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Pedigree Analysis and Optimisation of the Breeding Programme of the Markiesje and the Stabyhoun

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Pedigree Analysis and Optimisation of the Breeding Programme of the Markiesje and the Stabyhoun Pedigree analysis and optimisation of the breeding programme of the Markiesje and the Stabyhoun Aiming to improve health and welfare and maintain genetic diversity Harmen Doekes REG.NR.: 920809186050 Major thesis Animal Breeding and Genetics (ABG-80436) January, 2016 Supervisors/examiners: Piter Bijma - Animal Breeding and Genomics Centre, Wageningen University Kor Oldenbroek - Centre for Genetic Resources the Netherlands (CGN), Wageningen UR Jack Windig - Animal Breeding & Genomics Centre, Wageningen UR Livestock Research Thesis: Animal Breeding and Genomics Centre Pedigree analysis and optimisation of the breeding programme of the Markiesje and the Stabyhoun Aiming to improve health and welfare and maintain genetic diversity Harmen Doekes REG.NR.: 920809186050 Major thesis Animal Breeding and Genetics (ABG-80436) January, 2016 Supervisors: Kor Oldenbroek - Centre for Genetic Resources the Netherlands (CGN), Wageningen UR Jack Windig - Animal Breeding & Genomics Centre, Wageningen UR Livestock Research Examiners: Piter Bijma - Animal Breeding and Genomics Centre, Wageningen University Kor Oldenbroek - Centre for Genetic Resources the Netherlands (CGN), Wageningen UR Commissioned by: Nederlandse Markiesjes Vereniging Nederlandse Vereniging voor Stabij- en Wetterhounen Preface This major thesis is submitted in partial fulfilment of the requirements for the degree of Master of Animal Sciences of Wageningen University, the Netherlands. It comprises an unpublished study on the genetic status of two Dutch dog breeds, the Markiesje and the Stabyhoun. that was commissioned by the Breed Clubs of the breeds, the ‘Nederlandse Markiesjes Vereniging’ and the ‘Nederlandse Vereniging voor Stabij- en Wetterhounen’. It was written for readers with limited pre-knowledge. Although the thesis focusses on two breeds, it addresses issues that are found in many dog breeds. The study was conducted in 2015 at the chair group Animal Breeding & Genetics of Wageningen University, under supervision of Kor Oldenbroek and Jack Windig. I would like to thank my supervisors for their useful feedback, technical support and communication with the Breed Clubs and other relevant contacts. I am furthermore grateful to the various people of the Breed Clubs who provided me with the breeds’ studbooks and adequately answered my questions. Throughout the execution of the research project I have developed my general research skills. An example of such a skill is independent decision making. Although my supervisors steered the direction of the project, I was largely free to decide on what to focus (which was both a challenge and a useful experience). In addition to developing my general research skills, I have enlarged my knowledge of population genetics and have gained insight into the world of pedigree dogs. I sincerely hope that the results of this study can support the Breed Clubs in optimising their breeding programmes and thereby maintain genetic diversity and improve the animal health and welfare in both breeds. Wageningen, January 2016 Harmen Doekes Contents Summary ................................................................................................................................................. 4 Samenvatting (Dutch summary) .............................................................................................................. 5 1. Introduction ......................................................................................................................................... 6 1.1. Dog domestication and the development of breeds ...................................................................... 6 1.2. The emergence of inherited disorders .......................................................................................... 7 1.3. The dog genome, genetic diversity, inbreeding and coancestry ................................................... 8 1.4. Prevention and restriction of inherited disorders ........................................................................ 10 1.5. National initiatives to improve purebred dog health- and welfare ............................................. 12 1.6. The Markiesje ............................................................................................................................. 13 1.7. The Stabyhoun ............................................................................................................................ 15 1.8. Aim and research questions ........................................................................................................ 19 2. Materials and methods ....................................................................................................................... 21 2.1. Pedigree analysis ........................................................................................................................ 21 2.2. Analysis of inherited disorders ................................................................................................... 24 2.3. Simulation of breeding strategies ............................................................................................... 25 3. Results Markiesje .............................................................................................................................. 27 3.1. Pedigree analysis ........................................................................................................................ 27 3.2. Inherited disorders ...................................................................................................................... 32 3.3. Simulation of breeding strategies ............................................................................................... 34 4. Results Stabyhoun ............................................................................................................................. 37 4.1. Pedigree analysis ........................................................................................................................ 37 4.2. Inherited disorders ...................................................................................................................... 42 4.3. Simulation of breeding strategies ............................................................................................... 47 5. Discussion ......................................................................................................................................... 50 6. Conclusion and recommendations ..................................................................................................... 55 References ............................................................................................................................................. 56 Appendices ............................................................................................................................................... i Appendix I. Markiesje: distributions of general population parameters ............................................. ii Appendix II. Markiesjes affected by neuropathology: decomposition of COI and founder contributions ....................................................................................................................................... iv Appendix III. Stabyhoun: distributions of general population parameters........................................ vii Appendix IV. Dog Breed Management: input baseline simulations .................................................. ix Summary The strong artificial selection pressure and the management in (small) closed populations has led to a considerable amount of inbreeding and loss of genetic diversity in many dog breeds, which has resulted in the manifestation of inherited disorders. In this study, two of the nine original Dutch dog breeds, the Markiesje (studbook since 1970s) and the Stabyhoun (studbook since 1940s), were extensively analysed with the aim to formulate breeding recommendations that can support the Breed Clubs in maintaining genetic diversity and improving health and welfare in their breeds. First, a pedigree analysis was performed in which general population parameters and parameters related to genetic diversity were calculated. Second, the prevalence of inherited disorders found in the breeds was estimated and potential risk factors for these disorders were identified. Last, the effectiveness of various breeding strategies on reducing the inbreeding rate was evaluated using computer simulations. The Markiesje is a small breed with 120 pups born per year. In the Markiesje population, 26.2% of the males and 36.7% of the females were selected for breeding. The average litter size was 4.2 pups and the generation interval 3.4 years. The Stabyhoun is a larger breed with 700 pups born per year. In the Stabyhoun population, 7.8% of the males and 17.8% of the females were selected for breeding. The average litter size was 6.3 pups and the generation interval 4.4 years. Respectively 13% and 33% of the genetic diversity originally present in the 54 founders of the population Markiesjes and the 30 founders of the population Stabyhouns has been lost. In general, both breeds have had an unacceptably high risk on accumulating inherited disorders, with inbreeding rates per generation exceeding 1% (effective population size < 50). The inbreeding and coancestry rates were, however, found to be decreasing in both breeds. The effective number of founders and the founder genome equivalent of respectively 14.6 and 4.1 for the Markiesje and 6.3 and 1.5 for the Stabyhoun,
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