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26-27 March 2004 Meat Animal Research CenterClay Center, NE
R.L.Quaas
DNA Sire IdentificationDNA Sire IdentificationDick Quaas
Cornell University
Dick Quaas
Cornell University
26-27 March 2004 Meat Animal Research CenterClay Center, NE
R.L.Quaas
Parentage TestingParentage 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 CenterClay Center, NE
R.L.Quaas
Genetic BasisGenetic 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)
26-27 March 2004 Meat Animal Research CenterClay Center, NE
R.L.Quaas
Genetic Basis: 1st ExampleGenetic 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 CenterClay Center, NE
R.L.Quaas
Genetic Basis: 2nd ExampleGenetic 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 CenterClay Center, NE
R.L.Quaas
Genetic Basis: Marker AllelesGenetic 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 CenterClay Center, NE
R.L.Quaas
Genetic Basis: Sire IdentificationGenetic 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 CenterClay Center, NE
R.L.Quaas
ExclusionsExclusions
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 CenterClay Center, NE
R.L.Quaas
ExclusionsExclusions
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 CenterClay Center, NE
R.L.Quaas
ExclusionsExclusions
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 CenterClay Center, NE
R.L.Quaas
ExclusionsExclusions
A1 A2 A1 A2 A1 A2 A1 A2S x0135 117 119 254 270 201 201 219 237S x7087 117 119 266 268 197 199 -1 -1S x9003 119 123 260 268 201 201 237 237S x9053 107 119 268 268 197 197 213 213C x2013 117 123 260 270 201 201 237 237
bm1824 BM1862Sire or Calf ID
BL1067 BM1706
26-27 March 2004 Meat Animal Research CenterClay Center, NE
R.L.Quaas
Multiple SiresMultiple Sires
A1 A2 A1 A2 A1 A2 A1 A2S x0135 117 119 254 270 201 201 219 237S x9003 119 123 260 268 201 201 237 237C x2013 117 123 260 270 201 201 237 237
bm1824 BM1862Sire or Calf ID
BL1067 BM1706
Markers 1-3: Bulls equally likely to be sireMarker 4:Bull 2 twice as likely
Probability Bull 1 is Sire = 1/3Probability Bull 2 is Sire = 2/3
26-27 March 2004 Meat Animal Research CenterClay Center, NE
R.L.Quaas
Errors & ConsequencesErrors & Consequences
Genotypes not 100% accurate Most frequent: Heterozygote with similar
alleles -- differ by 2 -- read as homozygote of shorter alleleE.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 CenterClay Center, NE
R.L.Quaas
Factors Affecting ID RateFactors 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
polymorphicSome breeds might have only 1 or 2 alleles
@ some markersReduces effective # of markers
26-27 March 2004 Meat Animal Research CenterClay Center, NE
R.L.Quaas
Factors Affecting ID RateFactors Affecting ID Rate
# of potential sires – fewer is better
26-27 March 2004 Meat Animal Research CenterClay Center, NE
R.L.Quaas
26-27 March 2004 Meat Animal Research CenterClay Center, NE
R.L.Quaas
26-27 March 2004 Meat Animal Research CenterClay Center, NE
R.L.Quaas
Factors Affecting ID RateFactors 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 togetherSeparate 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 CenterClay Center, NE
R.L.Quaas
Factors Affecting ID RateFactors Affecting ID Rate
Laboratory precision Trade-off
PrecisionCost
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 CenterClay Center, NE
R.L.Quaas
Factors Affecting ID RateFactors 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 CenterClay Center, NE
R.L.Quaas
Factors Affecting ID RateFactors Affecting ID Rate
Unknown sire(s) -----Original Message-----
From: Bonnie Long Sent: Saturday, July 05, 2003 6:49 PMTo: Dick Quaas
We gathered a feral bull today ...
26-27 March 2004 Meat Animal Research CenterClay Center, NE
R.L.Quaas
26-27 March 2004 Meat Animal Research CenterClay Center, NE
R.L.Quaas
JP’s Sire Matching ProgramJP’s Sire Matching Program
26-27 March 2004 Meat Animal Research CenterClay Center, NE
R.L.Quaas
Results: Mule Camp 01HB02 calvesResults: 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 CenterClay Center, NE
R.L.Quaas
Group01HB02 135 7097 9053 9053 min 135 7097 9053 9053 ???
200020012002200320142016201820192029203220332034203721042110
Exclusions Probabilities
26-27 March 2004 Meat Animal Research CenterClay Center, NE
R.L.Quaas
Group01HB02 135 7097 9053 9053 min 135 7097 9053 9053 ???
2000 4 2 3 1 12001 4 2 5 2 22002 5 5 4 3 32003 6 1 4 4 12014 7 2 4 3 22016 5 0 3 3 02018 4 2 3 2 22019 6 2 3 5 22029 7 5 5 1 12032 1 2 1 4 12033 3 2 3 4 22034 6 5 4 2 22037 7 3 4 0 02104 5 1 5 2 12110 2 1 1 2 1
Exclusions Probabilities
26-27 March 2004 Meat Animal Research CenterClay Center, NE
R.L.Quaas
Group01HB02 135 7097 9053 9053 min 135 7097 9053 9053 ???
2000 4 2 3 1 12001 4 2 5 2 22002 5 5 4 3 32003 6 1 4 4 12014 7 2 4 3 22016 5 0 3 3 02018 4 2 3 2 22019 6 2 3 5 22029 7 5 5 1 12032 1 2 1 4 12033 3 2 3 4 22034 6 5 4 2 22037 7 3 4 0 02104 5 1 5 2 12110 2 1 1 2 1
2 3 7 3 15
Exclusions Probabilities
26-27 March 2004 Meat Animal Research CenterClay Center, NE
R.L.Quaas
Group01HB02 135 7097 9053 9053 min 135 7097 9053 9053 ???
2000 4 2 3 1 1 0 6 0 90 42001 4 2 5 2 2 0 53 0 26 212002 5 5 4 3 3 0 0 1 24 752003 6 1 4 4 1 0 97 0 0 32014 7 2 4 3 2 0 76 0 3 212016 5 0 3 3 0 0 100 0 0 02018 4 2 3 2 2 0 52 0 27 212019 6 2 3 5 2 0 79 0 0 212029 7 5 5 1 1 0 0 0 97 32032 1 2 1 4 1 80 8 9 0 32033 3 2 3 4 2 0 79 0 0 212034 6 5 4 2 2 0 0 0 79 212037 7 3 4 0 0 0 0 0 100 02104 5 1 5 2 1 0 94 0 2 42110 2 1 1 2 1 1 73 12 4 10
2 3 7 3 15 4.8 13.6 8.2 10.2 3.3
Exclusions Probabilities
26-27 March 2004 Meat Animal Research CenterClay Center, NE
R.L.Quaas
Value of Dam Genotype ????Value of Dam Genotype ????
calf 135 7087 9003 9053 Minimum 135 7087 9003 9053 ???2000 4 2 3 1 1 0 6 0 90 4
2 2 2 1 1 5 11 1 80 4
2032 1 2 1 4 1 80 8 9 0 31 2 1 4 1 42 24 31 0 3
2033 3 2 3 4 2 0 79 0 0 212 2 1 4 1 6 47 44 0 3
With 2 3 7 3 15 4.8 13.6 8.2 10.2 3.3W/O 3 4 7 3 17 4.5 13.6 8.8 10.6 2.5
Exclusions Probability Bull is Sire
26-27 March 2004 Meat Animal Research CenterClay Center, NE
R.L.Quaas