DNA Sire Identification

1. DNA Sire Identification Dick Quaas Cornell University Meat Animal Research CenterClay Center, NE

2. Parentage Testing • Pedigree Validation • Putative sire & dam • Yes/No answer • Sire determination: which of several ‘possibles'? • Conclusive answer (almost), e.g., for registration paper • Likelihood of each ‘possible’ is actually the sire Meat Animal Research CenterClay Center, NE

3. Genetic Basis • Every animal has 2 alleles @ each marker • Alleles same = homozygous • Alleles different = heterozygous • Animal’s particular pair of alleles = genotype • Calf gets a copy of : • 1 of sire’s 2 alleles • 1 of dam’s 2 alleles • Calf ‘must’ have at least 1 allele in common with its sire (& dam) Meat Animal Research CenterClay Center, NE

4. Genetic Basis: 1st Example • Sire genotype: 102/112 • Dam genotype: 106/108 • Calf must have 102 or 112 AND 106 or 108 • Possible calf genotypes: • 102/106  102/108 • 112/106 112/106 Meat Animal Research CenterClay Center, NE

5. Genetic Basis: 2nd Example • Calf genotype: 108/112 • Sire genotype: 106/112 • Dam genotype: 112/112 • Both can’t be a parent • 112 came from sire OR dam, not both • Neither could have transmitted the 108 Meat Animal Research CenterClay Center, NE

6. Genetic Basis: Marker Alleles • Current 12 markers are Microsatellites • Chunks of DNA of different lengths • Allele = length of chunk = # of base pairs • Examples (Mule Camp 01HB02 calves) • Marker 1: 107, 117, 119, 123 • Marker 2: 254, 260, 264, 266, 268, 270 • Marker 3: 197, 199, 201, 205, 207, 209 • Missing 203 Meat Animal Research CenterClay Center, NE

7. Genetic Basis: Sire Identification • Cannot prove a bull is the sire • Can eliminate sires • Analogous to testing for dwarfism, homozygous black, homozygous polled, etc. • Can identify carrier sire if we see a dwarf, black, or horned calf • Can only give probability statement about sire not carrying recessive allele Meat Animal Research CenterClay Center, NE

8. Exclusions Meat Animal Research CenterClay Center, NE

9. Excluded Exclusions Meat Animal Research CenterClay Center, NE

10. Excluded Excluded Exclusions Meat Animal Research CenterClay Center, NE

11. Exclusions Meat Animal Research CenterClay Center, NE

12. Multiple Sires • Markers 1-3: Bulls equally likely to be sire • Marker 4: Bull 2 twice as likely • Probability Bull 1 is Sire = 1/3 • Probability Bull 2 is Sire = 2/3 Meat Animal Research CenterClay Center, NE

13. Errors & Consequences • Genotypes not 100% accurate • Most frequent: Heterozygote with similar alleles -- differ by 2 -- read as homozygote of shorter allele • E.g., 107/109 read as 107/107 • Consequence • Likely no match for many calves • Solution: allow for errors • Don’t eliminate with single exclusion Meat Animal Research CenterClay Center, NE

14. Factors Affecting ID Rate • # alleles/markers -- more is better • Composites > PB • Microsatellites > SNPs • # markers -- more is better • 12 is more than enough IF all markers highly polymorphic • Some breeds might have only 1 or 2 alleles @ some markers • Reduces effective # of markers Meat Animal Research CenterClay Center, NE

15. Factors Affecting ID Rate • # of potential sires – fewer is better Meat Animal Research CenterClay Center, NE

16. Meat Animal Research CenterClay Center, NE

17. Meat Animal Research CenterClay Center, NE

18. Factors Affecting ID Rate • # of potential sires – fewer is better • > ~10 ... many calves will have several ‘sires’ identified • Sort bulls that go into breeding pastures • Do NOT put brothers together • Separate bulls with similar genotypes • Software which allocates genotyped bulls to breeding pastures • Dams genotyped -- helps some • Probably not cost effective in a commercial herd Meat Animal Research CenterClay Center, NE

19. Factors Affecting ID Rate • Laboratory precision • Trade-off • Precision • Cost • Bell Ranch: Bulls’ DNA samples run 3 times; calves’ samples just once • Just need enough calves associated with sire for progeny test • Might double cost to get 10% more calves sire-IDed Meat Animal Research CenterClay Center, NE

20. Factors Affecting ID Rate • Unknown sire(s) • Our calculations are most accurate if the sire really is one of the specified bulls Meat Animal Research CenterClay Center, NE

21. Factors Affecting ID Rate • Unknown sire(s) • -----Original Message-----From: Bonnie Long Sent: Saturday, July 05, 2003 6:49 PMTo: Dick QuaasWe gathered a feral bull today ... Meat Animal Research CenterClay Center, NE

22. Meat Animal Research CenterClay Center, NE

23. JP’s Sire Matching Program Meat Animal Research CenterClay Center, NE

24. Results: Mule Camp 01HB02 calves • 4 sires (12 Gene Seek markers) • X0135 • X7087 • X9003 • X9053 • Dams • 1st calf heifers • Genotyped for 5 of the 12 markers • 40 calves (12 markers) Meat Animal Research CenterClay Center, NE

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29. Value of Dam Genotype ???? Meat Animal Research CenterClay Center, NE

30. Meat Animal Research CenterClay Center, NE