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
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
Meat Animal Research Center Clay Center, NE 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) 26-27 March 2004 Meat Animal Research Center Clay Center, NE
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
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
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
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
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
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
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
Meat Animal Research Center Clay Center, NE Exclusions 26-27 March 2004 Meat Animal Research Center Clay Center, NE
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
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
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 26-27 March 2004 Meat Animal Research Center Clay Center, NE
Factors Affecting ID Rate # of potential sires – fewer is better 26-27 March 2004 Meat Animal Research Center Clay Center, NE
Meat Animal Research Center Clay Center, NE 26-27 March 2004 Meat Animal Research Center Clay Center, NE
Meat Animal Research Center Clay Center, NE 26-27 March 2004 Meat Animal Research Center Clay Center, NE
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 26-27 March 2004 Meat Animal Research Center Clay Center, NE
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
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
Factors Affecting ID Rate Unknown sire(s) -----Original Message----- From: Bonnie Long Sent: Saturday, July 05, 2003 6:49 PM To: Dick Quaas We gathered a feral bull today ... 26-27 March 2004 Meat Animal Research Center Clay Center, NE
Meat Animal Research Center Clay Center, NE 26-27 March 2004 Meat Animal Research Center Clay Center, NE
JP’s Sire Matching Program 26-27 March 2004 Meat Animal Research Center Clay Center, NE
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
Meat Animal Research Center Clay Center, NE 26-27 March 2004 Meat Animal Research Center Clay Center, NE
Meat Animal Research Center Clay Center, NE 26-27 March 2004 Meat Animal Research Center Clay Center, NE
Meat Animal Research Center Clay Center, NE 26-27 March 2004 Meat Animal Research Center Clay Center, NE
Meat Animal Research Center Clay Center, NE 26-27 March 2004 Meat Animal Research Center Clay Center, NE
Meat Animal Research Center Clay Center, NE Value of Dam Genotype ???? 26-27 March 2004 Meat Animal Research Center Clay Center, NE
Meat Animal Research Center Clay Center, NE 26-27 March 2004 Meat Animal Research Center Clay Center, NE