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.     

Genetic characterization and breed assignment in five Italian sheep breeds using microsatellite markers

The knowledge of the genetic relationship and admixture among neighbouring populations is crucial for conservation efforts. The aim of this study was to analyse the genetic diversity of five Italian sheep breeds (Appenninica, Garfagnina Bianca, Massese, Pomarancina and Zerasca) using a panel of 24 microsatellite markers. Blood samples from 226 individuals belonging to the aforementioned populations were obtained and genotyped. All the investigated breeds showed a significant heterozygote deficiency caused by the high level of inbreeding indicated also by the high level of F_IS (0.146). Genetic differentiation between breeds was moderate (F_ST = 0.05) but significant and the individuals could be assigned to their breeds with an high success rate even if the inter-individual distances showed that few animals clustered separately from the other individuals of the same breed, especially for Pomarancina breed. The genetic distances reflect the historical knowledge of these breeds and some patterns of ancestral and recent gene flow between neighbour populations arise. The clustering analysis detects the presence of six clusters. Massese and Zerasca breeds were grouped together as well as Appenninica and Pomarancina with the latter forming two distinct clusters equally represented. The formation of this last breed is occurred with the absorption of individuals of the Appenninica breed and the gene flow probably continued in these recent years allowing the presence of a population substructure for Pomarancina breed. Such substructure supports the high level of heterozygote deficiency found for this breed despite the relatively high population size. The five populations analysed presented some genetic similarities but a clear uniqueness of the populations has been showed for almost all of them. Special attention to monitor genetic variability and to organize mating plans should be given especially for the three endangered breeds.     

Litter size at birth in purebred dogs--a retrospective study of 224 breeds

Despite the long history of purebred dogs and the large number of existing breeds, few studies of canine litter size based upon a large number of breeds exist. Previous studies are either old or include only one or a few selected breeds. The aim of this large-scale retrospective study was to estimate the mean litter size in a large population of purebred dogs and to describe some factors that might influence the litter size. A total of 10,810 litters of 224 breeds registered in the Norwegian Kennel Club from 2006 to 2007 were included in the study. The overall mean litter size at birth was 5.4 (± 0.025). A generalized linear mixed model with a random intercept for breed revealed that the litter size was significantly influenced by the size of the breed, the method of mating and the age of the bitch. A significant interaction between breed size and age was detected, in that the expected number of puppies born decreased more for older bitches of large breeds. Mean litter size increased with breed size, from 3.5 (± 0.04) puppies in miniature breeds to 7.1 (± 0.13) puppies in giant breeds. No effect on litter size was found for the season of birth or the parity of the bitch. The large number of breeds and the detail of the registered information on the litters in this study are unique. In conclusion, the size of the breed, the age of the bitch and the method of mating were found to influence litter size in purebred dogs when controlling for breed, with the size of the breed as the strongest determinant.     

Physicochemical characterization and functional site analysis of lactoferrin gene of Vechur cow

The Bos indicus Vechur breed cow milk is known for its medicinal value and the breed is listed under the category of critically maintained breeds by the Food and Agriculture Organization. The lactoferrin protein in milk is known for its nutritional value. Gene polymorphisms have been reported for Bovine lactoferrin. Mutations in the evolutionarily conserved sites tend to impair protein function and are related with the physicochemical difference between the known variants with 11 SNPs within the wild type. Structural differences are located due to these SNPs that may lead to functional variations. The structural variation is seen primarily in the first 48 residues at 5' end in all the samples modelled. Out of 11 SNPs 5 amino acid variations fall under alpha helix and beta sheet region, this might be of functional significance. This result may provide evidence that the SNPs detected in lactoferrin gene might have potential effects on milk composition. Our result demonstrates one major domain that could be a common binding pocket to all the samples, and important as an active site common to all the breeds that could be utilized for effective drug designing. Moreover, at some SNP positions in Vechur breed, antimicrobial peptides were located indicating importance of those residues for enhanced antimicrobial activity in lactoferrin of Vechur breed. Second binding pocket found in N- lobe region with the three required residues aspartic acid, histidine and tyrosine for iron binding, was considered as major binding site.     

The pet dogs ability for learning from a human demonstrator in a detour task is independent from the breed and age

There are many indications and much practical knowledge about the different tasks which various breeds of dogs are selected for. Correspondingly these different breeds are known to possess different physical and mental abilities. We hypothesized that commonly kept breeds will show differences in their problem solving ability in a detour task around a V-shaped fence, and also, that breed differences will affect their learning ability from a human demonstrator, who demonstrates a detour around the fence. Subjects were recruited in Hungarian pet dog schools. We compared the results of the 10 most common breeds in our sample when they were tested in the detour task without human demonstration. There was no significant difference between the latencies of detour, however, there was a trend that German Shepherd dogs were the quickest and Giant Schnauzers were the slowest in this test. For testing the social learning ability of dogs we formed three breed groups (“utility”, “shepherd” and “hunting”). There were no significant differences between these, all the breed groups learned equally well from the human demonstrator. However, we found that dogs belonging to the “shepherd” group looked back more frequently to their owner than the dogs in the “hunting” group. Further, we have found that the age of pet dogs did not affect their social learning ability in the detour task. Our results showed that the pet status of a dog has probably a stronger effect on its cognitive performance and human related behaviour than its age or breed. These results emphasize that socialization and common activities with the dog might overcome the possible breed differences, if we give the dogs common problem solving, or social learning tasks.     

Scrotal circumference of Australian beef bulls

Normal range for scrotal circumference in Australian beef bulls was established using more than 300,000 measurements of breed, management group, age, liveweight, and scrotal circumference. The data used were derived from Australian bull breeders and two large research projects in northern Australia. Most bulls were within 250 to 750 kg liveweight and 300 to 750 days of age. The differences between breeds and variances within breeds were higher when scrotal circumference was predicted from age rather than liveweight, because of variance in growth rates. The average standard deviation for predicted scrotal circumference from liveweight and age was 25 and 30 mm, respectively. Scrotal circumference by liveweight relationships have a similar pattern across all breeds, except in Waygu, with a 50 to 70 mm range in average scrotal circumference at liveweights between 250 and 750 kg. Temperate breed bulls tended to have higher scrotal circumference at the same liveweight than tropically adapted breeds. Five groupings of common beef breeds in Australian were identified, within which there were similar predictions of scrotal circumference from liveweight. It was concluded that liveweight and breed are required to identify whether scrotal circumference is within normal range for Australian beef bulls that experience a wide range of nutritional conditions.     

家畜合成群体保留杂种优势的预测与培育效果评价

摘要：合成群体是由两个或多个组分品种培育的一个品种,旨在不与其他品种杂交就可利用杂种优势,因而被认为是利用杂种优势的一种替代方法。合成群体培育的成效在于其保留杂种优势的高低。本文综述了家畜合成群体保留杂种优势、相对生产效率和生产性能的预测及其培育效果的评价方式。合成群体包含了所有类型的杂种优势,只要避免近交,就可以保持一定的杂种优势。其高低取决于参与杂交的品种数目和所占血缘比例。合成群体的生产性能取决于各组分品种的育种值和保留杂种优势。合成群体的培育效果可通过理论预测、估计实际保留杂种优势、考察群体的遗传变异或者与有关品种比较等方式加以评价。     

Influence of somatic cell donor breed on reproductive performance and comparison of prenatal growth in cloned canines

Using in vivo–flushed oocytes from a homogenous dog population and subsequent embryo transfer after nuclear transfer, we studied the effects of donor cells collected from 10 different breeds on cloning efficiency and perinatal development of resulted cloned puppies. The breeds were categorized into four groups according to their body weight: small (≤9 kg), medium (>9–20 kg), large (>20–40 kg), and ultra large (>40 kg). A total of 1611 cloned embryos were transferred into 454 surrogate bitches for production of cloned puppies. No statistically significant differences were observed for initial pregnancy rates at Day 30 of embryo transfer for the donor cells originated from different breeds. However, full-term pregnancy rates were 16.5%, 11.0%, 10.0%, and 7.1% for the donor cells originated from ultra-large breed, large, medium, and small breeds, respectively, where pregnancy rate in the ultra-large group was significantly higher compared with the small breeds (P < 0.01). Perinatal mortality until weaning was significantly higher in small breeds (33.3%) compared with medium, large, or ultra-large breeds where no mortality was observed. The mean birth weight of cloned pups significantly increased proportional to breed size. The highest litter size was examined in ultra-large breeds. There was no correlation between the number of embryo transferred and litter size. Taken together, the efficiency of somatic cell cloning and fetal survival after embryo transfer may be affected significantly by selecting the appropriate genotype.     

Validation of a urine metabolome fingerprint in dog for phenotypic classification

Selective breeding of dogs over hundreds of years has inadvertently resulted in breed-specific propensities to particular diseases. Furthermore, it has likely induced more subtle affects on the physiology of certain breeds and moved them from their evolutionary optima. In the absence of obvious disease phenotypes such subtle changes could have yet unrecognised breed-specific implications for health and well-being. Here we have applied NMR metabolomics as a discovery-driven approach to identify the impact of breed on the urinary profile of dog and to determine if non-disease-related breed differences can be identified. Multiple urines were collected non-invasively over a two-week period from seven neutered male Labrador retrievers and miniature Schnauzers. Following NMR analyses by 1-dimensional ¹H and 2-dimensional ¹H J-resolved (JRES) spectroscopy, principal component analysis revealed that the metabolic variability within each individual is relatively small compared to inter-individual variability, and that some separation between breeds was evident. A supervised model, using partial least squares discriminant analysis (PLS-DA) with class based upon breed, was trained using the JRES data. The model predicted correctly the breed of seven additional urines, yielding a model sensitivity and specificity of 100%. Several significant metabolic differences between the breeds were identified. A second model was developed using PLS-DA with class based upon individual dogs, which again achieved high classification accuracy for the test set. Overall, this confirms that canine urine is information-rich and that breed is a major determinant of urinary metabolic fingerprints. In the future this may enable a more accurate development of specific nutritional care for an individual or breed.     

Dynamics of genomic architecture during composite breed development in cattle

Some livestock breeds face the challenge of reduced genetic variation, increased inbreeding depression owing to genetic drift and selection. Hybridization can reverse these processes and increase levels of productivity and adaptation to various environmental stressors. Samples from American Brangus were used to evaluate the indicine/taurine composition through nine generations (~45 years) after the hybridization process was completed. The purpose was to determine how hybridization alters allelic combinations of a breed over time when genetic factors such as selection and drift are operating. Furthermore, we explored genomic regions with deviations from the expected composition from the progenitor breeds and related these regions to traits under selection. The Brangus composition deviated from the theoretical expectation, defined by the breed association, of 62.5% taurine, showing taurine composition to be 70.4 ± 0.6%. Taurine and indicine proportion were not consistent across chromosomes. Furthermore, these non-uniform areas were found to be associated with traits that were probably under selection such as intermuscular fat and average daily gain. Interestingly, the sex chromosomes were predominantly taurine, which could be due to the composite being formed particularly in the final cross that resulted in progeny designated as purebred Brangus. This work demonstrated the process of new breed formation on a genomic level. It suggests that factors like genetic drift, selection and complementarity shift the genetic architecture into a uniquely different population. These findings are important to better understand how hybridization and crossbreeding systems shape the genetic architecture of composite populations.     

Patterns of molecular genetic variation among cat breeds

Genetic variation in cat breeds was assessed utilizing a panel of short tandem repeat (STR) loci genotyped in 38 cat breeds and 284 single-nucleotide polymorphisms (SNPs) genotyped in 24 breeds. Population structure in cat breeds generally reflects their recent ancestry and absence of strong breed barriers between some breeds. There is a wide range in the robustness of population definition, from breeds demonstrating high definition to breeds with as little as a third of their genetic variation partitioning into a single population. Utilizing the STRUCTURE algorithm, there was no clear demarcation of the number of population subdivisions; 16 breeds could not be resolved into independent populations, the consequence of outcrossing in established breeds to recently developed breeds with common ancestry. These 16 breeds were divided into 6 populations. Ninety-six percent of cats in a sample set of 1040 were correctly assigned to their classified breed or breed group/population. Average breed STR heterozygosities ranged from moderate (0.53; Havana, Korat) to high (0.85; Norwegian Forest Cat, Manx). Most of the variation in cat breeds was observed within a breed population (83.7%), versus 16.3% of the variation observed between populations. The hierarchical relationships of cat breeds is poorly defined as demonstrated by phylogenetic trees generated from both STR and SNP data, though phylogeographic grouping of breeds derived completely or in part from Southeast Asian ancestors was apparent.     

Horse personality: Variation between breeds

Anecdotal evidence from horse owners and handlers suggests the existence of breed typical behaviour and personality in horses. This is further supported by current research on heritability of personality characteristics in a range of species. The Horse Personality Questionnaire (HPQ) is a 25-item rating method that has previously been shown to be reliable for the assessment of personality in horses. Principal component analysis on HPQ data has identified six underlying personality components in horses. These are Dominance, Anxiousness, Excitability, Protection, Sociability and Inquisitiveness. Using the HPQ a survey of 1223 horses of eight different breeds was completed. Data were analysed to explore any differences in personality between breeds across the six personality components. Breed differences in personality were identified, and it was noted that variability between breeds varied between personality components. Anxiousness and Excitability showed the most variation between breeds, whilst Dominance and Protection showed the least variance. The results identified breed typical personalities that were comparable to results from previous studies as well as anecdotal evidence provided by the popular equine literature. The results are discussed in terms of the potential selection pressures that may have resulted in these differences.     

Levels and Patterns of Genetic Diversity and Population Structure in Domestic Rabbits

Over thousands of years humans changed the genetic and phenotypic composition of several organisms and in the process transformed wild species into domesticated forms. From this close association, domestic animals emerged as important models in biomedical and fundamental research, in addition to their intrinsic economical and cultural value. The domestic rabbit is no exception but few studies have investigated the impact of domestication on its genetic variability. In order to study patterns of genetic structure in domestic rabbits and to quantify the genetic diversity lost with the domestication process, we genotyped 45 microsatellites for 471 individuals belonging to 16 breeds and 13 wild localities. We found that both the initial domestication and the subsequent process of breed formation, when averaged across breeds, culminated in losses of ~20% of genetic diversity present in the ancestral wild population and domestic rabbits as a whole, respectively. Despite the short time elapsed since breed diversification we uncovered a well-defined structure in domestic rabbits where the F_ST between breeds was 22%. However, we failed to detect deeper levels of structure, probably consequence of a recent and single geographic origin of domestication together with a non-bifurcating process of breed formation, which were often derived from crosses between two or more breeds. Finally, we found evidence for intrabreed stratification that is associated with demographic and selective causes such as formation of strains, colour morphs within the same breed, or country/breeder of origin. These additional layers of population structure within breeds should be taken into account in future mapping studies.     

Genetic diversity among chicken breeds estimated through randomly amplified polymorphic DNA.

The randomly amplified polymorphic DNA (RAPD) markers were used to detect polymorphism among five breeds of chicken i.e. White Leghorn and Rhodes Island Red (selected for part period egg production and egg mass respectively), Red Cornish and White Plymouth Rock (selected for early body weights) and Kadaknath (native breed). Twelve of the fifty random primers screened yielded distinct polymorphic RAPD profiles. Of the total 96 fragments amplified, about 25% showed polymorphism. Using the RAPD data matrix, the within population and between population genetic similarity was estimated. The selected improved breeds showed higher within population genetic similarity in comparison to the native breed. The two meat type breeds showed a high level of genetic similarity between themselves. The White Leghorn breed showed a low genetic similarity with other breeds. The native breed showed highest similarity with Rhodes Island Red. The dendogram was constructed to show phylogenetic relationship among these breeds. As expected, the genetic distances were lowest within similar type breeds and were highest between dissimilar type breeds. The results indicated the effectiveness of RAPD in detecting polymorphism between chicken populations and their applicability in population studies and establishing genetic relationships among the chicken populations.     

Genetic analysis, breed assignment and conservation priorities of three native Danish horse breeds

A genetic analysis was performed on three indigenous Danish horse breeds using 12 microsatellite markers from a standard kit for parental testing. These three breeds are all considered endangered based on their small population sizes. Genetic variation in these three breeds was comparable to other horse breeds in Europe, and they do not seem to be at immediate danger of extinction caused by genetic deterioration. The Knabstrupper breed had more genetic variation, as measured by expected heterozygosity and allelic richness, than the other two breeds (Frederiksborg and Jutland). F(ST) statistics and population assignments confirmed population differentiation into three distinct breeds. The Frederiksborg and Knabstrupper breeds were closer to each other than to the Jutland breed. When establishing conservation priorities for the breeds, the priorities will depend on the conservation goals. Different methods for establishing conservation priorities are also discussed.     

Breeding goats for meat production: 2. Crossbreeding and formation of composite population

This review, the second in the series on breeding goats for meat production, examines the role of crossbreeding and composite population in improving economically important traits necessary for commercial production of meat goats. In general, the crossbreeding of indigenous goats or established breeds with one or more breeds (Alpine, Beetal, Boer, Jamunapari, Nubian and Saanen) that have demonstrated genetic merit in the performance traits of economical importance rely on specific cross and back cross to achieve increased productivity. Concurrently, the combining of desirable morphological characteristics and production performance of two or more breeds in composite populations has had considerable success in other livestock and poultry species, invigorating interest in the breeding of meat goats for commercial production. There have been a number of studies, world-wide, on evaluation of indigenous goats or established breeds and their crosses, including crossbreds derived from exotic breeds that are summarized. Furthermore, the Boer breed developed in South Africa has considerable potential for rapid and permanent improvement of meat production from goats, and studies on the Boer-sired crossbred offspring are highlighted.     

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.     

Genotype imputation in the domestic dog

Application of imputation methods to accurately predict a dense array of SNP genotypes in the dog could provide an important supplement to current analyses of array-based genotyping data. Here, we developed a reference panel of 4,885,283 SNPs in 83 dogs across 15 breeds using whole genome sequencing. We used this panel to predict the genotypes of 268 dogs across three breeds with 84,193 SNP array-derived genotypes as inputs. We then (1) performed breed clustering of the actual and imputed data; (2) evaluated several reference panel breed combinations to determine an optimal reference panel composition; and (3) compared the accuracy of two commonly used software algorithms (Beagle and IMPUTE2). Breed clustering was well preserved in the imputation process across eigenvalues representing 75 % of the variation in the imputed data. Using Beagle with a target panel from a single breed, genotype concordance was highest using a multi-breed reference panel (92.4 %) compared to a breed-specific reference panel (87.0 %) or a reference panel containing no breeds overlapping with the target panel (74.9 %). This finding was confirmed using target panels derived from two other breeds. Additionally, using the multi-breed reference panel, genotype concordance was slightly higher with IMPUTE2 (94.1 %) compared to Beagle; Pearson correlation coefficients were slightly higher for both software packages (0.946 for Beagle, 0.961 for IMPUTE2). Our findings demonstrate that genotype imputation from SNP array-derived data to whole genome-level genotypes is both feasible and accurate in the dog with appropriate breed overlap between the target and reference panels.     

Evaluating Evolutionary Divergence with Microsatellites

We report the use of microsatellites (MS) to track the recent evolution of swine. Allelic frequencies for nine MS loci linked on swine chromosome 6 (SSC6) representing four western and one Chinese swine breeds were used to estimate genetic distances and times of breed divergence. A phylogenetic tree was constructed which partitioned into western and Meishan breed branches. Yorkshire and Hampshire breeds exhibited the most recent divergence with a calculated distance of 391 years. The oldest divergence, of 2,227 years, was between Meishan and Hampshire swine. Estimates of breed divergence are consistent with historical records. Additional analysis suggests that polymorphic MS linked on a single chromosome are sufficient to determine evolutionary relationships within a single species. Received: 23 September 1996 / Accepted: 26 April 1997     

Breed- and gender-dependent differences in eye growth and form deprivation responses in chick

This study investigated the influences of breed and gender on the response to form deprivation and subsequent changes (recovery) when normal vision was restored. Two breeds of chickens, the White Leghorn and broiler cross, were compared, as well as male and female chicks for the White Leghorn breed. Normal eye growth was faster in the more rapidly growing broiler chicks; gender-differences were not as great as breed-differences although male White Leghorns ultimately became heavier and showed slightly greater normal eye growth than females. While both breeds showed high myopia and axial elongation in response to form deprivation, they differed significantly in the magnitude of their response, with White Leghorns showing more myopia and greater axial elongation and also recovering more slowly. Responses to form deprivation were similar for both genders, with respect to both the amount of myopia and axial elongation produced, although the female chicks recovered faster. Together these observations indicate that, although the overall pattern of response of form deprivation is consistent across both breed and gender, related quantitative differences in responses can be expected and need to be taken into account in experimental design and cross-study comparisons.Abbreviations WL White Leghorn chicks - BC broiler cross chicks - M male chicks - F female chicks - N normal eye - T treated eye - FD form deprivation - ACD anterior chamber depth - ALT axial lens thickness - VCD vitreous chamber depth - AL axial length