Assessing the relative importance of health and conformation traits in the cavalier king Charles spaniel.

peer reviewedBACKGROUND: The selection of a future breeding dog is a complicated task, in which disease characteristics and different traits have to be combined and weighed against one another. Truncation selection, that is the exclusion of affected animals, may be very inefficient when selecting on a large number of traits, and may result in a reduction of the genetic diversity in a population or breed. Selection could be facilitated by the use of a selection index that combines multiple traits or breeding values into one score. This however requires a consideration of their relative value according to their economic weight, which is difficult to express in monetary units for health traits. The use of a choice experiment to derive non-market values might be a solution to this problem. This is a pilot study to assess the potential use of choice experiments to ascertain the public preference and relative importance attached to health- and conformation traits in the selection of a Cavalier King Charles spaniel. The focus was on two prevalent disorders, mitral valve disease and syringomyelia, and on several important conformation traits such as muzzle length and eye shape. Based on available prior information, a Bayesian D-optimal design approach was used to develop a choice experiment and the resulting choice sets. RESULTS: Every participant (breeder or owner) in the choice experiment was presented with a total of 17 choice sets, in which at most four traits could vary to reduce the cognitive burden. A total of 114 respondents participated in the choice experiment and results showed that respondents (breeders/owners) current attitudes were directed towards health (syringomyelia and mitral valve disease), followed by eye shape and level of inbreeding. CONCLUSIONS: This approach identifies the value breeders and owners attach to certain traits in the breeding objective. The resulting relative weights, represented as the logworths obtained from the choice experiment, could be an alternative to economic weights. They could be implemented as a weight when breeding values are available, but more study on this topic will be necessary. A challenge in this approach is to scale up the experiment with additional traits. Moreover, for other traits, the genetic parameters and correlations should be known first, in order to include them in the health selection index as well

Genetic analysis of milk citrate predicted by milk mid-infrared spectra of Holstein cows in early lactation.

peer reviewedMilk citrate is regarded as an early biomarker of negative energy balance (NEB) in dairy cows during early lactation and serves as a suitable candidate phenotype for genomic selection due to its wide availability across a large number of cows through milk mid-infrared spectra prediction. However, its genetic background is not well known. Therefore, the objectives of this study were to (1) analyze the genetic parameters of milk citrate; (2) identify genomic regions associated with milk citrate; (3) analyze the functional annotation of candidate genes and quantitative trait loci (QTL) related to milk citrate in Walloon Holstein cows. In total, 134,517 test-day milk citrate phenotypes (mmol/L) collected within the first 50 d in milk (DIM) on 52,198 Holstein cows were used. These milk citrate phenotypes, predicted by milk mid-infrared spectra, were divided into 3 traits according to the first (citrate1), second (citrate2), and third to fifth parity (citrate3+). Genomic information for 566,170 SNPs was available for 4,479 animals. A multiple-trait repeatability model was used to estimate genetic parameters. A single-step genome-wide association study (GWAS) was used to identify candidate genes for citrate and post-GWAS analysis was done to investigate relationship and function of the identified candidate genes. The heritabilities estimated for citrate1, citrate2 and citrate3+ were 0.40, 0.37 and 0.35, respectively. The genetic correlations between the 3 traits ranged from 0.98 to 0.99. The genomic correlations between the 3 traits were also nearly 1.00 across the genomic regions (1 Mb) in the whole genome, which means that citrate can be considered as a single trait in the first 5 parities. In total, 603 significant SNPs located on 3 genomic regions (chromosome7 68.569 - 68.575 Mb, 14 1.31 - 3.05 Mb, and 20 54.00 - 64.28 Mb), were identified to be associated with milk citrate. We identified 89 candidate genes including GPT, ANKH, PPP1R16A and 32 QTL reported in the literature related to the identified significant SNPs. These identified QTL were mainly reported associated with milk fatty acids and metabolic diseases in dairy cows. This study suggests that milk citrate in Holstein cows is highly heritable and has the potential to be used as an early proxy for the NEB of Holstein cows in a breeding objective

Sustainable breeding of pedigree dogs

Breeding practices in purebred dogs are highly criticized since the BBC documentary in 2008. Selection for morphological extreme traits has resulted in various anatomical abnormalities and disorders in the pedigree dog population. Furthermore, selection for breed conformity further increased the number of disorders present in these breeds as a result of inbreeding practices and the use of few popular sires. As most dog breeds are closed populations, these problems will only enhance over the years. This PhD project made an assessment of the current state of the genetic diversity of pedigree dogs in Belgium. This was investigated in 23 pedigree dog breeds, including 14 native Belgian breeds (Bichon frisé, Bloodhound, Bouvier des Ardennes, Bouvier des Flandres, Griffon Belge, Griffon Bruxellois, Petit Brabançon, Laekenois shepherd, Malinois shepherd, Tervueren shepherd, Groenendael shepherd, Papillon, Phalène and Schipperke), and 9 other popular breeds (Australian shepherd, Border Collie, Boxer, Cavalier King Charles spaniel, German shepherd, Golden retriever, Labrador retriever, Irish setter and Rottweiler). Both genealogical and microsatellite information were used to calculate genetic diversity parameters, including inbreeding and effective population size. Both methods reveal low genetic diversity, especially in native Belgian breeds with small population sizes. Eight of the Belgian breeds are at risk of extinction, as measured by the low effective population size under 50. These breeds include the Bouvier des Ardennes, Petit Brabançon, Griffon Belge, Griffon Bruxellois, Laekenois shepherd, Phalène, Schipperke and Bichon frisé. For these breeds measures such as optimal contribution selection or genetic rescue should be applied to augment their genetic diversity. All breeds should be monitored continuously, and specially breeding practices such as the extensive use of popular sires should be avoided. Varieties of breeds resulting from selection based on phenotype only, and their effect on the genetic diversity have been studied as well. Using clustering techniques and principle component analysis, 4 breed groups were studied: the Belgian shepherds comprising Laekenois-, Groenendael-, Tervueren- and Malinois shepherd, the Belgian Griffons comprising Griffon Belge, Griffon Bruxellois and Petit Brabançon, the Bouviers comprising Bouvier des Ardennes and Bouvier des Flandres and the Continental Toy spaniels comprising Phalène and Papillon. The Continental Toy spaniels and Belgian Griffons were not distinguishable from each other, confirming their common breed history. As they belong to the endangered breeds, encouragements should be made to cross between these breed varieties, in order to ensure their future. In the Belgian shepherds, two main groups were identified (Malinois-Laekenois and Tervueren-Groenendael), confirming their common ancestors. These large subpopulations can be maintained as long as their genetic diversity stays at a high level. In the Belgian Bouviers, complete separation was shown, despite their common breed history. However, the Bouvier des Ardennes has been a recently reestablished breed with very low genetic diversity, and therefore, we advised to maintain an open-breed policy, allowing crosses with related breeds such as the Bouvier des Flandres or Picardy shepherd. A major consequence of inbreeding and the use of popular sires is the appearance of genetic disorders. Many of these are of complex inheritance, with both genetics and environment playing its role. Removing all affected animals of the breeding pool would only augment the problems, and therefore, this PhD project investigated alternative strategies, such as selection based on estimated breeding values (EBVs). Hip- and elbow dysplasia (HD and ED) are two highly prevalent disorders in many large dog breeds. An analysis was made in 9 breeds (Labrador retriever, Golden retriever, German shepherd, Rottweiler, Malinois shepherd, Tervueren shepherd, Irish setter, Boxer and Border Collie), and their genetic correlation was assessed. Results indicated that both disorders were indeed heritable, and found a positive genetic correlation. Heritability estimates for HD ranged between 0.01 and 0.67, and for ED between 0.40 and 0.81. However, analysis indicated that the estimations of ED heritability resulted in very high standard errors, demonstrating that selection based on EBVs is not yet possible. For HD, estimations of heritability were possible if over 400 screening results were available, which was the case in the Golden retriever, Labrador retriever, Border Collie, Rottweiler and German shepherd. Other disorders that were studied within this PhD project were syringomyelia and chiari-malformation (SM/CM) in the Cavalier King Charles spaniel. Here, 12 years of screening were evaluated in mainly Dutch and Belgian dogs. Analysis demonstrated the overall presence of CM in the population, making it a breed specific trait, probably through selection on specific characteristics such as a short muzzle length. This indicated that selection was not possible. SM on the other hand was shown to be heritable. Our PhD project indicated that current screening procedure could be ameliorated by using the width of the syrinx as a direct measure instead of the division into classes. This was demonstrated by the higher heritability of the width of the syrinx (0.301) compared to the classes (0.127). Lastly, mitral valve disease (MVD) was studied within an international population of Cavalier King Charles spaniels. This PhD project used two different estimation methods, namely a linear model and a threshold model. Analysis indicated that MVD was heritable, with degree of heritability ranging between 0.24 and 0.30, and that it was highest when analyzed using a threshold model. This indicated that selection based on EBVs was possible for MVD as well. When selecting a breeding animal, a breeder has to consider multiple traits and disorders, and not exclude all affected animals from the breeding pool. This PhD project investigated the relative preference of traits in the Cavalier King Charles spaniel, including health traits and conformation traits, as well as inbreeding and price of the dog. This was accomplished by means of a choice experiment, and indicated an overall preference for health characteristics. The price of the dog seemed not to be of any importance. As a result of this PhD, awareness has been raised among breeders and the Belgian Kennel Club KMSH (Koninklijke Maatschappij Sint-Hubertus). This resulted in a number of measures to augment the health status and genetic diversity of the Belgian pedigree dogs, such as for example the setup of an advice tool similar to the mate select program. This tool will assist breeders in the choice of their ideal breeding animal. A large step has been covered towards healthier pedigree dogs.status: publishe

Inteelt en genetische diversiteit van 23 populaties van honden in België op basis van afstammingsgegevens van de KMSH

nrpages: 41status: publishe

Effect of dog breed 'varieties' on population genetic structure

status: publishe

Wat is genomische selectie? Toepassingen in de Vlaamse melkveesector

status: publishe

Half of 23 Belgian dog breeds has a compromised genetic diversity, as revealed by genealogical and molecular data analysis

The genetic diversity in 23 dog breeds raised in Belgium was investigated using both genealogical analysis and microsatellite markers. Some of these breeds are native breeds, with only small populations maintained. Pedigree and molecular data, obtained from the Belgian kennel club, were used to calculate the inbreeding coefficients, realised effective population size as well as probabilities of gene origin and average observed heterozygosity. Inbreeding coefficients ranged from 0.8 to 44.7% and realised effective population size varied between 3.2 and 829.1, according to the used method and breed. Mean observed heterozygosity ranged from 0.47 to 0.73. Both pedigree and molecular methods reveal low genetic diversity and presence of bottlenecks, especially in native Belgian breeds with small population sizes. Furthermore, principal component analysis on the set of investigated diversity parameters revealed no groups of breeds that could be identified in which similar breeding strategies could be applied to maintain genetic diversity.status: publishe