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Chapard L, Meyermans R, Gorssen W, Hooyberghs K, Meurrens I, De Smet S, Buys N, Janssens S. Early life jumping traits: Are they good proxies for success in show jumping competitions in Belgian warmblood horses? J Anim Breed Genet 2024; 141:138-152. [PMID: 37882486 DOI: 10.1111/jbg.12834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/22/2023] [Accepted: 10/14/2023] [Indexed: 10/27/2023]
Abstract
The main goal of the Belgian Warmblood horse studbook (BWP) is to breed successful competition horses, with emphasis on show jumping. However, competition results are only available later in life and competition traits are lowly heritable. Hence, the use of phenotypes that record performance-related traits at an early life stage could help increase genetic progress. In this study, we evaluated the potential of eleven linear scored early life jumping traits assessed during jumping in freedom (2-5 years old) or under the saddle (4-6 years old) as proxies for later success in show jumping competitions. To this end, we estimated their heritabilities and genetic correlations with the competition trait, adjusted fence height, by using 2170 free jumping records, 1588 jumping under saddle records, 674,527 show jumping competition records and almost 81,000 informative horses in the pedigree. As participation of young horses in these contests is on a voluntary basis, a pre-selection most probably exists. To verify this hypothesis, we investigated the association between participation to young horse contests and participation to show jumping competitions later on (called here start status phenotype). We also estimated heritabilities for "start status in free jumping contest", "start status in jumping under saddle contest" and "start status in free jumping or jumping under saddle contest" by fitting threshold models. Furthermore, we calculated genetic correlations between these traits and adjusted fence height and calculated the correlations between EBVs for start status in young horse contests and EBVs for success in competitions. Estimated heritabilities of early life jumping traits ranged between 0.05 and 0.30. Their genetic correlations with adjusted fence height were moderate to high (rg = 0.37-0.63). Relatively more horses that participated in young horse contests competed later on compared to horses that did not participate in young horse contests (p-value < 0.001). They were also significantly more successful in show jumping competitions. Furthermore, start status in young horse contests was moderately heritable in BWP horses (h2 = 0.56-0.65) and moderately to highly correlated with later success in competitions (rg = 0.30-0.77). Hence, we showed that ELJ traits are good proxies for later success in competitions and that a pre-selection of horses occurs in young horse contests. It is suggested to stimulate participation to young horse contests to achieve a more representative sample of the population. Early life jumping traits can therefore optimize the genetic progress for show jumping performance.
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Affiliation(s)
- Léa Chapard
- Department of Biosystems, Center for Animal Breeding and Genetics, KU Leuven, Leuven, Belgium
| | - Roel Meyermans
- Department of Biosystems, Center for Animal Breeding and Genetics, KU Leuven, Leuven, Belgium
| | - Wim Gorssen
- Department of Biosystems, Center for Animal Breeding and Genetics, KU Leuven, Leuven, Belgium
| | - Katrijn Hooyberghs
- Department of Biosystems, Center for Animal Breeding and Genetics, KU Leuven, Leuven, Belgium
| | | | - Stefaan De Smet
- Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Nadine Buys
- Department of Biosystems, Center for Animal Breeding and Genetics, KU Leuven, Leuven, Belgium
| | - Steven Janssens
- Department of Biosystems, Center for Animal Breeding and Genetics, KU Leuven, Leuven, Belgium
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Kowalski E, Aluwé M, Ampe B, Janssens S, Buys N, De Smet S, Millet S. Effect of sire type and a by-product based diet on performance and meat quality in growing-finishing pigs. Animal 2024; 18:101106. [PMID: 38442542 DOI: 10.1016/j.animal.2024.101106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 02/02/2024] [Accepted: 02/02/2024] [Indexed: 03/07/2024] Open
Abstract
For many years, pig production has focused on maximizing performance by selecting for maximal muscle growth and feeding diets that allow the animals to express their genetic potential. However, it is unclear whether this selection for muscle deposition has affected the capacity of pigs to cope with by-product-based diets, which rely on fat as the primary energy source instead of starches and sugars. Therefore, an experiment was set up to investigate if different types of boars affect how their progeny cope with alternative ingredients in the diet, with a possible need for adapted breeding schemes. Two types of boars within the Piétrain sire line were used based on either a high or low estimated breeding value for daily feed intake (HFI: high feed intake, low feed intake). When their progeny reached 14 weeks of age, two dietary strategies were compared: a control (CON) vs a by-product-based diet high in fat and fiber (HFF). The CON diet was mainly based on cereals (corn, wheat, barley) and soybean meal. The HFF diet was formulated to contain the same net energy, CP and digestible amino acid levels without any cereals or soybean meal. In total 192 animals were included in the experiment (48 animals/type of boar/diet) and performance, digestibility, carcass and meat quality were compared. None of the parameters showed a significant interaction (P < 0.05) between the type of boar and diet, suggesting that shifting to diets that are less prone to feed-food competition is equally feasible in different types of pigs. Type of boar did affect performance, carcass quality and intramuscular fat content. HFI pigs showed higher daily feed intake (DFI) and daily gain (P < 0.001), with no significant difference in feed conversion ratio (P = 0.205), lower carcass quality (P < 0.001) and higher intramuscular fat content (P = 0.030). For both boar types, pigs fed the CON diet performed better, with a higher daily gain (P = 0.028), DFI (P = 0.011) and dressing yield (P = 0.009) and better digestibility (P < 0.001), but without differences in feed conversion ratio or meat quality. In conclusion, there was no indication that pigs differing in feed intake capacity cope differently with a high-fat, high-fiber diet based on by-products. Different types of pigs may cope well with diets that are less prone to feed-food competition.
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Affiliation(s)
- E Kowalski
- Flanders Research Institute for Agriculture, Fisheries and Food, Animal Sciences Unit, 9090, Melle, Belgium; Ghent University, Laboratory for Animal Nutrition and Animal Product Quality, Department of Animal Sciences and Aquatic Ecology, 9000 Ghent, Belgium
| | - M Aluwé
- Flanders Research Institute for Agriculture, Fisheries and Food, Animal Sciences Unit, 9090, Melle, Belgium
| | - B Ampe
- Flanders Research Institute for Agriculture, Fisheries and Food, Animal Sciences Unit, 9090, Melle, Belgium
| | - S Janssens
- KU Leuven, Center of Animal Breeding and Genetics, Department of Biosystems, 3001, Heverlee, Belgium
| | - N Buys
- KU Leuven, Center of Animal Breeding and Genetics, Department of Biosystems, 3001, Heverlee, Belgium
| | - S De Smet
- Ghent University, Laboratory for Animal Nutrition and Animal Product Quality, Department of Animal Sciences and Aquatic Ecology, 9000 Ghent, Belgium
| | - S Millet
- Flanders Research Institute for Agriculture, Fisheries and Food, Animal Sciences Unit, 9090, Melle, Belgium.
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Meyermans R, Heylen O, Bouhuijzen Wenger J, Martens J, Buys N, Janssens S. The novel IMAGE001 genotyping array as a valuable alternative for genetic diversity screening in chicken: a demonstration in a local chicken breed in Belgium. Poult Sci 2024; 103:103221. [PMID: 37988999 PMCID: PMC10667748 DOI: 10.1016/j.psj.2023.103221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/13/2023] [Accepted: 10/18/2023] [Indexed: 11/23/2023] Open
Abstract
Screening for genetic diversity in livestock species breeds is of utmost importance, especially for local, small populations that are at the risk of extinction. Luckily, recent developments in technology increase access to genotyping, also for numerically small breeds. One of these new technologies is the IMAGE001 single nucleotide polymorphism genotyping array that includes markers for 6 different species (cow, pig, sheep, chicken, horse and goat). For our current study, we studied the Turkey-headed Malines chicken, a local chicken breed in Belgium, for the first time. A total of 110 animals were genotyped, together with 29 samples from 4 supposedly related breeds. The genotypes were used to assess the genetic diversity of this local breed. Our analysis revealed an average inbreeding coefficient of 0.20 through runs of homozygosity analysis, and effective population size estimation based on linkage disequilibrium indicated a low genetic diversity (Ne = 34). Moreover, a principal component analysis and a genetic differentiation study (FST) were performed using these marker data to position the Turkey-headed Malines relative to the 4 other indigenous Belgian chicken breeds. Finally, we discussed the practical implications of the overlap between the IMAGE001 array and other existing chicken genotyping arrays. This study is the first use of the novel IMAGE001 array to evaluate a local chicken breed, and demonstrates it as a viable option for genomic characterization a breed. Moreover, with this research, we are able to provide a good basis for further evaluation of the Belgian chicken heritage.
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Affiliation(s)
- Roel Meyermans
- Department of Biosystems, Center for Animal Breeding and Genetics, KU Leuven, 3001 Leuven, Belgium.
| | - Olivier Heylen
- OTEAS Consulting & Statistics (Agriculture, Environment & Ecology), 2221 Booischot, Belgium; Steunpunt Levend Erfgoed vzw, 9860 Oosterzele, Belgium
| | | | - Jan Martens
- Steunpunt Levend Erfgoed vzw, 9860 Oosterzele, Belgium
| | - Nadine Buys
- Department of Biosystems, Center for Animal Breeding and Genetics, KU Leuven, 3001 Leuven, Belgium
| | - Steven Janssens
- Department of Biosystems, Center for Animal Breeding and Genetics, KU Leuven, 3001 Leuven, Belgium
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Chakkingal Bhaskaran B, Meyermans R, Gorssen W, Maes GE, Buyse J, Janssens S, Buys N. The forgotten variable? Does the euthanasia method and sample storage condition influence an organisms transcriptome - a gene expression analysis on multiple tissues in pigs. BMC Genomics 2023; 24:769. [PMID: 38093185 PMCID: PMC10720124 DOI: 10.1186/s12864-023-09794-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/08/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Transcriptomic studies often require collection of fresh tissues post euthanasia. The chosen euthanasia method might have the potential to induce variations in gene expressions that are unlinked with the experimental design. The present study compared the suitability of 'nitrogen gas in foam' (ANOXIA) in comparison to a non-barbiturate anaesthetic, T-61® (T61), for euthanizing piglets used in transcriptome research. Further, the effect of common tissue storage conditions, RNAlater™ (RL) and snap freezing in liquid nitrogen (LN2), on gene expression profiles were also analysed. RESULTS On comparison of the 3'mRNA-Seq data generated from pituitary, hypothalamus, liver and lung tissues, no significant differential expression in the protein coding genes were detected between the euthanasia methods. This implies that the nitrogen anoxia method could be a suitable alternative for euthanasia of piglets used in transcriptomic research. However, small nuclear RNAs (snRNAs) that constitute the eukaryotic spliceosomal machinery were found to be significantly higher (log2fold change ≥ 2.0, and adjusted p value ≤ 0.1) in pituitary samples collected using ANOXIA. Non-protein coding genes like snRNAs that play an important role in pre-mRNA splicing can subsequently modify gene expression. Storage in RL was found to be superior in preserving RNA compared to LN2 storage, as evidenced by the significantly higher RIN values in representative samples. However, storage in RL as opposed to LN2, also influenced differential gene expression in multiple tissues, perhaps as a result of its inability to inhibit biological activity during storage. Hence such external sources of variations should be carefully considered before arriving at research conclusions. CONCLUSIONS Source of biological variations like euthanasia method and storage condition can confound research findings. Even if we are unable to prevent the effect of these external factors, it will be useful to identify the impact of these variables on the parameter under observation and thereby prevent misinterpretation of our results.
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Affiliation(s)
- B Chakkingal Bhaskaran
- Department of Biosystems, Centre for Animal Breeding and Genetics, KU Leuven, Kasteelpark Arenberg 30, Box 2472, Leuven, 3001, Belgium.
| | - R Meyermans
- Department of Biosystems, Centre for Animal Breeding and Genetics, KU Leuven, Kasteelpark Arenberg 30, Box 2472, Leuven, 3001, Belgium
| | - W Gorssen
- Department of Biosystems, Centre for Animal Breeding and Genetics, KU Leuven, Kasteelpark Arenberg 30, Box 2472, Leuven, 3001, Belgium
| | - G E Maes
- Centre for Human Genetics, Genomics Core, UZ-KU Leuven, Leuven, Belgium
| | - J Buyse
- Department of Biosystems, Laboratory of Livestock Physiology, KU Leuven, Kasteelpark Arenberg 30, Box 2472, Leuven, 3001, Belgium
| | - S Janssens
- Department of Biosystems, Centre for Animal Breeding and Genetics, KU Leuven, Kasteelpark Arenberg 30, Box 2472, Leuven, 3001, Belgium
| | - N Buys
- Department of Biosystems, Centre for Animal Breeding and Genetics, KU Leuven, Kasteelpark Arenberg 30, Box 2472, Leuven, 3001, Belgium.
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Gorssen W, Winters C, Meyermans R, Chapard L, Hooyberghs K, Janssens S, Huisman A, Peeters K, Mulder H, Buys N. A promising resilience parameter for breeding: the use of weight and feed trajectories in growing pigs. J Anim Sci Biotechnol 2023; 14:101. [PMID: 37525252 PMCID: PMC10391771 DOI: 10.1186/s40104-023-00901-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/31/2023] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND Increasing resilience is a priority in modern pig breeding. Recent research shows that general resilience can be quantified via variability in longitudinal data. The collection of such longitudinal data on weight, feed intake and feeding behaviour in pigs has been facilitated by the development of technologies such as automated feeding stations. The goal of this study was to investigate resilience traits, which were estimated as deviations from longitudinal weight, feed intake and feeding behaviour data during the finishing phase. A dataset with 324,207 records between the age of 95 and 155 days on 5,939 Piétrain pigs with known pedigree and genomic information was used. We provided guidelines for a rigid quality control of longitudinal body weight data, as we found that outliers can significantly affect results. Gompertz growth curve analysis, linear modelling and trajectory analyses were used for quantifying resilience traits. RESULTS To our knowledge, this is the first study comparing resilience traits from longitudinal body weight, feed intake and feeding behaviour data in pigs. We demonstrated that the resilience traits are lowly to moderately heritable for deviations in body weight (h2 = 2.9%-20.2%), in feed intake (9.4%-23.3%) and in feeding behaviour (16.2%-28.3%). Additionally, these traits have good predictive abilities in cross-validation analyses. Deviations in individual body weight and feed intake trajectories are highly correlated (rg = 0.78) with low to moderate favourable genetic correlations with feed conversion ratio (rg = 0.39-0.49). Lastly, we showed that some resilience traits, such as the natural logarithm of variances of observed versus predicted body weights (lnvarweight), are more robust to lower observation frequencies and are repeatable over three different time periods of the finishing phase. CONCLUSIONS Our results will help future studies investigating resilience traits and resilience-related traits. Moreover, our study provides first results on standardization of quality control and efficient data sampling from automated feeding station data. Our findings will be valuable for breeding organizations as they offer evidence that pigs' general resilience can be selected on with good accuracy. Moreover, this methodology might be extended to other species to quantify resilience based on longitudinal data.
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Affiliation(s)
- Wim Gorssen
- Center for Animal Breeding and Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30 - Box 2472, 3001, Leuven, Belgium
| | - Carmen Winters
- Laboratory for Biological Psychology, KU Leuven, Tiensestraat 102 - Box 3714, 3000, Leuven, Belgium
| | - Roel Meyermans
- Center for Animal Breeding and Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30 - Box 2472, 3001, Leuven, Belgium
| | - Léa Chapard
- Center for Animal Breeding and Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30 - Box 2472, 3001, Leuven, Belgium
| | - Katrijn Hooyberghs
- Center for Animal Breeding and Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30 - Box 2472, 3001, Leuven, Belgium
| | - Steven Janssens
- Center for Animal Breeding and Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30 - Box 2472, 3001, Leuven, Belgium
| | - Abe Huisman
- Hendrix Genetics, P.O. Box 114, 5830 AC, Boxmeer, The Netherlands
| | - Katrijn Peeters
- Hendrix Genetics, P.O. Box 114, 5830 AC, Boxmeer, The Netherlands
| | - Han Mulder
- Research Animal Breeding and Genomics, Wageningen University, P.O. Box 338, 6700 AH, Wageningen, the Netherlands
| | - Nadine Buys
- Center for Animal Breeding and Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30 - Box 2472, 3001, Leuven, Belgium.
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Chapard L, Van Thillo A, Meyermans R, Gorssen W, Buys N, Janssens S. Adjusted fence height: an improved phenotype for the genetic evaluation of show jumping performance in Warmblood horses. Genet Sel Evol 2023; 55:12. [PMID: 36823617 PMCID: PMC9948484 DOI: 10.1186/s12711-023-00786-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 02/09/2023] [Indexed: 02/25/2023] Open
Abstract
BACKGROUND Show jumping is one of the most popular disciplines in the horse sector, which makes success in show jumping competitions an important breeding goal for many studbooks. Therefore, the genetic evaluation of show jumping performance is of major interest and this is the case for two Belgian Warmblood studbooks: the Belgian Warmblood horse and Zangersheide. In this study, first an improved phenotype for show jumping performance was developed, i.e. adjusted fence height based on a new non-arbitrary method to scale ranking and competition level, which are two major components of success in competitions. Second, we assessed the importance of including a rider effect in genetic models for show jumping performance, this effect being under debate in sport horse breeding. Third, genetic models based on elementary performances and one model based on a summarized performance were compared in terms of model fit, heritabilities and the stability of estimated breeding values to define the most suitable one for the genetic evaluation of show jumping performance. RESULTS In this study, more than 600,000 Belgian competition records and almost 81,000 horses were used. Genetic evaluations were developed based on elementary performances (Blom-transformed ranking and adjusted fence height) and on a summarized performance (highest level achieved). Estimated heritabilities of Blom-transformed ranking, adjusted fence height and highest level achieved were 0.09, 0.12 and 0.39, respectively. Including a rider effect improved the models for genetic evaluations. Estimated genetic correlations between the studied models were moderate to high (rg = 0.60-0.99). With the best fit model, the accuracy of the estimated breeding value (EBV) for adjusted fence height reached 0.70 for a larger number of stallions and for stallions that tended to be younger. CONCLUSIONS We recommend breeders to implement this new phenotype 'adjusted fence height' in breeding programs. It is moderately to highly correlated with Blom-transformed ranking and highest level achieved, a proxy for lifetime success, and is available for selection candidates from an early age onwards.
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Affiliation(s)
- Léa Chapard
- Department of Biosystems, Center for Animal Breeding and Genetics, KU Leuven, Kasteelpark Arenberg 30, 3001, Leuven, Belgium.
| | - Anna Van Thillo
- grid.5596.f0000 0001 0668 7884Department of Biosystems, Center for Animal Breeding and Genetics, KU Leuven, Kasteelpark Arenberg 30, 3001 Leuven, Belgium
| | - Roel Meyermans
- grid.5596.f0000 0001 0668 7884Department of Biosystems, Center for Animal Breeding and Genetics, KU Leuven, Kasteelpark Arenberg 30, 3001 Leuven, Belgium
| | - Wim Gorssen
- grid.5596.f0000 0001 0668 7884Department of Biosystems, Center for Animal Breeding and Genetics, KU Leuven, Kasteelpark Arenberg 30, 3001 Leuven, Belgium
| | - Nadine Buys
- grid.5596.f0000 0001 0668 7884Department of Biosystems, Center for Animal Breeding and Genetics, KU Leuven, Kasteelpark Arenberg 30, 3001 Leuven, Belgium
| | - Steven Janssens
- grid.5596.f0000 0001 0668 7884Department of Biosystems, Center for Animal Breeding and Genetics, KU Leuven, Kasteelpark Arenberg 30, 3001 Leuven, Belgium
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Gorssen W, Winters C, Meyermans R, D’Hooge R, Janssens S, Buys N. Estimating genetics of body dimensions and activity levels in pigs using automated pose estimation. Sci Rep 2022; 12:15384. [PMID: 36100692 PMCID: PMC9470733 DOI: 10.1038/s41598-022-19721-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 09/02/2022] [Indexed: 11/09/2022] Open
Abstract
Pig breeding is changing rapidly due to technological progress and socio-ecological factors. New precision livestock farming technologies such as computer vision systems are crucial for automated phenotyping on a large scale for novel traits, as pigs’ robustness and behavior are gaining importance in breeding goals. However, individual identification, data processing and the availability of adequate (open source) software currently pose the main hurdles. The overall goal of this study was to expand pig weighing with automated measurements of body dimensions and activity levels using an automated video-analytic system: DeepLabCut. Furthermore, these data were coupled with pedigree information to estimate genetic parameters for breeding programs. We analyzed 7428 recordings over the fattening period of 1556 finishing pigs (Piétrain sire x crossbred dam) with two-week intervals between recordings on the same pig. We were able to accurately estimate relevant body parts with an average tracking error of 3.3 cm. Body metrics extracted from video images were highly heritable (61–74%) and significantly genetically correlated with average daily gain (rg = 0.81–0.92). Activity traits were low to moderately heritable (22–35%) and showed low genetic correlations with production traits and physical abnormalities. We demonstrated a simple and cost-efficient method to extract body dimension parameters and activity traits. These traits were estimated to be heritable, and hence, can be selected on. These findings are valuable for (pig) breeding organizations, as they offer a method to automatically phenotype new production and behavioral traits on an individual level.
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Meyermans R, Bartley K, Janssens S, Burgess STG, Buys N. Screening for antibodies against the sheep scab mite (Psoroptes ovis) Pso o 2 antigen in experimentally infested Swifter sheep may fail to identify affected animals. VLAAMS DIERGEN TIJDS 2021. [DOI: 10.21825/vdt.v90i5.20903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Sheep scab, caused by Psoroptes ovis mites, represents a significant threat to sheep health and welfare. Infestations are diagnosed by parasite identification in skin scrapings, and more recently with a commercial ELISA against serum antibodies to the Pso o 2 mite allergen. However, little is known about the performance of the ELISA in non-UK sheep populations. In this study, six Swifter sheep were experimentally infested with P. ovis. Lesion sizes were monitored and serum IgG against Pso o 2 and the novel Pso-EIP-1 antigens were measured by ELISA. Although all sheep showed signs of infestation, serum from two animals failed to react with Pso o 2. However, they did react to Pso-EIP-1. This indicates that cases of sheep scab in (Swifter) sheep may remain undetected using the Pso o 2 ELISA, which may have implications for routine screening of non- UK sheep breeds.
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Lamberigts C, Wang Y, Dierckx T, Buys N, Everaert N, Buyse J. The influence of thyroid state on hypothalamic AMP-activated protein kinase pathways in broilers. Gen Comp Endocrinol 2021; 311:113838. [PMID: 34181935 DOI: 10.1016/j.ygcen.2021.113838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 12/12/2022]
Abstract
To investigate whether there are important interactions in play in broilers between thyroid hormones and the central regulation of energy homeostasis through AMP-activated protein kinase (AMPK), we induced a functional hyperthyroid and hypothyroid state in broiler chicks, and quantified systemic and hypothalamic AMPK related gene expression and related protein. Thyroid state was manipulated through dietary supplementation of triiodothyronine (T3) or methimazole (MMI) for 7 days. A hypothalamic AMPK suppressor, 0.1% α-lipoic acid (α-LA) was used to assess the effects of the T3 and MMI feed formulations on the AMPK pathways. Feed intake and body weight were reduced in both hypothyroid and hyperthyroid conditions. In hyperthyroid conditions (T3 supplementation) expression of the AMPKα1 subunit increased, while in hypothyroid conditions (MMI supplementation) active phosphorylated AMPK levels in the hypothalamus dropped, but gene expression of the AMPKα1 and α2 subunit increased. For FAS and ACC (involved in fatty acid metabolism), and CRH, TRH and CNR1 (anorexigenic neuropeptides stimulating energy expenditure) there were indications that their regulation in response to thyroid state might be modulated through AMPK pathways. Our results indicate that the expression of hypothalamic AMPK as well as that of several other genes from AMPK pathways are involved in thyroid-hormone-induced changes in appetite, albeit differently according to thyroid state.
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Affiliation(s)
- C Lamberigts
- Laboratory of Livestock Physiology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30, 3001 Leuven, Belgium
| | - Y Wang
- Laboratory of Livestock Physiology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30, 3001 Leuven, Belgium
| | - T Dierckx
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Herestraat 49 box 1030, 3000 Leuven, Belgium
| | - N Buys
- Laboratory of Livestock Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30, 3001 Leuven, Belgium
| | - N Everaert
- Precision Livestock and Nutrition Laboratory, Teaching and Research Centre (TERRA), Gembloux AgroBioTech, University of Liège, Passage des Déportés 2, 5030 Gembloux, Belgium
| | - J Buyse
- Laboratory of Livestock Physiology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30, 3001 Leuven, Belgium.
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Heyrman E, Millet S, Tuyttens FAM, Ampe B, Janssens S, Buys N, Wauters J, Vanhaecke L, Aluwé M. On-farm prevalence of and potential risk factors for boar taint. Animal 2021; 15:100141. [PMID: 33573941 DOI: 10.1016/j.animal.2020.100141] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 10/30/2020] [Accepted: 11/09/2020] [Indexed: 10/22/2022] Open
Abstract
Boar taint is an unpleasant taste and odor that can occur in entire male pigs and is caused by androstenone, skatole, and to a lesser extent indole accumulating in fat tissue. In the present observational study, we evaluated an extensive list of such potential risk factors which influence boar taint: social hierarchy and puberty attainment, housing, health, preslaughter conditions, season, feed, carcass composition, slaughter weight or age, and breed. Details on these factors were collected by interviews with the participating farmers, observations on each farm by trained observers and farmers, as well as slaughterhouse data. Twenty-two farms (in West- and East-Flanders, ranging from 160 to 600 sows, selected on suitability) raising entire male pigs were included in the study to evaluate the link between boar taint and potential risk factors related to the farm and slaughter batch (114 slaughter batches and 16 791 entire male pigs in total). Average olfactory boar taint prevalence was 1.8 ± 0.8%. Boar taint prevalence varied also within farms up to a maximum range between slaughter batches of 9.1% which suggests an effect of factors varying between slaughter batches such as season or other variables varying between slaughter batches. Less aggressive behavior at the end of fattening as well as lower skin lesion scores at fattening as well as at slaughter could be associated with less boar taint. The same might be said for sexual behavior, though less convincingly from this study. Measures that reduce aggression and stress have therefore have the potential to lower boar taint prevalence. The same might be said for sexual behavior, though less convincingly from this study. Furthermore, boar taint prevalence was generally higher in winter than in summer, which is relevant from a planning perspective for the slaughterhouses to seek alternative markets. Finally, increased CP gave significantly lower boar taint prevalences. This may to some extent be explained by the negative association between boar taint and lean meat percentage, as increased dietary CP levels promote the carcass lean meat percentages which can then be associated with lower boar taint levels.
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Affiliation(s)
- E Heyrman
- ILVO (Flanders Research Institute for Agriculture, Fisheries and Food), Animal Sciences Unit, 9090 Melle, Belgium; KU Leuven, Livestock Genetics, Department of Biosystems, 3001 Heverlee, Belgium
| | - S Millet
- ILVO (Flanders Research Institute for Agriculture, Fisheries and Food), Animal Sciences Unit, 9090 Melle, Belgium
| | - F A M Tuyttens
- ILVO (Flanders Research Institute for Agriculture, Fisheries and Food), Animal Sciences Unit, 9090 Melle, Belgium
| | - B Ampe
- ILVO (Flanders Research Institute for Agriculture, Fisheries and Food), Animal Sciences Unit, 9090 Melle, Belgium
| | - S Janssens
- KU Leuven, Livestock Genetics, Department of Biosystems, 3001 Heverlee, Belgium
| | - N Buys
- KU Leuven, Livestock Genetics, Department of Biosystems, 3001 Heverlee, Belgium
| | - J Wauters
- Ghent University, Faculty of Veterinary Medicine, Department of Veterinary Public Health and Food Safety, Laboratory of Chemical Analysis, 9820 Merelbeke, Belgium
| | - L Vanhaecke
- Ghent University, Faculty of Veterinary Medicine, Department of Veterinary Public Health and Food Safety, Laboratory of Chemical Analysis, 9820 Merelbeke, Belgium
| | - M Aluwé
- ILVO (Flanders Research Institute for Agriculture, Fisheries and Food), Animal Sciences Unit, 9090 Melle, Belgium.
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11
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Gorssen W, Meyermans R, Janssens S, Buys N. A publicly available repository of ROH islands reveals signatures of selection in different livestock and pet species. Genet Sel Evol 2021; 53:2. [PMID: 33397285 PMCID: PMC7784028 DOI: 10.1186/s12711-020-00599-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 12/11/2020] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Runs of homozygosity (ROH) have become the state-of-the-art method for analysis of inbreeding in animal populations. Moreover, ROH are suited to detect signatures of selection via ROH islands and are used in other applications, such as genomic prediction and genome-wide association studies (GWAS). Currently, a vast amount of single nucleotide polymorphism (SNP) data is available online, but most of these data have never been used for ROH analysis. Therefore, we performed a ROH analysis on large medium-density SNP datasets in eight animal species (cat, cattle, dog, goat, horse, pig, sheep and water buffalo; 442 different populations) and make these results publicly available. RESULTS The results include an overview of ROH islands per population and a comparison of the incidence of these ROH islands among populations from the same species, which can assist researchers when studying other (livestock) populations or when looking for similar signatures of selection. We were able to confirm many known ROH islands, for example signatures of selection for the myostatin (MSTN) gene in sheep and horses. However, our results also included multiple other ROH islands, which are common to many populations and not identified to date (e.g. on chromosomes D4 and E2 in cats and on chromosome 6 in sheep). CONCLUSIONS We are confident that our repository of ROH islands is a valuable reference for future studies. The discovered ROH island regions represent a unique starting point for new studies or can be used as a reference for future studies. Furthermore, we encourage authors to add their population-specific ROH findings to our repository.
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Affiliation(s)
- Wim Gorssen
- Livestock Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30, Box 2472, 3001, Leuven, Belgium
| | - Roel Meyermans
- Livestock Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30, Box 2472, 3001, Leuven, Belgium
| | - Steven Janssens
- Livestock Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30, Box 2472, 3001, Leuven, Belgium
| | - Nadine Buys
- Livestock Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30, Box 2472, 3001, Leuven, Belgium.
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12
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Alden LE, Matthews LR, Wagner S, Fyfe T, Randall C, Regehr C, White M, Buys N, Carey MG, Corneil W, White N, Fraess-Phillips A, Krutop E. Systematic literature review of psychological interventions for first responders. Work & Stress 2020. [DOI: 10.1080/02678373.2020.1758833] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- L. E. Alden
- Department of Psychology, University of British Columbia, Vancouver, Canada
| | - L. R. Matthews
- Faculty of Health Sciences, University of Sydney, Sydney, Australia
| | - S. Wagner
- School of Health Sciences, University of Northern British Columbia, Prince George, Canada
| | - T. Fyfe
- School of Health Sciences, University of Northern British Columbia, Prince George, Canada
| | - C. Randall
- School of Allied Health Sciences, Griffith University, Brisbane, Australia
| | - C. Regehr
- Faculty of Social Work, University of Toronto, Toronto Ontario, Canada
| | - M. White
- Department of Family Practice, University of British Columbia, Vancouver, Canada
| | - N. Buys
- School of Allied Health Sciences, Griffith University, Brisbane, Australia
| | - M. G. Carey
- School of Nursing, University of Rochester, Rochester, NY, USA
| | - W. Corneil
- School of Health Sciences, University of Ottawa, Ottawa, Canada
| | - N. White
- School of Health Sciences, University of Northern British Columbia, Prince George, Canada
| | - A. Fraess-Phillips
- School of Health Sciences, University of Northern British Columbia, Prince George, Canada
| | - E. Krutop
- School of Health Sciences, University of Northern British Columbia, Prince George, Canada
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13
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Meyermans R, Gorssen W, Buys N, Janssens S. How to study runs of homozygosity using PLINK? A guide for analyzing medium density SNP data in livestock and pet species. BMC Genomics 2020; 21:94. [PMID: 31996125 PMCID: PMC6990544 DOI: 10.1186/s12864-020-6463-x] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 01/08/2020] [Indexed: 12/01/2022] Open
Abstract
Background PLINK is probably the most used program for analyzing SNP genotypes and runs of homozygosity (ROH), both in human and in animal populations. The last decade, ROH analyses have become the state-of-the-art method for inbreeding assessment. In PLINK, the --homozyg function is used to perform ROH analyses and relies on several input settings. These settings can have a large impact on the outcome and default values are not always appropriate for medium density SNP array data. Guidelines for a robust and uniform ROH analysis in PLINK using medium density data are lacking, albeit these guidelines are vital for comparing different ROH studies. In this study, 8 populations of different livestock and pet species are used to demonstrate the importance of PLINK input settings. Moreover, the effects of pruning SNPs for low minor allele frequencies and linkage disequilibrium on ROH detection are shown. Results We introduce the genome coverage parameter to appropriately estimate FROH and to check the validity of ROH analyses. The effect of pruning for linkage disequilibrium and low minor allele frequencies on ROH analyses is highly population dependent and such pruning may result in missed ROH. PLINK’s minimal density requirement is crucial for medium density genotypes and if set too low, genome coverage of the ROH analysis is limited. Finally, we provide recommendations for the maximal gap, scanning window length and threshold settings. Conclusions In this study, we present guidelines for an adequate and robust ROH analysis in PLINK on medium density SNP data. Furthermore, we advise to report parameter settings in publications, and to validate them prior to analysis. Moreover, we encourage authors to report genome coverage to reflect the ROH analysis’ validity. Implementing these guidelines will substantially improve the overall quality and uniformity of ROH analyses.
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Affiliation(s)
- R Meyermans
- Department of Biosystems, Livestock Genetics, KU Leuven, Kasteelpark Arenberg 30 - Box 2472, 3001, Leuven, Belgium
| | - W Gorssen
- Department of Biosystems, Livestock Genetics, KU Leuven, Kasteelpark Arenberg 30 - Box 2472, 3001, Leuven, Belgium
| | - N Buys
- Department of Biosystems, Livestock Genetics, KU Leuven, Kasteelpark Arenberg 30 - Box 2472, 3001, Leuven, Belgium
| | - S Janssens
- Department of Biosystems, Livestock Genetics, KU Leuven, Kasteelpark Arenberg 30 - Box 2472, 3001, Leuven, Belgium.
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14
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Meyermans R, Gorssen W, Wijnrocx K, Lenstra JA, Vellema P, Buys N, Janssens S. Unraveling the genetic diversity of Belgian Milk Sheep using medium-density SNP genotypes. Anim Genet 2019; 51:258-265. [PMID: 31881555 PMCID: PMC7065072 DOI: 10.1111/age.12891] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 07/23/2019] [Accepted: 11/13/2019] [Indexed: 01/05/2023]
Abstract
The present study focuses on the Belgian Milk Sheep in Flanders (Belgium) and compares its genetic diversity and relationship with the Flemish Sheep, the Friesian Milk Sheep, the French Lacaune dairy sheep and other Northern European breeds. For this study, 94 Belgian Milk Sheep, 23 Flemish Sheep and 22 Friesian Milk Sheep were genotyped with the OvineSNP50 array. In addition, 29 unregistered animals phenotypically similar to Belgian Milk Sheep were genotyped using the 15K ISGC chip. Both Belgian and Friesian Milk Sheep as well as the East Friesian Sheep were found to be less diverse than the other seven breeds included in this study. Genomic inbreeding coefficients based on runs of homozygosity (ROH) were estimated at 14.5, 12.4 and 10.2% for Belgian Milk Sheep, Flemish Sheep and Friesian Milk Sheep respectively. Out of 29 unregistered Belgian Milk Sheep, 28 mapped in the registered Belgian Milk Sheep population. Ancestry analysis, PCA and FST calculations showed that Belgian Milk Sheep are more related to Friesian Milk Sheep than to Flemish Sheep, which was contrary to the breeders' expectations. Consequently, breeders may prefer to crossbreed Belgian Milk Sheep with Friesian sheep populations (Friesian Milk Sheep or East Friesian Sheep) in order to increase diversity. This research underlines the usefulness of SNP chip genotyping and ROH analyses for monitoring genetic diversity and studying genetic links in small livestock populations, profiting from internationally available genotypes. As assessment of genetic diversity is vital for long-term breed survival, these results will aid flockbooks to preserve genetic diversity.
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Affiliation(s)
- R Meyermans
- Livestock Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30 - 2472, 3001, Leuven, Belgium
| | - W Gorssen
- Livestock Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30 - 2472, 3001, Leuven, Belgium
| | - K Wijnrocx
- Livestock Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30 - 2472, 3001, Leuven, Belgium
| | - J A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, 3584CM, Utrecht, The Netherlands
| | - P Vellema
- Department of Small Ruminant Health, GD Animal Health, PO Box 9, 7400 AA, Deventer, The Netherlands
| | - N Buys
- Livestock Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30 - 2472, 3001, Leuven, Belgium
| | - S Janssens
- Livestock Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30 - 2472, 3001, Leuven, Belgium
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15
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Gorssen W, Meyermans R, Buys N, Janssens S. SNP genotypes reveal breed substructure, selection signatures and highly inbred regions in Piétrain pigs. Anim Genet 2019; 51:32-42. [PMID: 31809557 PMCID: PMC7003864 DOI: 10.1111/age.12888] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2019] [Indexed: 12/19/2022]
Abstract
The Piétrain pig originates from the Belgian village Piétrain some time between 1920 and 1950. Owing to its superior conformation, the Piétrain has spread worldwide since the 1960s. As initial population sizes were limited and close inbreeding was commonplace, the breed’s genetic diversity has been questioned. Therefore, this study examines Piétrain breed substructure, diversity and selection signatures using SNP data in comparison with Duroc, Landrace and Large White populations. Principal component analysis indicated three subpopulations, and FST analysis showed that US Piétrains differ most from European Piétrains. Average inbreeding based on runs of homozygosity (ROH) segments larger than 4 Mb ranged between 16.7 and 20.9%. The highest chromosomal inbreeding levels were found on SSC8 (42.7%). ROH islands were found on SSC8, SSC15 and SSC18 in all Piétrain populations, but numerous population‐specific ROH islands were also detected. Moreover, a large ROH island on SSC8 (34–126 Mb) appears nearly fixed in all Piétrain populations, with a unique genotype. Chromosomal ROH patterns were similar between Piétrain populations. This study shows that Piétrain populations are genetically diverging, with at least three genetically distinct populations worldwide. Increasing genetic diversity in local Piétrain populations by introgression from other Piétrain populations seems to be only limited. Moreover, a unique 90 Mb region on SSC8 appeared largely fixed in the Piétrain breed, indicating that fixation was already present before the 1960s. We believe that strong selection and inbreeding during breed formation fixed these genomic regions in Piétrains. Finally, we hypothesize that independent coat color selection may have led to large ROH pattern similarities on SSC8 between unrelated pig breeds.
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Affiliation(s)
- W Gorssen
- Livestock Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30-2472, B-3001, Leuven, Belgium
| | - R Meyermans
- Livestock Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30-2472, B-3001, Leuven, Belgium
| | - N Buys
- Livestock Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30-2472, B-3001, Leuven, Belgium
| | - S Janssens
- Livestock Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30-2472, B-3001, Leuven, Belgium
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16
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Solé M, Ablondi M, Binzer-Panchal A, Velie BD, Hollfelder N, Buys N, Ducro BJ, François L, Janssens S, Schurink A, Viklund Å, Eriksson S, Isaksson A, Kultima H, Mikko S, Lindgren G. Inter- and intra-breed genome-wide copy number diversity in a large cohort of European equine breeds. BMC Genomics 2019; 20:759. [PMID: 31640551 PMCID: PMC6805398 DOI: 10.1186/s12864-019-6141-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 09/25/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Copy Number Variation (CNV) is a common form of genetic variation underlying animal evolution and phenotypic diversity across a wide range of species. In the mammalian genome, high frequency of CNV differentiation between breeds may be candidates for population-specific selection. However, CNV differentiation, selection and its population genetics have been poorly explored in horses. RESULTS We investigated the patterns, population variation and gene annotation of CNV using the Axiom® Equine Genotyping Array (670,796 SNPs) from a large cohort of individuals (N = 1755) belonging to eight European horse breeds, varying from draught horses to several warmblood populations. After quality control, 152,640 SNP CNVs (individual markers), 18,800 segment CNVs (consecutive SNP CNVs of same gain/loss state or both) and 939 CNV regions (CNVRs; overlapping segment CNVs by at least 1 bp) compared to the average signal of the reference (Belgian draught horse) were identified. Our analyses showed that Equus caballus chromosome 12 (ECA12) was the most enriched in segment CNV gains and losses (~ 3% average proportion of the genome covered), but the highest number of segment CNVs were detected on ECA1 and ECA20 (regardless of size). The Friesian horses showed private SNP CNV gains (> 20% of the samples) on ECA1 and Exmoor ponies displayed private SNP CNV losses on ECA25 (> 20% of the samples). The Warmblood cluster showed private SNP CNV gains located in ECA9 and Draught cluster showed private SNP CNV losses located in ECA7. The length of the CNVRs ranged from 1 kb to 21.3 Mb. A total of 10,612 genes were annotated within the CNVRs. The PANTHER annotation of these genes showed significantly under- and overrepresented gene ontology biological terms related to cellular processes and immunity (Bonferroni P-value < 0.05). We identified 80 CNVRs overlapping with known QTL for fertility, coat colour, conformation and temperament. We also report 67 novel CNVRs. CONCLUSIONS This work revealed that CNV patterns, in the genome of some European horse breeds, occurred in specific genomic regions. The results provide support to the hypothesis that high frequency private CNVs residing in genes may potentially be responsible for the diverse phenotypes seen between horse breeds.
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Affiliation(s)
- Marina Solé
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | - Michela Ablondi
- Department of Veterinary Science, Università di Parma, Parma, Italy
| | - Amrei Binzer-Panchal
- Department of Medical Sciences, Array and Analysis Facility, Uppsala University, Uppsala, Sweden
| | - Brandon D Velie
- Faculty of Life and Environmental Science, University of Sydney, Sydney, NSW, Australia
| | - Nina Hollfelder
- Department of Medical Sciences, Array and Analysis Facility, Uppsala University, Uppsala, Sweden
| | - Nadine Buys
- Livestock Genetics, Department of Biosystems, KU Leuven, 3001, Leuven, Belgium
| | - Bart J Ducro
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, the Netherlands
| | - Liesbeth François
- Livestock Genetics, Department of Biosystems, KU Leuven, 3001, Leuven, Belgium
| | - Steven Janssens
- Livestock Genetics, Department of Biosystems, KU Leuven, 3001, Leuven, Belgium
| | - Anouk Schurink
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, the Netherlands.,Centre for Genetic Resources, the Netherlands (CGN), Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, the Netherlands
| | - Åsa Viklund
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Susanne Eriksson
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anders Isaksson
- Department of Medical Sciences, Array and Analysis Facility, Uppsala University, Uppsala, Sweden
| | - Hanna Kultima
- Department of Medical Sciences, Array and Analysis Facility, Uppsala University, Uppsala, Sweden
| | - Sofia Mikko
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Gabriella Lindgren
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Livestock Genetics, Department of Biosystems, KU Leuven, 3001, Leuven, Belgium
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17
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Affiliation(s)
- E. Decuypere
- Laboratory for Physiology and Immunology of Domestic Animals, Department of Animal Production, Faculty of Agricultural and Applied Biological Sciences, K.U. Leuven, Kardinaal Mercierlaan 92, B-3001 Leuven, Belgium
| | - J. Buyse
- Laboratory for Physiology and Immunology of Domestic Animals, Department of Animal Production, Faculty of Agricultural and Applied Biological Sciences, K.U. Leuven, Kardinaal Mercierlaan 92, B-3001 Leuven, Belgium
| | - N. Buys
- Seghersgentec, Kapellebaan 15, 9255 Buggenhout, Belgium
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18
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François L, Hoskens H, Velie BD, Stinckens A, Tinel S, Lamberigts C, Peeters L, Savelkoul HFJ, Tijhaar E, Lindgren G, Janssens S, Ducro BJ, Buys N, Schurink AA. Genomic Regions Associated with IgE Levels against Culicoides spp. Antigens in Three Horse Breeds. Genes (Basel) 2019; 10:genes10080597. [PMID: 31398914 PMCID: PMC6723964 DOI: 10.3390/genes10080597] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/25/2019] [Accepted: 08/06/2019] [Indexed: 11/16/2022] Open
Abstract
Insect bite hypersensitivity (IBH), which is a cutaneous allergic reaction to antigens from Culicoides spp., is the most prevalent skin disorder in horses. Misdiagnosis is possible, as IBH is usually diagnosed based on clinical signs. Our study is the first to employ IgE levels against several recombinant Culicoides spp. allergens as an objective, independent, and quantitative phenotype to improve the power to detect genetic variants that underlie IBH. Genotypes of 200 Shetland ponies, 127 Icelandic horses, and 223 Belgian Warmblood horses were analyzed while using a mixed model approach. No single-nucleotide polymorphism (SNP) passed the Bonferroni corrected significance threshold, but several regions were identified within and across breeds, which confirmed previously identified regions of interest and, in addition, identifying new regions of interest. Allergen-specific IgE levels are a continuous and objective phenotype that allow for more powerful analyses when compared to a case-control set-up, as more significant associations were obtained. However, the use of a higher density array seems necessary to fully employ the use of IgE levels as a phenotype. While these results still require validation in a large independent dataset, the use of allergen-specific IgE levels showed value as an objective and continuous phenotype that can deepen our understanding of the biology underlying IBH.
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Affiliation(s)
- Liesbeth François
- Livestock Genetics, Department of Biosystems, KU Leuven, B-3001 Leuven, Belgium
| | - Hanne Hoskens
- Department of Human Genetics, KU Leuven, B-3000 Leuven, Belgium
| | - Brandon D Velie
- School of Life & Environmental Sciences, B19-603 University of Sydney, Sydney, NSW 2006,Australia
| | - Anneleen Stinckens
- Livestock Genetics, Department of Biosystems, KU Leuven, B-3001 Leuven, Belgium
| | - Susanne Tinel
- Livestock Genetics, Department of Biosystems, KU Leuven, B-3001 Leuven, Belgium
| | - Chris Lamberigts
- Research Group Livestock Physiology, Department of Biosystems, KU Leuven, Leuven, B-3001 Leuven, Belgium
| | - Liesbet Peeters
- Biomedical Research Institute, Hasselt University, B-3590 Diepenbeek, Belgium
| | - Huub F J Savelkoul
- Cell Biology and Immunology Group, Wageningen University & Research, 6700 AH Wageningen, The Netherlands
| | - Edwin Tijhaar
- Cell Biology and Immunology Group, Wageningen University & Research, 6700 AH Wageningen, The Netherlands
| | - Gabriella Lindgren
- Livestock Genetics, Department of Biosystems, KU Leuven, B-3001 Leuven, Belgium
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Steven Janssens
- Livestock Genetics, Department of Biosystems, KU Leuven, B-3001 Leuven, Belgium
| | - Bart J Ducro
- Animal Breeding and Genomics, Wageningen University & Research, 6700 AH Wageningen, The Netherlands
| | - Nadine Buys
- Livestock Genetics, Department of Biosystems, KU Leuven, B-3001 Leuven, Belgium
| | - And Anouk Schurink
- Animal Breeding and Genomics, Wageningen University & Research, 6700 AH Wageningen, The Netherlands.
- Centre for Genetic Resources, The Netherlands (CGN), Wageningen University & Research, 6700 AH Wageningen, The Netherlands.
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19
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Schurink A, da Silva VH, Velie BD, Dibbits BW, Crooijmans RPMA, Franҫois L, Janssens S, Stinckens A, Blott S, Buys N, Lindgren G, Ducro BJ. Copy number variations in Friesian horses and genetic risk factors for insect bite hypersensitivity. BMC Genet 2018; 19:49. [PMID: 30060732 PMCID: PMC6065148 DOI: 10.1186/s12863-018-0657-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 07/19/2018] [Indexed: 12/04/2022] Open
Abstract
Background Many common and relevant diseases affecting equine welfare have yet to be tested regarding structural variants such as copy number variations (CNVs). CNVs make up a substantial proportion of total genetic variability in populations of many species, resulting in more sequence differences between individuals than SNPs. Associations between CNVs and disease phenotypes have been established in several species, but equine CNV studies have been limited. Aim of this study was to identify CNVs and to perform a genome-wide association (GWA) study in Friesian horses to identify genomic loci associated with insect bite hypersensitivity (IBH), a common seasonal allergic dermatitis observed in many horse breeds worldwide. Results Genotypes were obtained using the Axiom® Equine Genotyping Array containing 670,796 SNPs. After quality control of genotypes, 15,041 CNVs and 5350 CNV regions (CNVRs) were identified in 222 Friesian horses. Coverage of the total genome by CNVRs was 11.2% with 49.2% of CNVRs containing genes. 58.0% of CNVRs were novel (i.e. so far only identified in Friesian horses). A SNP- and CNV-based GWA analysis was performed, where about half of the horses were affected by IBH. The SNP-based analysis showed a highly significant association between the MHC region on ECA20 and IBH in Friesian horses. Associations between the MHC region on ECA20 and IBH were also detected based on the CNV-based analysis. However, CNVs associated with IBH in Friesian horses were not often in close proximity to SNPs identified to be associated with IBH. Conclusions CNVs were identified in a large sample of the Friesian horse population, thereby contributing to our knowledge on CNVs in horses and facilitating our understanding of the equine genome and its phenotypic expression. A clear association was identified between the MHC region on ECA20 and IBH in Friesian horses based on both SNP- and CNV-based GWA studies. These results imply that MHC contributes to IBH sensitivity in Friesian horses. Although subsequent analyses are needed for verification, nucleotide differences, as well as more complex structural variations like CNVs, seem to contribute to IBH sensitivity. IBH should be considered as a common disease with a complex genomic architecture. Electronic supplementary material The online version of this article (10.1186/s12863-018-0657-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anouk Schurink
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700, AH, Wageningen, the Netherlands.
| | - Vinicius H da Silva
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700, AH, Wageningen, the Netherlands.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7023, 75007, Uppsala, Sweden.,Department of Animal Ecology, Netherlands Institute of Ecology, NIOO-KNAW, 6708, PB, Wageningen, the Netherlands
| | - Brandon D Velie
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7023, 75007, Uppsala, Sweden
| | - Bert W Dibbits
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700, AH, Wageningen, the Netherlands
| | - Richard P M A Crooijmans
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700, AH, Wageningen, the Netherlands
| | - Liesbeth Franҫois
- KU Leuven, Department of Biosystems, Livestock Genetics, P.O. Box 2456, 3001, Heverlee, Belgium
| | - Steven Janssens
- KU Leuven, Department of Biosystems, Livestock Genetics, P.O. Box 2456, 3001, Heverlee, Belgium
| | - Anneleen Stinckens
- KU Leuven, Department of Biosystems, Livestock Genetics, P.O. Box 2456, 3001, Heverlee, Belgium
| | - Sarah Blott
- Reproductive Biology, Faculty of Medicine and Health Sciences, The University of Nottingham, Leicestershire, LE12 5RD, UK
| | - Nadine Buys
- KU Leuven, Department of Biosystems, Livestock Genetics, P.O. Box 2456, 3001, Heverlee, Belgium
| | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7023, 75007, Uppsala, Sweden
| | - Bart J Ducro
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700, AH, Wageningen, the Netherlands
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Heyrman E, Millet S, Tuyttens FAM, Ampe B, Janssens S, Buys N, Wauters J, Vanhaecke L, Aluwé M. On farm intervention studies on reduction of boar taint prevalence: Feeding strategies, presence of gilts and time in lairage. Res Vet Sci 2018; 118:508-516. [PMID: 29758535 DOI: 10.1016/j.rvsc.2018.05.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/23/2018] [Accepted: 05/07/2018] [Indexed: 10/16/2022]
Abstract
One of the challenges in the production of entire male pigs is the occurrence of boar taint. We separately tested the effect of 3 management strategies to reduce boar taint on respectively 2, 3, and 6 Flemish pig farms: 1) adapted feeding strategies, 2) presence of gilts in the compartment, and 3) varying lairage duration at the slaughterhouse. A commercialized feed concept resulted in a significant reduction of olfactory boar taint prevalence when fed for 2 weeks (T2W) compared to control (T-CON) (P = 0.030). For T2W and when fed for 3 weeks (T3W), androstenone (AND) (P = 0.002 for T2W, P = 0.029 for T3W) and skatole (SKA) (P < 0.001 for T2W and T3W) were significantly reduced compared to T-CON. Olfactory boar taint prevalence was significantly reduced when feeding 5% dried chicory roots (FI5%) (P = 0.032), but not for 3% dried chicory roots (FI3%) (P = 0.958). SKA concentration was significantly lower when feeding FI5% (P < 0.001) and when feeding FI3% (P = 0.034). Rearing entire male pigs separately from gilts and increasing lairage duration from <1 h to >3 h did not significantly affect boar taint.
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Affiliation(s)
- E Heyrman
- ILVO (Flanders Research Institute for Agriculture, Fisheries and Food), Animal Sciences Unit, 9090 Melle, Belgium; KU Leuven, Livestock Genetics, Department of Biosystems, 3001 Heverlee, Belgium
| | - S Millet
- ILVO (Flanders Research Institute for Agriculture, Fisheries and Food), Animal Sciences Unit, 9090 Melle, Belgium
| | - F A M Tuyttens
- ILVO (Flanders Research Institute for Agriculture, Fisheries and Food), Animal Sciences Unit, 9090 Melle, Belgium
| | - B Ampe
- ILVO (Flanders Research Institute for Agriculture, Fisheries and Food), Animal Sciences Unit, 9090 Melle, Belgium
| | - S Janssens
- KU Leuven, Livestock Genetics, Department of Biosystems, 3001 Heverlee, Belgium
| | - N Buys
- KU Leuven, Livestock Genetics, Department of Biosystems, 3001 Heverlee, Belgium
| | - J Wauters
- Ghent University, Faculty of Veterinary Medicine, Department of Veterinary Public Health and Food Safety, Laboratory of Chemical Analysis, 9820 Merelbeke, Belgium
| | - L Vanhaecke
- Ghent University, Faculty of Veterinary Medicine, Department of Veterinary Public Health and Food Safety, Laboratory of Chemical Analysis, 9820 Merelbeke, Belgium
| | - M Aluwé
- ILVO (Flanders Research Institute for Agriculture, Fisheries and Food), Animal Sciences Unit, 9090 Melle, Belgium.
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Bulens A, Van Beirendonck S, Van Thielen J, Buys N, Driessen B. Rearing finishing pigs with intact tails: Do they benefit from an enriched environment? J Vet Behav 2018. [DOI: 10.1016/j.jveb.2017.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Wijnrocx K, François L, Goos P, Buys N, Janssens S. Assessing the relative importance of health and conformation traits in the cavalier king Charles spaniel. Canine Genet Epidemiol 2018; 5:1. [PMID: 29403647 PMCID: PMC5778675 DOI: 10.1186/s40575-017-0056-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 12/01/2017] [Indexed: 12/02/2022] Open
Abstract
Background 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.
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Affiliation(s)
- Katrien Wijnrocx
- 3KU Leuven Department of Biosystems, Livestock Genetics, Kasteelpark Arenberg 30, box 2456, 3001 Leuven, Belgium
| | - Liesbeth François
- 3KU Leuven Department of Biosystems, Livestock Genetics, Kasteelpark Arenberg 30, box 2456, 3001 Leuven, Belgium
| | - Peter Goos
- 1KU Leuven Department of Biosystems, MeBioS, Kasteelpark Arenberg 30, box 2456, 3001 Leuven, Belgium.,2Department of Engineering Management, University of Antwerp, Prinsstraat 13, 2000 Antwerp, Belgium
| | - Nadine Buys
- 3KU Leuven Department of Biosystems, Livestock Genetics, Kasteelpark Arenberg 30, box 2456, 3001 Leuven, Belgium
| | - Steven Janssens
- 3KU Leuven Department of Biosystems, Livestock Genetics, Kasteelpark Arenberg 30, box 2456, 3001 Leuven, Belgium
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Bulens A, Van Beirendonck S, Van Thielen J, Buys N, Driessen B. Hiding walls for fattening pigs: Do they affect behavior and performance? Appl Anim Behav Sci 2017. [DOI: 10.1016/j.applanim.2017.06.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Wijnrocx K, Van Bruggen LWL, Eggelmeijer W, Noorman E, Jacques A, Buys N, Janssens S, Mandigers PJJ. Twelve years of chiari-like malformation and syringomyelia scanning in Cavalier King Charles Spaniels in the Netherlands: Towards a more precise phenotype. PLoS One 2017; 12:e0184893. [PMID: 28934242 PMCID: PMC5608246 DOI: 10.1371/journal.pone.0184893] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 09/03/2017] [Indexed: 11/18/2022] Open
Abstract
Chiari-like malformation (CM), syringomyelia (SM) and middle ear effusion (also called PSOM) are three conditions that frequently occur in Cavalier King Charles Spaniels (CKCS). Both CM and SM are currently screened in the Netherlands prior to breeding and are graded according to the British Veterinary Association's Kennel Club (BVA/KC) scheme. This study evaluated the prevalence and estimated genetic parameter of CM, SM and middle ear effusion from 12 years of screening results. For SM, the classical method using the BVA/KC scheme, was compared with exact measuring of the central canal dilation. For CM, the BVA/KC scheme was compared with a more detailed scheme. Next to this the presence of microchip artifacts was assessed. 1249 screening of 1020 dogs were re-evaluated. Results indicated the presence of CM in all dogs, suggesting it has become a breed-specific characteristic. And although different grades of CM were observed, the condition did not deteriorate over time. SM was present in 39% of the dogs and a clear age effect was demonstrated, with SM increasing with age. This emphasizes the importance of screening at appropriate age, since SM can worsen with increasing age. One alternative is to promote repeated measures. The presence of middle ear effusion in this study was 19%-21% for dogs younger than 3 years, and 32%-38% for dogs older than 3 years. In as much as 60%, microchip artifacts were noticed, leading to the recommendation to place microchips in another location in breeds that are susceptible to developing SM. Finally, this study estimated the heritability of CM in this population, due to the lack of phenotypic variance, to be very low at 0.02-0.03. The heritability for SM central canal dilatation to be 0.30, compared to 0.13 for the classical BVA/KC method, using a model including the age effect and the combined effect of veterinary clinic and year of the evaluation. Genetic correlations were rather small, ranging from 0.16-0.33. As a conclusion, screening for SM and CM in the entire population should be maintained, and a selection scheme against SM should be based on estimated breeding values for the exact measurement of the central canal dilatation.
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Affiliation(s)
- Katrien Wijnrocx
- KU Leuven Department of Biosystems, Livestock Genetics, Leuven, Belgium
| | - Leonie W. L. Van Bruggen
- University of Utrecht, Department of Clinical Sciences of Companion Animals, Utrecht, The Netherlands
| | - Wieteke Eggelmeijer
- University of Utrecht, Department of Clinical Sciences of Companion Animals, Utrecht, The Netherlands
| | | | | | - Nadine Buys
- KU Leuven Department of Biosystems, Livestock Genetics, Leuven, Belgium
| | - Steven Janssens
- KU Leuven Department of Biosystems, Livestock Genetics, Leuven, Belgium
| | - Paul J. J. Mandigers
- University of Utrecht, Department of Clinical Sciences of Companion Animals, Utrecht, The Netherlands
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Bulens A, Van Beirendonck S, Van Thielen J, Buys N, Driessen B. A two-level pen for fattening pigs: Effects on behavior, performance, and postslaughter measurements. J Anim Sci 2017; 95:616-625. [PMID: 28380603 DOI: 10.2527/jas.2016.0831] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Concurrent with a tendency toward higher slaughter weights of fattening pigs, minimum requirements for space allowance are increasing. Allowing pigs more space in existing standard pens, however, leads to a decrease in the number of pigs per pen, which jeopardizes the economic viability of the pig farm. A possible solution includes creating a two-level pen by constructing a second level in an existing pen, to enable an increase in space allowance per pig with the same number of pigs. We investigated the effect of such a pen on the behavior, performance, and postslaughter results of fattening pigs during the entire fattening period (30 to 110 kg). A total of 444 pigs were distributed over standard control pens (0.74 m/pig) and two-level pens (0.99 m/pig). Feed was provided only in a trough at the ground level of the pen. The results show that the increased space allowance and choice of levels in two-level pens influenced the pigs' behavior in a positive way, as they performed less manipulation of pen mates ( < 0.0001). Moreover, pigs lay down more ( = 0.0007) and showed less head knocking ( = 0.005) in two-level pens, suggesting that they were calmer. In line with the behavioral results, pigs in two-level pens had fewer lesions on tails ( = 0.006), ears ( = 0.008), and shoulders ( = 0.01). Growth performance was not affected ( > 0.05), but postslaughter measurements revealed fewer livers with white spots in pigs from two-level pens. This result might be related to lower disease pressure in pens with lower stocking densities. In conclusion, a two-level pen seemed to have positive effects on the behavior of pigs (in terms of pen mate manipulation) and the increase in space allowance seemed to make the pigs calmer. The use of the second level by heavier pigs should, however, be further studied to investigate whether this extra space could be fully counted for the minimal space requirements.
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Bulens A, Van Beirendonck S, Van Thielen J, Buys N, Driessen B. A two-level pen for fattening pigs: Effects on behavior, performance, and postslaughter measurements. J Anim Sci 2017. [DOI: 10.2527/jas2016.0831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Velie BD, Shrestha M, Francois L, Schurink A, Stinckens A, Blott S, Ducro BJ, Mikko S, Thomas R, Sundquist M, Eriksson S, Buys N, Lindgren G. P6017 A high density genome-wide scan for genetic risk factors of insect bite hypersensitivity (IBH): A Horsegene Project Initiative. J Anim Sci 2016. [DOI: 10.2527/jas2016.94supplement4156a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Coussé A, Francois L, Stinckens A, Buys N, Elansary M, Abos R, Saegerman C, Druet T, Losson B, Georges M, Sarre C, Claerebout E, Hubin X. P6038 Tackling the itch: GWAS-based candidate genes for psoroptic mange sensitivity in Belgian Blue cattle. J Anim Sci 2016. [DOI: 10.2527/jas2016.94supplement4167a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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François L, Jäderkvist Fegraeus K, Eriksson S, Andersson LS, Tesfayonas YG, Viluma A, Imsland F, Buys N, Mikko S, Lindgren G, Velie BD. Conformation Traits and Gaits in the Icelandic Horse are Associated with Genetic Variants in Myostatin (MSTN). J Hered 2016; 107:431-7. [PMID: 27208149 DOI: 10.1093/jhered/esw031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 05/11/2016] [Indexed: 11/13/2022] Open
Abstract
Many genes are known to have an influence on conformation and performance traits; however, the role of one gene, Myostatin (MSTN), has been highlighted in recent studies on horses. Myostatin acts as a repressor in the development and regulation of differentiation and proliferative growth of skeletal muscle. Several studies have examined the link between MSTN, conformation, and performance in racing breeds, but no studies have investigated the relationship in Icelandic horses. Icelandic horses, a highly unique breed, are known both for their robust and compact conformation as well as their additional gaits tölt and pace. Three SNPs (g.65868604G>T [PR8604], g.66493737C>T [PR3737], and g.66495826A>G [PR5826]) flanking or within equine MSTN were genotyped in 195 Icelandic horses. The SNPs and haplotypes were analyzed for association with official estimated breeding values (EBV) for conformation traits (n = 11) and gaits (n = 5). The EBV for neck, withers, and shoulders was significantly associated with both PR8604 and PR3737 (P < 0.05). PR8604 was also associated with EBV for total conformation (P = 0.05). These associations were all supported by the haplotype analysis. However, while SNP PR5826 showed a significant association with EBVs for leg stance and hooves (P < 0.05), haplotype analyses for these traits failed to fully support these associations. This study demonstrates the possible role of MSTN on both the form and function of horses from non-racing breeds. Further analysis of Icelandic horses as well as other non-racing breeds would be beneficial and likely help to completely understand the influence of MSTN on conformation and performance in horses.
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Affiliation(s)
- Liesbeth François
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden (François, Jäderkvist Fegraeus, Eriksson, Andersson, Tesfayonas, Viluma, Mikko, Lindgren, and Velie); KU Leuven, Department of Biosystems, Livestock Genetics, Leuven 3001, Belgium (François and Buys); and Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden (Imsland)
| | - Kim Jäderkvist Fegraeus
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden (François, Jäderkvist Fegraeus, Eriksson, Andersson, Tesfayonas, Viluma, Mikko, Lindgren, and Velie); KU Leuven, Department of Biosystems, Livestock Genetics, Leuven 3001, Belgium (François and Buys); and Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden (Imsland)
| | - Susanne Eriksson
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden (François, Jäderkvist Fegraeus, Eriksson, Andersson, Tesfayonas, Viluma, Mikko, Lindgren, and Velie); KU Leuven, Department of Biosystems, Livestock Genetics, Leuven 3001, Belgium (François and Buys); and Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden (Imsland)
| | - Lisa S Andersson
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden (François, Jäderkvist Fegraeus, Eriksson, Andersson, Tesfayonas, Viluma, Mikko, Lindgren, and Velie); KU Leuven, Department of Biosystems, Livestock Genetics, Leuven 3001, Belgium (François and Buys); and Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden (Imsland)
| | - Yohannes G Tesfayonas
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden (François, Jäderkvist Fegraeus, Eriksson, Andersson, Tesfayonas, Viluma, Mikko, Lindgren, and Velie); KU Leuven, Department of Biosystems, Livestock Genetics, Leuven 3001, Belgium (François and Buys); and Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden (Imsland)
| | - Agnese Viluma
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden (François, Jäderkvist Fegraeus, Eriksson, Andersson, Tesfayonas, Viluma, Mikko, Lindgren, and Velie); KU Leuven, Department of Biosystems, Livestock Genetics, Leuven 3001, Belgium (François and Buys); and Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden (Imsland)
| | - Freyja Imsland
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden (François, Jäderkvist Fegraeus, Eriksson, Andersson, Tesfayonas, Viluma, Mikko, Lindgren, and Velie); KU Leuven, Department of Biosystems, Livestock Genetics, Leuven 3001, Belgium (François and Buys); and Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden (Imsland)
| | - Nadine Buys
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden (François, Jäderkvist Fegraeus, Eriksson, Andersson, Tesfayonas, Viluma, Mikko, Lindgren, and Velie); KU Leuven, Department of Biosystems, Livestock Genetics, Leuven 3001, Belgium (François and Buys); and Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden (Imsland)
| | - Sofia Mikko
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden (François, Jäderkvist Fegraeus, Eriksson, Andersson, Tesfayonas, Viluma, Mikko, Lindgren, and Velie); KU Leuven, Department of Biosystems, Livestock Genetics, Leuven 3001, Belgium (François and Buys); and Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden (Imsland)
| | - Gabriella Lindgren
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden (François, Jäderkvist Fegraeus, Eriksson, Andersson, Tesfayonas, Viluma, Mikko, Lindgren, and Velie); KU Leuven, Department of Biosystems, Livestock Genetics, Leuven 3001, Belgium (François and Buys); and Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden (Imsland)
| | - Brandon D Velie
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden (François, Jäderkvist Fegraeus, Eriksson, Andersson, Tesfayonas, Viluma, Mikko, Lindgren, and Velie); KU Leuven, Department of Biosystems, Livestock Genetics, Leuven 3001, Belgium (François and Buys); and Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden (Imsland)
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Velie BD, Shrestha M, Franҫois L, Schurink A, Tesfayonas YG, Stinckens A, Blott S, Ducro BJ, Mikko S, Thomas R, Swinburne JE, Sundqvist M, Eriksson S, Buys N, Lindgren G. Using an Inbred Horse Breed in a High Density Genome-Wide Scan for Genetic Risk Factors of Insect Bite Hypersensitivity (IBH). PLoS One 2016; 11:e0152966. [PMID: 27070818 PMCID: PMC4829256 DOI: 10.1371/journal.pone.0152966] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 03/22/2016] [Indexed: 11/19/2022] Open
Abstract
While susceptibility to hypersensitive reactions is a common problem amongst humans and animals alike, the population structure of certain animal species and breeds provides a more advantageous route to better understanding the biology underpinning these conditions. The current study uses Exmoor ponies, a highly inbred breed of horse known to frequently suffer from insect bite hypersensitivity, to identify genomic regions associated with a type I and type IV hypersensitive reaction. A total of 110 cases and 170 controls were genotyped on the 670K Axiom Equine Genotyping Array. Quality control resulted in 452,457 SNPs and 268 individuals being tested for association. Genome-wide association analyses were performed using the GenABEL package in R and resulted in the identification of two regions of interest on Chromosome 8. The first region contained the most significant SNP identified, which was located in an intron of the DCC netrin 1 receptor gene. The second region identified contained multiple top SNPs and encompassed the PIGN, KIAA1468, TNFRSF11A, ZCCHC2, and PHLPP1 genes. Although additional studies will be needed to validate the importance of these regions in horses and the relevance of these regions in other species, the knowledge gained from the current study has the potential to be a step forward in unraveling the complex nature of hypersensitive reactions.
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Affiliation(s)
- Brandon D. Velie
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- * E-mail:
| | - Merina Shrestha
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Liesbeth Franҫois
- Research Group Livestock Genetics, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Anouk Schurink
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, the Netherlands
| | - Yohannes G. Tesfayonas
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anneleen Stinckens
- Research Group Livestock Genetics, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Sarah Blott
- School of Veterinary Medicine & Science, University of Nottingham, Leicestershire, United Kingdom
| | - Bart J. Ducro
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, the Netherlands
| | - Sofia Mikko
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ruth Thomas
- Exmoor Pony Society, Cullompton, United Kingdom
| | - June E. Swinburne
- Animal DNA Diagnostics Ltd, Cambridgeshire, United Kingdom
- Animal Health Trust, Newmarket, United Kingdom
| | | | - Susanne Eriksson
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Nadine Buys
- Research Group Livestock Genetics, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Gabriella Lindgren
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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31
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Wijnrocx K, François L, Stinckens A, Janssens S, Buys N. Half of 23 Belgian dog breeds has a compromised genetic diversity, as revealed by genealogical and molecular data analysis. J Anim Breed Genet 2016; 133:375-83. [DOI: 10.1111/jbg.12203] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 01/30/2016] [Indexed: 11/27/2022]
Affiliation(s)
- K. Wijnrocx
- Department of Biosystems; KU Leuven, Livestock Genetics; 3001 Leuven Belgium
| | - L. François
- Department of Biosystems; KU Leuven, Livestock Genetics; 3001 Leuven Belgium
| | - A. Stinckens
- Department of Biosystems; KU Leuven, Livestock Genetics; 3001 Leuven Belgium
| | - S. Janssens
- Department of Biosystems; KU Leuven, Livestock Genetics; 3001 Leuven Belgium
| | - N. Buys
- Department of Biosystems; KU Leuven, Livestock Genetics; 3001 Leuven Belgium
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32
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Willems E, Guerrero-Bosagna C, Decuypere E, Janssens S, Buyse J, Buys N, Jensen P, Everaert N. Differential Expression of Genes and DNA Methylation associated with Prenatal Protein Undernutrition by Albumen Removal in an avian model. Sci Rep 2016; 6:20837. [PMID: 26861190 PMCID: PMC4748411 DOI: 10.1038/srep20837] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 01/07/2016] [Indexed: 11/17/2022] Open
Abstract
Previously, long-term effects on body weight and reproductive performance have been demonstrated in the chicken model of prenatal protein undernutrition by albumen removal. Introduction of such persistent alterations in phenotype suggests stable changes in gene expression. Therefore, a genome-wide screening of the hepatic transcriptome by RNA-Seq was performed in adult hens. The albumen-deprived hens were created by partial removal of the albumen from eggs and replacement with saline early during embryonic development. Results were compared to sham-manipulated hens and non-manipulated hens. Grouping of the differentially expressed (DE) genes according to biological functions revealed the involvement of processes such as ‘embryonic and organismal development’ and ‘reproductive system development and function’. Molecular pathways that were altered were ‘amino acid metabolism’, ‘carbohydrate metabolism’ and ‘protein synthesis’. Three key central genes interacting with many DE genes were identified: UBC, NR3C1, and ELAVL1. The DNA methylation of 9 DE genes and 3 key central genes was examined by MeDIP-qPCR. The DNA methylation of a fragment (UBC_3) of the UBC gene was increased in the albumen-deprived hens compared to the non-manipulated hens. In conclusion, these results demonstrated that prenatal protein undernutrition by albumen removal leads to long-term alterations of the hepatic transcriptome in the chicken.
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Affiliation(s)
- Els Willems
- KU Leuven, Department of Biosystems, Laboratory of Livestock Physiology, Kasteelpark Arenberg 30 box 2456, 3001 Leuven, Belgium.,Linköping University, IFM Biology, AVIAN Behavioural Genomics and Physiology Group, Linköping 581 83, Sweden
| | - Carlos Guerrero-Bosagna
- Linköping University, IFM Biology, AVIAN Behavioural Genomics and Physiology Group, Linköping 581 83, Sweden
| | - Eddy Decuypere
- KU Leuven, Department of Biosystems, Laboratory of Livestock Physiology, Kasteelpark Arenberg 30 box 2456, 3001 Leuven, Belgium
| | - Steven Janssens
- KU Leuven, Department of Biosystems, Research Group Livestock Genetics, Kasteelpark Arenberg 30 box 2456, 3001 Leuven, Belgium
| | - Johan Buyse
- KU Leuven, Department of Biosystems, Laboratory of Livestock Physiology, Kasteelpark Arenberg 30 box 2456, 3001 Leuven, Belgium
| | - Nadine Buys
- KU Leuven, Department of Biosystems, Research Group Livestock Genetics, Kasteelpark Arenberg 30 box 2456, 3001 Leuven, Belgium
| | - Per Jensen
- Linköping University, IFM Biology, AVIAN Behavioural Genomics and Physiology Group, Linköping 581 83, Sweden
| | - Nadia Everaert
- KU Leuven, Department of Biosystems, Laboratory of Livestock Physiology, Kasteelpark Arenberg 30 box 2456, 3001 Leuven, Belgium.,University of Liège, Gembloux Agro-Bio Tech, Precision Livestock and Nutrition Unit, Passage des Déportés 2, 5030 Gembloux, Belgium
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33
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Peeters LM, Janssens S, Brebels M, Buys N. Genetic parameters and estimated breeding values of insect bite hypersensitivity in Belgian Warmblood horses. Vet J 2015; 206:420-2. [PMID: 26586216 DOI: 10.1016/j.tvjl.2015.08.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Revised: 07/29/2015] [Accepted: 08/09/2015] [Indexed: 10/23/2022]
Abstract
Genetic factors involved in susceptibility to insect bite hypersensitivity (IBH) in Belgian Warmblood horses (BWP) were investigated. Data relating to 3409 horses were collected using a questionnaire, administered to owners during sport competitions, BWP breeding days, breeder visits and after phone calls. Horses were classified as IBH-affected or unaffected, based on two 'disease classifiers': a lifetime record, based on owner information (life_status) and another based on whether or not the horse was showing clinical signs at the time of questioning (clin_status). IBH prevalence was 10% based on life_status, and 6.2% based on clin_status. The heritabilities estimated using threshold animal models varied from 0.65 to 0.78 on the underlying scale (0.18-0.26 on the observed scale). These research findings indicate that susceptibility to IBH is a heritable trait in BWP.
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Affiliation(s)
- Liesbet M Peeters
- Department of Biosystems, Katholieke Universiteit Leuven, BE-3001 Heverlee, Belgium.
| | - Steven Janssens
- Department of Biosystems, Katholieke Universiteit Leuven, BE-3001 Heverlee, Belgium
| | - Machteld Brebels
- Department of Biosystems, Katholieke Universiteit Leuven, BE-3001 Heverlee, Belgium
| | - Nadine Buys
- Department of Biosystems, Katholieke Universiteit Leuven, BE-3001 Heverlee, Belgium
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34
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Bulens A, Van Beirendonck S, Van Thielen J, Buys N, Driessen B. Straw applications in growing pigs: Effects on behavior, straw use and growth. Appl Anim Behav Sci 2015. [DOI: 10.1016/j.applanim.2015.04.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Van den Broeke A, Aluwé M, Tuyttens FAM, Ampe B, Vanhaecke L, Wauters J, Janssens S, Coussé A, Buys N, Millet S. An intervention study demonstrates effects of MC4R genotype on boar taint and performances of growing-finishing pigs. J Anim Sci 2015; 93:934-43. [PMID: 26020871 DOI: 10.2527/jas.2014-8184] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Asp298Asn polymorphism of the melanocortin-4 receptor (MC4R) in pigs is known to affect economically important traits such as growth rate and backfat thickness. We have assessed the possible use of this polymorphism as a molecular marker to perform genetic selection toward lower boar taint levels without compromising growth performance and carcass and meat quality in commercial boars and gilts. Homozygous boars and gilts of the AA genotype and GG genotype were compared in an intervention study with a 2 × 2 design to assess main effects and possible interactions between sex and genotype. The concentrations of the 3 boar taint compounds androstenone ( = 0.044), skatole ( = 0.049), and indole ( = 0.006) were significantly higher in fat of AA boars compared to GG boars. However, no effect on the sensory analysis of the fat samples could be observed. Between 20 and 115 kg BW, AA pigs showed higher ADFI than GG pigs ( < 0.001). An interaction between genotype and sex was observed for ADG ( = 0.044): AA boars had a significantly higher ADG than GG boars but there was no significant difference between the gilts. Daily lean meat gain tended to be higher in boars compared to gilts ( = 0.051), independent of genotype. Similarly, boars showed higher G:F compared to gilts ( < 0.001), without effect of genotype. Genotype and sex affected several carcass quality parameters but there was no interaction. Pigs of the AA genotype displayed a lower dressing percentage ( = 0.005), lower ham width ( = 0.024), lower muscle thickness ( = 0.011), and higher fat thickness ( < 0.001), resulting in a lower lean meat percentage ( < 0.001) in comparison with GG pigs. Gilts had a significantly higher dressing percentage ( < 0.001), higher muscle thickness ( < 0.001), higher ham width ( < 0.001), and lower ham angle ( < 0.001) compared to boars. Other than the boar taint compounds, meat quality was not affected by genotype. Pork of gilts was darker ( = 0.014) and less exudative during cooking ( < 0.001) and contained more intramuscular fat ( = 0.013). These results indicate that genetic selection against boar taint is possible using this marker. This will also result in lower feed intake and ADG and, consequently, better carcass quality.
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36
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Elansary M, Stinckens A, Ahariz N, Cambisano N, Coppieters W, Grindflek E, van Son M, Buys N, Georges M. On the use of the transmission disequilibrium test to detect pseudo-autosomal variants affecting traits with sex-limited expression. Anim Genet 2015; 46:395-402. [PMID: 25996251 DOI: 10.1111/age.12296] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2015] [Indexed: 11/29/2022]
Abstract
We herein describe the realization of a genome-wide association study for scrotal hernia and cryptorchidism in Norwegian and Belgian commercial pig populations. We have used the transmission disequilibrium test to avoid spurious associations due to population stratification. By doing so, we obtained genome-wide significant signals for both diseases with SNPs located in the pseudo-autosomal region in the vicinity of the pseudo-autosomal boundary. By further analyzing these signals, we demonstrate that the observed transmission disequilibria are artifactual. We determine that transmission bias at pseudo-autosomal markers will occur (i) when analyzing traits with sex-limited expression and (ii) when the allelic frequencies at the marker locus differ between X and Y chromosomes. We show that the bias is due to the fact that (i) sires will preferentially transmit the allele enriched on the Y (respectively X) chromosome to affected sons (respectively daughters) and (ii) dams will appear to preferentially transmit the allele enriched on the Y (respectively X) to affected sons (respectively daughters), as offspring inheriting the other allele are more likely to be non-informative. We define the conditions to mitigate these issues, namely by (i) extracting information from maternal meiosis only and (ii) ignoring trios for which sire and dam have the same heterozygous genotype. We show that by applying these rules to scrotal hernia and cryptorchidism, the pseudo-autosomal signals disappear, confirming their spurious nature.
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Affiliation(s)
- Mahmoud Elansary
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Bd de Colonster B43, 4000, Liège, Belgium
| | - Anneleen Stinckens
- Unit of Livestock Genetics, Division of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30, 3001, Leuven, Belgium
| | - Naima Ahariz
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Bd de Colonster B43, 4000, Liège, Belgium
| | - Nadine Cambisano
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Bd de Colonster B43, 4000, Liège, Belgium
| | - Wouter Coppieters
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Bd de Colonster B43, 4000, Liège, Belgium
| | - Eli Grindflek
- (The Norwegian Pig Breeders Association) NORSVIN, Hamar, Norway
| | - Maren van Son
- (The Norwegian Pig Breeders Association) NORSVIN, Hamar, Norway
| | - Nadine Buys
- Unit of Livestock Genetics, Division of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30, 3001, Leuven, Belgium
| | - Michel Georges
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Bd de Colonster B43, 4000, Liège, Belgium
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37
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Wauters J, Vanden Bussche J, Verplanken K, Bekaert KM, Aluwé M, Van den Broeke A, Coussé A, Buys N, Vanhaecke L. Development of a quantitative method for the simultaneous analysis of the boar taint compounds androstenone, skatole and indole in porcine serum and plasma by means of ultra-high performance liquid chromatography coupled to high resolution mass spectrometry. Food Chem 2015; 187:120-9. [PMID: 25977006 DOI: 10.1016/j.foodchem.2015.04.066] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 11/18/2014] [Accepted: 04/07/2015] [Indexed: 12/28/2022]
Abstract
Boar taint is an off-odour occurring while heating meat or fat from boars. A method detecting the three compounds (androstenone, skatole and indole) simultaneously in blood would offer substantial advantages since it would allow monitoring the impact of rearing strategies. Therefore, a UHPLC-HR-Orbitrap-MS analysis method is optimized and validated for the quantification of these compounds in plasma or serum. Sample pre-treatment involved an extraction with diethylether followed by a centrifugal filtration (30 kDa). Limits of detection and quantification varied between 0.5 and 1 μg L(-1) and 2 and 3 μg L(-1) for the three compounds, respectively. Besides, an excellent repeatability (RSD < 7.6%), within-laboratory reproducibility (RSD<10.5%), recovery (87-97%) and linearity (R(2)>0.99) were recorded. Correlations between serum/plasma and fat levels of the boar taint compounds were positive for skatole (r(serum) = 0.39 and r(plasma) = 0.84) and androstenone (r(serum) = 0.73-0.78 and r(plasma) = 0.32-0.80).
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Affiliation(s)
- J Wauters
- Ghent University, Faculty of Veterinary Medicine, Department of Veterinary Public Health and Food Safety, Laboratory of Chemical Analysis, Salisburylaan 133, B-9820 Merelbeke, Belgium.
| | - J Vanden Bussche
- Ghent University, Faculty of Veterinary Medicine, Department of Veterinary Public Health and Food Safety, Laboratory of Chemical Analysis, Salisburylaan 133, B-9820 Merelbeke, Belgium.
| | - K Verplanken
- Ghent University, Faculty of Veterinary Medicine, Department of Veterinary Public Health and Food Safety, Laboratory of Chemical Analysis, Salisburylaan 133, B-9820 Merelbeke, Belgium.
| | - K M Bekaert
- Ghent University, Faculty of Veterinary Medicine, Department of Veterinary Public Health and Food Safety, Laboratory of Chemical Analysis, Salisburylaan 133, B-9820 Merelbeke, Belgium.
| | - M Aluwé
- Institute of Agricultural and Fisheries Research (ILVO), Animal Sciences Unit, Scheldeweg 68, B-9090 Melle, Belgium.
| | - A Van den Broeke
- Institute of Agricultural and Fisheries Research (ILVO), Animal Sciences Unit, Scheldeweg 68, B-9090 Melle, Belgium.
| | - A Coussé
- KU Leuven University, Science, Engineering and Technology Group, Department of Biosystems (BIOSYST), Division of Gene Technology, Kasteelpark Arenberg 21, B-3001 Heverlee, Belgium.
| | - N Buys
- KU Leuven University, Science, Engineering and Technology Group, Department of Biosystems (BIOSYST), Division of Gene Technology, Kasteelpark Arenberg 21, B-3001 Heverlee, Belgium.
| | - L Vanhaecke
- Ghent University, Faculty of Veterinary Medicine, Department of Veterinary Public Health and Food Safety, Laboratory of Chemical Analysis, Salisburylaan 133, B-9820 Merelbeke, Belgium.
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Sun J, Sun J, Wang N, Buys N. Validation of a New Attribution Style Inventory for Chinese Patients with Schizophrenia. Eur Psychiatry 2015. [DOI: 10.1016/s0924-9338(15)30807-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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39
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De Keyser K, Berth M, Christensen N, Willaert S, Janssens S, Ducatelle R, Goddeeris B, De Cock H, Buys N. Assessment of plasma anti-elastin antibodies for use as a diagnostic aid for chronic progressive lymphoedema in Belgian Draught Horses. Vet Immunol Immunopathol 2015; 163:16-22. [DOI: 10.1016/j.vetimm.2014.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 11/01/2014] [Accepted: 11/05/2014] [Indexed: 11/25/2022]
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40
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Stinckens A, Vereijken A, Ons E, Konings P, Van As P, Cuppens H, Moreau Y, Sakai R, Aerts J, Goddeeris B, Buys N, Vanmechelen K, Cassiman J. Art meets science: The Cosmopolitan Chicken Research Project. Facts Views Vis Obgyn 2015; 7:163-72. [PMID: 26977265 PMCID: PMC4788331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The Cosmopolitan Chicken Project is an artistic undertaking of renowned artist Koen Vanmechelen. In this project, the artist interbreeds domestic chickens from different countries aiming at the creation of a true Cosmopolitan Chicken as a symbol for global diversity. The unifying theme is the chicken and the egg, symbols that link scientific, political, philosophical and ethical issues. The Cosmopolitan Chicken Research Project is the scientific component of this artwork. Based on state of the art genomic techniques, the project studies the effect of the crossing of chickens on the genetic diversity. Also, this research is potentially applicable to the human population. The setup of the CC®P is quite different from traditional breeding experiments: starting from the crossbreed of two purebred chickens (Mechelse Koekoek x Poule de Bresse), every generation is crossed with a few animals from another breed. For 26 of these purebred and crossbred populations, genetic diversity was measured (1) under the assumption that populations were sufficiently large to maintain all informative SNP within a generation and (2) under the circumstances of the CCP breeding experiment. Under the first assumption, a steady increase in genetic diversity was witnessed over the consecutive generations, thus indeed indicating the creation of a "Cosmopolitan Chicken Genome". However, under the conditions of the CCP, which reflects the reality within the human population, diversity is seen to fluctuate within given boundaries instead of steadily increasing. A reflection on this might be that this is because, in humans, an evolutionary optimum in genetic diversity is reached. Key words.
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Affiliation(s)
- A. Stinckens
- Division of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium.
| | - A. Vereijken
- Hendrix Genetics, Research & Technology Centre, Boxmeer, the Netherlands.
| | - E. Ons
- Hendrix Genetics, Research & Technology Centre, Boxmeer, the Netherlands.
| | - P. Konings
- STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, Department of Electrical Engineering (ESAT), KU Leuven, Leuven, Belgium.
,iMinds Medical IT, KU Leuven, Leuven, Belgium.
| | - P. Van As
- Hendrix Genetics, Research & Technology Centre, Boxmeer, the Netherlands.
| | - H. Cuppens
- Center for Human Genetics, KU Leuven, Leuven, Belgium.
| | - Y. Moreau
- STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, Department of Electrical Engineering (ESAT), KU Leuven, Leuven, Belgium.
,iMinds Medical IT, KU Leuven, Leuven, Belgium.
| | - R. Sakai
- STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, Department of Electrical Engineering (ESAT), KU Leuven, Leuven, Belgium.
,iMinds Medical IT, KU Leuven, Leuven, Belgium.
| | - J. Aerts
- STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, Department of Electrical Engineering (ESAT), KU Leuven, Leuven, Belgium.
,iMinds Medical IT, KU Leuven, Leuven, Belgium.
| | - B. Goddeeris
- Division of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium.
| | - N. Buys
- Division of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium.
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41
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Peeters LM, Janssens S, Coussé A, Buys N. Insect bite hypersensitivity in Belgian warmblood horses: prevalence and risk factors. VLAAMS DIERGEN TIJDS 2014. [DOI: 10.21825/vdt.v83i5.16636] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Insect bite hypersensitivity (IBH) is an allergic reaction to the bites of certain Culicoides spp. or other insects. In this study, risk factors for IBH in Belgian warmblood horses stabled or grazing in Flanders (Belgium) were investigated. IBH records (n=3409) were collected in 2009 and 2011 using a questionnaire and face-to-face interviews. The classification of IBH-affected versus unaffected horses was based on the owner’s statement, and the reported IBH lifetime prevalence was 10%. Thirty eight percent of IBH affected horses had no clinical symptoms at the time of questioning. When only the presence or absence of clinical symptoms at the time of questioning was taken into account, the prevalence of IBH symptoms was 6.2%. Seventy percent of IBH-affected horses were treated with IBH measures to reduce clinical symptoms. Model selection was based on backwards elimination in a logistic regression framework starting with 17 factors. The age of the horse, vegetation of surrounding pasture and stud size were found to be significantly associated with the self-reported IBH status.
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42
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Schroyen M, Janssens S, Stinckens A, Brebels M, Bertolini F, Lamberigts C, Bekaert K, Vanhaecke L, Aluwé M, Tuyttens FAM, Millet S, Buys N. The MC4R c.893G>A mutation: a marker for growth and leanness associated with boar taint odour in Belgian pig breeds. Meat Sci 2014; 101:1-4. [PMID: 25462375 DOI: 10.1016/j.meatsci.2014.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 08/18/2014] [Accepted: 08/18/2014] [Indexed: 10/24/2022]
Abstract
Since surgical castration of male piglets without anaesthesia is under heavy societal pressure, finding a sustainable solution to reduce boar taint has become urgent. One way to circumvent this animal welfare violation is raising entire male pigs whilst selecting against the tainted phenotype through marker-assisted selection. Since slaughtering at a lower weight is often suggested to reduce boar taint, selection using a marker for that trait could be a promising strategy. Therefore, in this study a melanocortin 4 receptor (MC4R) mutation, frequently described in different pig breeds as marker for fat content, weight gain and feed intake, was examined in relation to boar taint in pig breeds used in Belgian pig farms. Although results suggest an association between this mutation and a boar taint odour score assigned by experts, no association was found between the mutation and the concentration of the individual chemical boar taint components androstenone, skatole and indole.
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Affiliation(s)
- M Schroyen
- Livestock Genetics, Department Biosystems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 30, B-3001 Heverlee, Belgium
| | - S Janssens
- Livestock Genetics, Department Biosystems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 30, B-3001 Heverlee, Belgium
| | - A Stinckens
- Livestock Genetics, Department Biosystems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 30, B-3001 Heverlee, Belgium
| | - M Brebels
- Livestock Genetics, Department Biosystems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 30, B-3001 Heverlee, Belgium
| | - F Bertolini
- Livestock Genetics, Department Biosystems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 30, B-3001 Heverlee, Belgium
| | - C Lamberigts
- Livestock Genetics, Department Biosystems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 30, B-3001 Heverlee, Belgium
| | - K Bekaert
- Laboratory of Chemical Analysis, Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820 Merelbeke, Belgium
| | - L Vanhaecke
- Laboratory of Chemical Analysis, Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820 Merelbeke, Belgium
| | - M Aluwé
- Animal Sciences Unit, Institute for Agricultural and Fisheries Research (ILVO), Scheldeweg 68, B-9090 Melle, Belgium
| | - F A M Tuyttens
- Animal Sciences Unit, Institute for Agricultural and Fisheries Research (ILVO), Scheldeweg 68, B-9090 Melle, Belgium
| | - S Millet
- Animal Sciences Unit, Institute for Agricultural and Fisheries Research (ILVO), Scheldeweg 68, B-9090 Melle, Belgium
| | - N Buys
- Livestock Genetics, Department Biosystems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 30, B-3001 Heverlee, Belgium.
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De Keyser K, Janssens S, Peeters LM, Gasthuys F, Oosterlinck M, Buys N. Chronic progressive lymphedema in the Belgian draft horse in Belgium: clinical phenotyping, prevalence and risk factor analysis. VLAAMS DIERGEN TIJDS 2014. [DOI: 10.21825/vdt.v83i3.16651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Chronic progressive lymphedema (CPL) is a well-known problem in the Belgian draft horse. However, tools for clinical diagnosis have not been standardized. Therefore, the exact disease prevalence and the possible CPL risk factors have not been investigated in the Belgian breed yet. The aim of the present study was to assess a uniform CPL clinical examination method to increase diagnostic objectivity as well as to determine the occurrence and severity of lesions. Using univariate and stepwise multivariable logistic regression models, the association of factors, such as age-gender interaction, coat color and season, with CPL occurrence was examined. In this study, it was demonstrated that CPL is highly prevalent in the Belgian draft horse: 60.66% of the horses of the total sample were affected, including a large proportion of young horses (< 3 years), whereas 85.86% was affected in a subset of older horses (≥ 3 years). In the latter, the lesions were more explicit as CPL is a chronic disorder. In some horses (i.e. 14% of the yearlings), mild clinical symptoms appeared at approximately the age of one, while distinct onset of the disease occurred from the age of three onwards. The factors age-gender interaction, coat color and season, which are significantly associated with CPL occurrence, were identified and quantified. In this study, a standardized diagnostic protocol is proposed that will enhance future data collection and furthermore will offer a foundation for quantitative genetic research. Ultimately, it will help to reduce CPL occurrence in the Belgian draft horse by means of selection.
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de Keyser K, Janssens S, Buys N. Chronic progressive lymphoedema in draught horses. Equine Vet J 2014; 47:260-6. [DOI: 10.1111/evj.12256] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 02/18/2014] [Indexed: 01/17/2023]
Affiliation(s)
- K. de Keyser
- Livestock Genetics; Department of Biosystems; KU Leuven; Heverlee (Leuven) Belgium
| | - S. Janssens
- Livestock Genetics; Department of Biosystems; KU Leuven; Heverlee (Leuven) Belgium
| | - N. Buys
- Livestock Genetics; Department of Biosystems; KU Leuven; Heverlee (Leuven) Belgium
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De Keyser K, Janssens S, Peeters L, Foqué N, Gasthuys F, Oosterlinck M, Buys N. Genetic parameters for chronic progressive lymphedema in Belgian Draught Horses. J Anim Breed Genet 2014; 131:522-8. [DOI: 10.1111/jbg.12087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 02/14/2014] [Indexed: 11/30/2022]
Affiliation(s)
- K. De Keyser
- KU Leuven Department of Biosystems, Livestock Genetics; Leuven Belgium
| | - S. Janssens
- KU Leuven Department of Biosystems, Livestock Genetics; Leuven Belgium
| | - L.M. Peeters
- KU Leuven Department of Biosystems, Livestock Genetics; Leuven Belgium
| | - N. Foqué
- KU Leuven Department of Biosystems, Livestock Genetics; Leuven Belgium
| | - F. Gasthuys
- Department of Surgery and Anaesthesiology of Domestic Animals; Faculty of Veterinary Medicine; Ghent University; Merelbeke Belgium
| | - M. Oosterlinck
- Department of Surgery and Anaesthesiology of Domestic Animals; Faculty of Veterinary Medicine; Ghent University; Merelbeke Belgium
| | - N. Buys
- KU Leuven Department of Biosystems, Livestock Genetics; Leuven Belgium
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Verhelst R, Schroyen M, Buys N, Niewold T. Dietary polyphenols reduce diarrhea in enterotoxigenic Escherichia coli (ETEC) infected post-weaning piglets. Livest Sci 2014. [DOI: 10.1016/j.livsci.2013.11.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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47
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Cousse A, Abos R, Sarre C, Hubin X, Boccart C, Losson B, Saegerman C, Claerebout E, Georges M, Buys N. Phenotyping Belgian Blue cattle for their susceptibility to psoroptic mange. Commun Agric Appl Biol Sci 2014; 79:121-125. [PMID: 25864325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
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Palmans S, Janssens S, Van Meensel J, Aluwé M, Meirlaen S, De Campeneere S, Sonck B, Buys N, Millet S. Genotype X feed interactions in the genetic evaluation of Piétrain Boars. Commun Agric Appl Biol Sci 2014; 79:127-129. [PMID: 25864326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
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49
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Wijnrocx K, Janssens S, Buys N. Effect of dog breed 'varieties' on population genetic structure. Commun Agric Appl Biol Sci 2014; 79:206-211. [PMID: 25864339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
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Sedlacek L, Ramsauer B, Brazier J, Buys N, Marretta L. AML in der Schwangerschaft: Fallvorstellung. Z Geburtshilfe Neonatol 2013. [DOI: 10.1055/s-0033-1361360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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