1. DNA Sire Identification Meat Animal Research Center Clay Center, NE
Dick Quaas
Cornell University
26-27 March 2004
Meat Animal Research Center Clay Center, NE

2. Meat Animal Research Center Clay Center, NE
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
26-27 March 2004
Meat Animal Research Center Clay Center, NE

3. Meat Animal Research Center Clay Center, NE
Genetic Basis
Every animal has 2 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)
26-27 March 2004
Meat Animal Research Center Clay 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
26-27 March 2004
Meat Animal Research Center Clay 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
26-27 March 2004
Meat Animal Research Center Clay 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
26-27 March 2004
Meat Animal Research Center Clay 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
26-27 March 2004
Meat Animal Research Center Clay Center, NE

8. Meat Animal Research Center Clay Center, NE
Exclusions
Marker 1
Marker 2
Bull 1
107/117
260/264
Bull 2
117/119
260/260
Bull 3
119/123
266/268
Calf 1
117/123
260/270
Calf 2
107/107
264/268
26-27 March 2004
Meat Animal Research Center Clay Center, NE

9. Meat Animal Research Center Clay Center, NE
Exclusions
Marker 1
Marker 2
Bull 1
107/117
260/264
Bull 2
117/119
260/260
Bull 3
119/123
266/268
Calf 1
117/123
260/270
Calf 2
107/107
264/268
Excluded
26-27 March 2004
Meat Animal Research Center Clay Center, NE

10. Meat Animal Research Center Clay Center, NE
Exclusions
Marker 1
Marker 2
Bull 1
107/117
260/264
Bull 2
107/119
260/260
Bull 3
119/123
266/268
Calf 1
117/123
260/270
Calf 2
107/107
264/268
Excluded
Excluded
26-27 March 2004
Meat Animal Research Center Clay Center, NE

11. Meat Animal Research Center Clay Center, NE
Exclusions
26-27 March 2004
Meat Animal Research Center Clay Center, NE

12. Meat Animal Research Center Clay Center, NE
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
26-27 March 2004
Meat Animal Research Center Clay Center, NE

13. Meat Animal Research Center Clay Center, NE
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
26-27 March 2004
Meat Animal Research Center Clay 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 some markers
Reduces effective # of markers
26-27 March 2004
Meat Animal Research Center Clay Center, NE

15. Factors Affecting ID Rate
# of potential sires – fewer is better
26-27 March 2004
Meat Animal Research Center Clay Center, NE

16. Meat Animal Research Center Clay Center, NE
26-27 March 2004
Meat Animal Research Center Clay Center, NE

17. Meat Animal Research Center Clay Center, NE
26-27 March 2004
Meat Animal Research Center Clay Center, NE

18. Factors Affecting ID Rate
# of potential sires – fewer is better
> ~ 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
26-27 March 2004
Meat Animal Research Center Clay 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
26-27 March 2004
Meat Animal Research Center Clay 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
26-27 March 2004
Meat Animal Research Center Clay Center, NE

21. Factors Affecting ID Rate
Unknown sire(s)
-----Original Message----- From: Bonnie Long Sent: Saturday, July 05, :49 PM To: Dick Quaas We gathered a feral bull today ...
26-27 March 2004
Meat Animal Research Center Clay Center, NE

22. Meat Animal Research Center Clay Center, NE
26-27 March 2004
Meat Animal Research Center Clay Center, NE

23. JP’s Sire Matching Program
26-27 March 2004
Meat Animal Research Center Clay 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)
26-27 March 2004
Meat Animal Research Center Clay Center, NE

25. Meat Animal Research Center Clay Center, NE
26-27 March 2004
Meat Animal Research Center Clay Center, NE

26. Meat Animal Research Center Clay Center, NE
26-27 March 2004
Meat Animal Research Center Clay Center, NE

27. Meat Animal Research Center Clay Center, NE
26-27 March 2004
Meat Animal Research Center Clay Center, NE

28. Meat Animal Research Center Clay Center, NE
26-27 March 2004
Meat Animal Research Center Clay Center, NE

29. Meat Animal Research Center Clay Center, NE
Value of Dam Genotype ????
26-27 March 2004
Meat Animal Research Center Clay Center, NE

30. Meat Animal Research Center Clay Center, NE
26-27 March 2004
Meat Animal Research Center Clay Center, NE