1. KIZZI ROBERTS A SURVEY OF RELATIONSHIPS AMONG RARE BREEDS OF SWINE

2. BREED DIVERSITY Over 70 different breeds of pigs Vertical integration within the industry Consumer demand for lean, uniform product Yorkshire, Landrace, Chester White, Duroc, Berkshire, Large White The American Livestock Breed Conservancy (ALBC) was founded to protect rare breeds of livestock and poultry Approximately 180 livestock and poultry breeds

3. IMPORTANCE OF BREED DIVERSITY Industry breeds share similar genetic makeup Bred to thrive in a specific environment Confined feeding operations Less popular breeds of pigs are more genetically diverse Able to tolerate harsh living conditions Disease Resistance More self sufficient

4. SWINE BREEDS Many breeds have unique traits not found in industry breeds ALBC lists 7 critical swine breeds Fewer than 200 registered each year Three breeds were selected from this list Guinea Hog Ossabaw Island Red Wattle

5. GUINEA HOG Small, hardy pigs Excellent foragers High fat content Good for subsistence farming Small size Thrive on rough forage

6. OSSABAW ISLAND Isolated feral herd on Ossabaw Island Small, hardy pig Large fat stores Good model for non insulin dependent diabetes

7. RED WATTLE Hardy, large pigs Rapid growth rate Lean, tender, flavorful meat Mild temperament

8. CHALLENGES OF CONSERVATION These breeds are not as popular Small carcass, high fat content, relatively slow growth rate Small breed population Difficult for farmers to find animals to purchase Not as many pig farmers As compared to other small farming operations Small herd size No confined feeding operations

9. CHALLENGES OF CONSERVATION Lack of pedigree information Old breeds Sometimes have no formal breed organization Reduced genetic diversity Due to small population and lack of pedigree data Inbreeding Not knowing relationships of animals makes planning matings difficult Ultimately reduces breed viability

10. INBREEDING High levels of homozygosity (inbreeding) Allows undesirable or lethal alleles to be expressed Reduction in genetic diversity Reduces breed viability

11. OBJECTIVE Determine relationships among rare breeds of pigs when pedigree data is incomplete or unknown so farmers can plan matings to reduce inbreeding Compare rare breeds to each other and to industry breeds Determine which breeds are more similar to popular breeds and which are more genetically diverse

12. METHODS Collect DNA samples from each breed 10-11 animals per breed Hair samples Samples genotyped at GeneSeek Determine relationships from genotypes

13. QUICK REVIEW DNA is composed of four nucleotides The sequence of nucleotides is important Codes for genes

14. ALLELE Two chromosomes Two forms of a gene Each form is an allele Allele A and Allele B An animal’s genotype is determined by which alleles it carries Homozygous means it has two forms of the same allele Either AA or BB Heterozygous means is carries a form of each allele AB Therefore there are 3 possible genotypes

15. HOW GENETIC TESTING CAN HELP Single Nucleotide Polymorphism (SNP) A change in a single nucleotide in DNA Creates two different alleles A or B Three different genotypes AA, AB, or BB Related individuals will have similar genetic makeup

16. GENETIC TESTING Swine 60k SNP chip Genotypes at over 60,000 sites Genotypes codes as A, H, or B In matrix form, SNP data can be used to measure the levels of hetero- and homozygosity

17. SNP DATA ALGA09ALGA460ALGA376ALGA047ALGA087ALGA300ALGA370ALGA131ALGA133 Setty's MC Wart Side Sow BBAABBBAA Setty's MC Big Old Stiff Boar BBAABBBAA Houdini BBHAHHHAH DNC Seymour Sample A BBAAHBBAH Rose DNC BBAAHBBAA DNC Junior BBAABBBAH Setty Lilly BBAABBBAA DNC Seymour Sample B BBAAHBBAH Samson BHAAABHAA Killian BBAABBBAA Barnett BBAAHBBAA

18. Relationships Count of similar homozygous alleles – Higher number of similar alleles between two individuals, indicates closer relationship Expressed as a proportion or percentage

19. PROPORTION OF SIMILAR ALLELES Setty's MC Wart Side Sow Setty's MC Big Old Stiff BoarHoudini DNC Seymour Sample A Rose DNC DNC Junior Setty Lilly DNC Seymo ur Sample BSamsonKillianBarnett Setty's MC Wart Side Sow 74.462.143.643.046.048.859.142.728.950.156.8 Setty's MC Big Old Stiff Boar 62.174.844.740.745.046.959.940.429.651.653.8 Houdini 43.644.776.143.457.340.447.243.127.849.647.1 DNC Seymour Sample A 43.040.743.476.646.157.243.575.929.251.648.8 Rose DNC 46.045.057.346.171.841.845.945.730.249.246.9 DNC Junior 48.846.940.457.241.868.747.656.830.250.347.6 Setty Lilly 59.159.947.243.545.947.673.043.227.851.055.2 DNC Seymour Sample B 42.740.443.175.945.756.843.276.129.151.248.5 Samson 28.929.627.829.230.2 27.829.154.229.728.9 Killian 50.151.649.651.649.250.351.051.229.770.047.5 Barnett 56.853.847.148.846.947.655.248.528.947.572.9

20. GROUPING INTO FAMILIES Order by shared number of alleles Rough estimate of close families This method does not give precise levels of relatedness

21. FAMILIES Family 1Family 3Family 5 SamsonKillianRose DNC Houdini Family 2Family 4 Setty's MC Wart Side SowDNC Seymour Setty's MC Big Old Stiff BoarDNC Junior Setty Lilly Barnett

22. CALCULATING THE RELATIONSHIPS Sampling of pigs with known relationships Calculate both pedigree relationships and number of shared genotypes

23. RELATIONSHIP MATRIX Plug count of homozygous alleles into regression formula to get relationships for Guinea hogs A relationship of 0.5 between two animals is equivalent to a sibling or parent-offspring relationship

24. GUINEA HOG RELATIONSHIP MATRIX Setty's MC Wart Side Sow Setty's MC Big Old BoarHoudini DNC Seymour Sample A Rose DNC DNC Junior Setty Lilly DNC Seymour Sample BSamsonKillianBarnett Setty's MC Wart Side Sow 0.8870.3860.3720.4520.5280.8070.364-0.0110.5640.743 Setty's MC Big Old Boar0.887 0.4180.3100.4240.4780.8280.3020.0080.6020.662 Houdini0.3860.418 0.3830.7580.3000.4850.374-0.0390.5500.482 DNC Seymour Sample A0.3720.3100.383 0.4540.7560.3841.2600.0000.6020.528 Rose DNC0.4520.4240.7580.454 0.3400.4500.4450.0260.5390.477 DNC Junior0.5280.4780.3000.7560.340 0.4950.7440.0250.5690.497 Setty Lilly0.8070.8280.4850.3840.4500.495 0.378-0.0400.5880.702 DNC Seymour Sample B0.3640.3020.3741.2600.4450.7440.378 -0.0040.5930.521 Samson-0.0110.008-0.0390.0000.0260.025-0.040-0.004 0.012-0.009 Killian0.5640.6020.5500.6020.5390.5690.5880.5930.012 0.493 Barnett0.7430.6620.4820.5280.4770.4970.7020.521-0.0090.493

25. PARTIAL PEDIGREE AnimalSireDam DNC GeorgeBiggers ArthurCelesky's Tulip DNC ChunkyBiggers ArthurSetty Rose Setty's MC Big Old Stiff BoarDNC GeorgeDNC Chunky Setty's MC Wart Side SowDNC GeorgeDNC Chunky DNC GabriellaSetty HoudiniCelesky's Tulip Brothers CGDNC GeorgeDNC Chunky Brothers GGDNC GeorgeDNC Gabriella Setty LillySetty HoudiniCelesky's Tulip Fall IvyBrothers CGBrothers GG DNC SeymourBiggers ArthurFall Ivy

26. EXAMPLE FAMILY TREE DNC George DNC Chunky Biggers Arthur Celesky’s Tulip Setty Rose Setty’s MC Big Old Stiff Boar Biggers Arthur

27. CALCULATED RELATIONSHIPS FROM PEDIGREE Animal Biggers A Celesk ys DNCGe org SettyR os DNCChu nk SettysBiSettysW a SettyHo u DNCGa bri BroCGBroGGSettyLilFallIvyDNCSey mo BiggersA1.0.5... 0.25.0.3750.6875 Celeskys.10.5..0.25.0.50.250.5 0.3750.1875 DNCGe org0.5 1.0.250.625.0.250.625 0.250.6250.5625 SettyRos...10.50.25....0.1250.0625 DNCChu nk0.5.0.250.510.625.. 0.125.0.3750.4375 SettysBi0.50.250.6250.250.6251.1250.625.0.1250.6250.3750.1250.5 SettysW a0.50.250.6250.250.625 1.125.0.1250.6250.3750.1250.5 SettyHou.......10.5.0.250.50.1250.0625 DNCGa bri.0.50.25..0.125 0.510.1250.6250.50.3750.1875 BroCG0.50.250.6250.250.625.0.1251.1250.3750.1250.750.625 BroGG0.250.50.625.0.1250.375 0.250.6250.3751.1250.3750.750.5 SettyLil.0.50.25..0.125 0.5 0.1250.37510.250.125 FallIvy0.375 0.6250.1250.3750.5 0.1250.3750.75 0.251.18750.7813 DNCSey mo0.68750.18750.56250.06250.43750.5 0.06250.18750.6250.50.1250.78131.1875

28. PEDIGREE VS SNP Setty Rose Setty Big Boar Setty WartSetty Houdini Setty LilyDNC Seymour Setty Rose0.25/.420.25/0.45./0.75./0.450.06/0.45 Setty Big Boar 0.25/0.420.62/0.88./0.420.13/0.830.5/0.30 Setty Wart0.25/0.450.62/0.88./0.390.13/0.810.5/0.36 Setty Houdini./0.75./0.42./0.390.5/0.490.06/0.38 Setty Lily./0.450.13/0.830.13/0.810.5/0.490.13/0.38 DNC Seymour 0.06/0.450.5/0.300.5/0.360.06/0.380.13/0.38 Pedigree Calculation/ SNP Calculation

29. FUTURE WORK Determine relationships in Ossabaw Island and Red Wattle pigs Compare SNP’s across breeds More complete picture of the origin of these breeds Provide information to producers and others interested in conservation of these breeds

31. THANK YOU NCR-SARE ALBC Jeannette Beranger Alison Martin Dr. Tim Safranski Dr. Bill Lamberson Producers Cheryl Fanning Kevin Fall Robert Long Megan Rolf Tasia Taxis

32. QUESTIONS?