUP with 9334 SNPs was considered the gold standard prediction. The pairwise breed F_st ranged from 0.040 (between the Irish Blackface and Scottish Blackface) to 0.282 (between the Border Leicester and Suffolk). Principal component analysis revealed that the Suffolk from Ireland and the Suffolk from New Zealand formed distinct, non-overlapping clusters. In contrast, the Texel from Ireland and that from New Zealand formed integrated, overlapping clusters. Composite animals such as the Belclare clustered close to its founder breeds (i.e., Finn, Galway, Lleyn and Texel). When all 9334 SNPs were used to predict breed composition, an animal that had a majority breed proportion predicted to be ≥0.90 was defined as purebred for the present study. As the panel density decreased, the predicted breed proportion threshold, used to identify animals as purebred, also decreased (≥0.85 with 6000 SNPs to ≥0.60 with 2000 SNPs). In all, results from the study suggest that breed composition for purebred and crossbred animals can be determined with SNP-BLUP using ≥5000 SNPs.     

Assessing genetic diversity and differentiation in Portuguese coarse-wool sheep breeds with microsatellite markers

Population structure and genetic diversity in the Portuguese native breeds of sheep Algarvia (AL), Badana (BA), Galega Bragançana (GB), Galega Mirandesa (GM), Mondegueira (MO) and Churra da Terra Quente (TQ), as well as the exotic Assaf (AS), were analyzed by typing 25 microsatellite markers in 210 individuals. The markers used exhibited high levels of polymorphism, with means for total and effective number of alleles per locus of 13.0 and 4.2, respectively, and an expected heterozygosity of 0.72 across loci. The mean number of alleles per locus and expected heterozygosity were highest in GM and GB, and lowest in AS. Exclusive alleles were found in 10 of the 25 markers analysed, mostly in the AS breed. The proportion of loci which were not in Hardy–Weinberg equilibrium in each breed ranged between 0.12 (GB) and 0.40 (AL and GM), mostly due to a lower than expected number of heterozygotes in those loci. All breeds showed a significant deficit in heterozygosity, which was more pronounced in GM (F_IS = 0.113) and BA (F_IS = 0.103), suggesting that inbreeding might be a major concern in these breeds. The analysis of relationships among breeds, assessed by different methods, indicates that AS and AL are the more distanced breeds relative to the others, while the closest relationships were observed between TQ with MO and GM with GB. The estimated F_ST indicates that only 0.049 of the total genetic variability can be attributed to differences among breeds, and this ratio dropped to 0.029 when only the native breeds were considered. The analysis of individual distances based on allele-sharing indicates that only AS and AL had a tendency for animals of the same breed to cluster together, while for the other breeds there was overlapping among breeds. The results of this study confirm that native breeds of sheep represent an important reservoir of genetic diversity, even though the level of differentiation among closely located breeds tends to be rather small. For several of the breeds analyzed, the levels of inbreeding currently observed cause some apprehension, and recommend the establishment of appropriate conservation strategies, aimed at minimizing inbreeding to avoid further losses of genetic diversity.     

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.     

Genetic variability in natural populations of Arabidopsis thaliana in northern Europe

Ten populations of the model plant Arabidopsis thaliana were collected along a north-south gradient in Norway and screened for microsatellite polymorphisms in 25 loci and variability in quantitative traits. Overall, the average levels of genetic diversity were found to be relatively high in these populations, compared to previously published surveys of within population variability. Six of the populations were polymorphic at microsatellite loci, resulting in an overall proportion of polymorphic loci of 18%, and a relatively high gene diversity for a selfing species (HE = 0.06). Of the overall variability, 12% was found within populations. Two of six polymorphic populations contained heterozygous individuals. Both FST and phylogenetic analyses showed no correlation between geographical and genetic distances. Haplotypic diversity patterns suggested postglacial colonization of Scandinavia from a number of different sources. Heritable variation was observed for many of the studied quantitative traits, with all populations showing variability in at least some traits, even populations with no microsatellite variability. There was a positive association between variability in quantitative traits and microsatellites within populations. Several quantitative traits exhibited QST values significantly less than FST, suggesting that selection may be acting to retard differentiation for these traits.     

Genomic variation and population structure detected by single nucleotide polymorphism arrays in Corriedale,Merino and Creole sheep

The aim of this study was to investigate the genetic diversity within and among three breeds of sheep: Corriedale, Merino and Creole. Sheep from the three breeds (Merino n = 110, Corriedale n = 108 and Creole n = 10) were genotyped using the Illumina Ovine SNP50 beadchip^®. Genetic diversity was evaluated by comparing the minor allele frequency (MAF) among breeds. Population structure and genetic differentiation were assessed using STRUCTURE software, principal component analysis (PCA) and fixation index (F_ST). Fixed markers (MAF = 0) that were different among breeds were identified as specific breed markers. Using a subset of 18,181 single nucleotide polymorphisms (SNPs), PCA and STUCTURE analysis were able to explain population stratification within breeds. Merino and Corriedale divergent lines showed high levels of polymorphism (89.4% and 86% of polymorphic SNPs, respectively) and moderate genetic differentiation (F_ST = 0.08) between them. In contrast, Creole had only 69% polymorphic SNPs and showed greater genetic differentiation from the other two breeds (F_ST = 0.17 for both breeds). Hence, a subset of molecular markers present in the OvineSNP50 is informative enough for breed assignment and population structure analysis of commercial and Creole breeds.     

Genetic characterization of four native Italian shepherd dog breeds and analysis of their relationship to cosmopolitan dog breeds using microsatellite markers

Very little research into genetic diversity of Italian native dog breeds has been carried out so far. In this study we aimed to estimate and compare the genetic diversity of four native Italian shepherd dog breeds: the Maremma, Bergamasco, Lupino del Gigante and Oropa shepherds. Therefore, some cosmopolitan dog breeds, which have been widely raised in Italy for a long time past, have also been considered to check possible influence of these dog populations on the Italian autochthonous breeds considered here. A total of 212 individuals, belonging to 10 different dog breeds, were sampled and genotyped using 18 autosomal microsatellite loci. We analyzed the genetic diversity of these breeds, within breed diversity, breed relationship and population structure. The 10 breeds considered in this study were clearly genetically differentiated from each other, regardless of current population sizes and the onset of separate breeding history. The level of genetic diversity explained 20% of the total genetic variation. The level of H_E found here is in agreement with that found by other studies. The native Italian breeds showed generally higher genetic diversity compared with the long established, well-defined cosmopolitan dog breeds. As the Border Collie seems closer to the Italian breeds than the other cosmopolitan shepherd dogs considered here, a possible utilization of this breed to improve working performance in Italian traditional working shepherd dogs cannot be ignored. The data and information found here can be utilized in the organization of conservation programs planned to reduce inbreeding and to minimize loss of genetic variability.