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Genetic Relationships and Inbreeding Coefficients of Swine Breeds

Genetic Relationships and Inbreeding Coefficients of Swine Breeds. Presented by Dr. Bill Lamberson University of Missouri . Background. Changes in the pork industry Vertical integration Use of limited number of breeds on a large scale Consumer demand for lean, uniform product

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Genetic Relationships and Inbreeding Coefficients of Swine Breeds

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  1. Genetic Relationships and Inbreeding Coefficients of Swine Breeds Presented by Dr. Bill Lamberson University of Missouri

  2. Background • Changes in the pork industry • Vertical integration • Use of limited number of breeds on a large scale • Consumer demand for lean, uniform product • Yorkshire/Large White, Landrace, Chester White, Duroc, Berkshire, Hampshire, Spot • Over 70 breeds of pigs worldwide • Many in danger of extinction • The American Livestock Conservancy (ALC) was founded to protect rare breeds of livestock and poultry • Approximately 180 livestock and poultry breeds • 7 breeds of pigs in US listed as critical

  3. Importance of Genetic Relationships • Pedigrees essential for producers to plan matings • Many pedigrees are incomplete or missing for rare breeds of pigs • Without pedigrees, producers have no way of knowing relationships between individuals • Greater chance of mating related individuals • Increased levels of inbreeding • Increased homozygousity • Ultimately reduces breed viability

  4. Importance of Breed Diversity • Industry breeds share similar genetic makeup • Bred to thrive in a specific environment • Confined feeding operations • Consumer demand for lean, uniform product • Yorkshire/Large White, Landrace, Chester White, Duroc, Berkshire, Hampshire, Spot • Less popular breeds of pigs are more genetically diverse • Able to tolerate harsh living conditions • Disease Resistance • More self sufficient

  5. Objective • Determine relationships between individuals where pedigree data is missing or incomplete. • Compare average relatedness of individuals within a breed to individuals in other breeds

  6. Materials and Methods • 10 breeds of swine • Range 4-20 individuals per breed • Heritage Breeds: Guinea, Ossabaw Island, Red Wattle, Saddleback, Mulefoot, and Tamworth • Commercial Breeds: Duroc, Landrace, Large White, and Pietrain • Hair samples submitted by producers and genotyped by GeneSeek using the Porcine 60k SNP chip • Publicly available data accessed online • http://datadryad.org/resource/doi:10.5061/dryad.v6f1g

  7. Materials and Methods (cont.) • SNP data converted to PED and MAP files for analysis in Plink • Plink used to construct a genomic relationship matrix (GRM) • Individuals or SNP’s not meeting the following criteria were removed: • Minor allele frequency greater than 0.05 • Call rate for individual greater than 0.90 • Inbreeding coefficient • Data set pruned first to include SNP’s in approximate linkage equilibrium • F value is inbreeding coefficient estimate • SAS used to analyze Plink output • Differences between breeds significant at α≤ 0.05

  8. Results Values with differing superscripts in columns are significantly different at α≤ 0.05

  9. Results (cont.) • Commercial breeds exhibit lower levels of relatedness and inbreeding • Endangered breeds show higher levels of relatedness and inbreeding

  10. Relationship between breeds • Multidimensional scaling (MDS) cluster plot

  11. Discussion • As expected, higher levels of relatedness and inbreeding were calculated for the endangered breeds • Factors contributing to this include small populations and lack of pedigree data • Outlying breeds such as Tamworth, Red Wattle and Durocmay carry unique genes not seen in breeds sharing similar genetic makeup

  12. Conclusion • Heritage breeds have many qualities worth preserving that are not seen in industry breeds and conservation efforts should continue

  13. Acknowledgements • SARE • American Livestock Conservancy • Producers • American Guinea Hog Association

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