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