Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium
Effective population size is an important parameter for the assessment of genetic diversity within a livestock population and its development over time. If pedigree information is not available, linkage disequilibrium (LD) analysis might offer an alternative perspective for the estimation of effecti...
| Autores principales: | , , , , , , , |
|---|---|
| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Wiley
2010
|
| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/1822 |
| _version_ | 1855519167296307200 |
|---|---|
| author | Flury, C. Tapio, M. Sonstegard, T.S. Drögemaller, C. Leeb, T. Simianer, H. Hanotte, Olivier H. Rieder, S. |
| author_browse | Drögemaller, C. Flury, C. Hanotte, Olivier H. Leeb, T. Rieder, S. Simianer, H. Sonstegard, T.S. Tapio, M. |
| author_facet | Flury, C. Tapio, M. Sonstegard, T.S. Drögemaller, C. Leeb, T. Simianer, H. Hanotte, Olivier H. Rieder, S. |
| author_sort | Flury, C. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Effective population size is an important parameter for the assessment of genetic diversity within a livestock population and its development over time. If pedigree information is not available, linkage disequilibrium (LD) analysis might offer an alternative perspective for the estimation of effective population size. In this study, 128 individuals of the Swiss Eringer breed were genotyped using the Illumina BovineSNP50 beadchip. We set bin size at 50 kb for LD analysis, assuming that LD for proximal single nucleotide polymorphism (SNP)-pairs reflects distant breeding history while LD from distal SNP-pairs would reflect near history. Recombination rates varied among different regions of the genome. The use of physical distances as an approximation of genetic distances (e.g. setting 1 Mb = 0.01 Morgan) led to an upward bias in LD-based estimates of effective population size for generations beyond 50, while estimates for recent history were unaffected. Correction for restricted sample size did not substantially affect these results. LD-based actual effective population size was estimated in the range of 87–149, whereas pedigree-based effective population size resulted in 321 individuals. For conservation purposes, requiring knowledge of recent history (<50 generations), approximation assuming constant recombination rate seemed adequate. |
| format | Journal Article |
| id | CGSpace1822 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2010 |
| publishDateRange | 2010 |
| publishDateSort | 2010 |
| publisher | Wiley |
| publisherStr | Wiley |
| record_format | dspace |
| spelling | CGSpace18222023-09-08T19:31:01Z Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium Flury, C. Tapio, M. Sonstegard, T.S. Drögemaller, C. Leeb, T. Simianer, H. Hanotte, Olivier H. Rieder, S. cattle genetics Effective population size is an important parameter for the assessment of genetic diversity within a livestock population and its development over time. If pedigree information is not available, linkage disequilibrium (LD) analysis might offer an alternative perspective for the estimation of effective population size. In this study, 128 individuals of the Swiss Eringer breed were genotyped using the Illumina BovineSNP50 beadchip. We set bin size at 50 kb for LD analysis, assuming that LD for proximal single nucleotide polymorphism (SNP)-pairs reflects distant breeding history while LD from distal SNP-pairs would reflect near history. Recombination rates varied among different regions of the genome. The use of physical distances as an approximation of genetic distances (e.g. setting 1 Mb = 0.01 Morgan) led to an upward bias in LD-based estimates of effective population size for generations beyond 50, while estimates for recent history were unaffected. Correction for restricted sample size did not substantially affect these results. LD-based actual effective population size was estimated in the range of 87–149, whereas pedigree-based effective population size resulted in 321 individuals. For conservation purposes, requiring knowledge of recent history (<50 generations), approximation assuming constant recombination rate seemed adequate. 2010-10 2010-06-08T14:53:52Z 2010-06-08T14:53:52Z Journal Article https://hdl.handle.net/10568/1822 en Limited Access Wiley Flury, C.; Tapio, M.; Sonstegard, T.; Drögemüller, C.; Leeb, T.; Simianer, H.; Hanotte, O.; Rieder, S. 2010. Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium. Journal of Animal Breeding and Genetics 127(5):339-347. |
| spellingShingle | cattle genetics Flury, C. Tapio, M. Sonstegard, T.S. Drögemaller, C. Leeb, T. Simianer, H. Hanotte, Olivier H. Rieder, S. Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium |
| title | Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium |
| title_full | Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium |
| title_fullStr | Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium |
| title_full_unstemmed | Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium |
| title_short | Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium |
| title_sort | effective population size of an indigenous swiss cattle breed estimated from linkage disequilibrium |
| topic | cattle genetics |
| url | https://hdl.handle.net/10568/1822 |
| work_keys_str_mv | AT fluryc effectivepopulationsizeofanindigenousswisscattlebreedestimatedfromlinkagedisequilibrium AT tapiom effectivepopulationsizeofanindigenousswisscattlebreedestimatedfromlinkagedisequilibrium AT sonstegardts effectivepopulationsizeofanindigenousswisscattlebreedestimatedfromlinkagedisequilibrium AT drogemallerc effectivepopulationsizeofanindigenousswisscattlebreedestimatedfromlinkagedisequilibrium AT leebt effectivepopulationsizeofanindigenousswisscattlebreedestimatedfromlinkagedisequilibrium AT simianerh effectivepopulationsizeofanindigenousswisscattlebreedestimatedfromlinkagedisequilibrium AT hanotteolivierh effectivepopulationsizeofanindigenousswisscattlebreedestimatedfromlinkagedisequilibrium AT rieders effectivepopulationsizeofanindigenousswisscattlebreedestimatedfromlinkagedisequilibrium |