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 ID: 1047439
Download Presentation The PPT/PDF document "Genetic Relationships and Inbreeding Coe..." is the property of its rightful owner. Permission is granted to download and print the materials on this web site for personal, non-commercial use only, and to display it on your personal computer provided you do not modify the materials and that you retain all copyright notices contained in the materials. By downloading content from our website, you accept the terms of this agreement.
1. Genetic Relationships and Inbreeding Coefficients of Swine BreedsPresented by Dr. Bill LambersonUniversity of Missouri
2. BackgroundChanges in the pork industry Vertical integrationUse of limited number of breeds on a large scaleConsumer demand for lean, uniform productYorkshire/Large White, Landrace, Chester White, Duroc, Berkshire, Hampshire, SpotOver 70 breeds of pigs worldwideMany in danger of extinctionThe American Livestock Conservancy (ALC) was founded to protect rare breeds of livestock and poultryApproximately 180 livestock and poultry breeds7 breeds of pigs in US listed as critical
3. Importance of Genetic RelationshipsPedigrees essential for producers to plan matingsMany pedigrees are incomplete or missing for rare breeds of pigsWithout pedigrees, producers have no way of knowing relationships between individualsGreater chance of mating related individualsIncreased levels of inbreedingIncreased homozygousity Ultimately reduces breed viability
4. Importance of Breed DiversityIndustry breeds share similar genetic makeupBred to thrive in a specific environmentConfined feeding operationsConsumer demand for lean, uniform productYorkshire/Large White, Landrace, Chester White, Duroc, Berkshire, Hampshire, SpotLess popular breeds of pigs are more genetically diverseAble to tolerate harsh living conditionsDisease ResistanceMore self sufficient
5. ObjectiveDetermine 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 Methods10 breeds of swineRange 4-20 individuals per breedHeritage Breeds: Guinea, Ossabaw Island, Red Wattle, Saddleback, Mulefoot, and TamworthCommercial Breeds: Duroc, Landrace, Large White, and PietrainHair samples submitted by producers and genotyped by GeneSeek using the Porcine 60k SNP chipPublicly 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 PlinkPlink used to construct a genomic relationship matrix (GRM)Individuals or SNP’s not meeting the following criteria were removed: Minor allele frequency greater than 0.05Call rate for individual greater than 0.90Inbreeding coefficient Data set pruned first to include SNP’s in approximate linkage equilibriumF value is inbreeding coefficient estimateSAS used to analyze Plink outputDifferences between breeds significant at α ≤ 0.05
8. ResultsBreednRFGuinea140.16a0.26aOssabaw Island100.37b0.47bRed Wattle50.49bc0.28aSaddleback220.14a0.15cMulefoot40.69d0.39abDuroc200.21a0.25aLandrace200.03e0.15cLarge White200.05ef0.15cPietrain200.07f0.12cTamworth200.46c0.41bValues with differing superscripts in columns are significantly different at α ≤ 0.05
9. Results (cont.)Commercial breeds exhibit lower levels of relatedness and inbreedingEndangered breeds show higher levels of relatedness and inbreeding
10. Relationship between breedsMultidimensional scaling (MDS) cluster plot
11. DiscussionAs expected, higher levels of relatedness and inbreeding were calculated for the endangered breedsFactors contributing to this include small populations and lack of pedigree dataOutlying breeds such as Tamworth, Red Wattle and Duroc may carry unique genes not seen in breeds sharing similar genetic makeup
12. ConclusionHeritage breeds have many qualities worth preserving that are not seen in industry breeds and conservation efforts should continue
13. AcknowledgementsSAREAmerican Livestock ConservancyProducersAmerican Guinea Hog Association