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DNA Sire Identification PowerPoint PPT Presentation


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DNA Sire Identification. Dick Quaas Cornell University. 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.

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DNA Sire Identification

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DNA Sire Identification

Dick Quaas

Cornell University

Meat Animal Research CenterClay Center, NE


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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


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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


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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


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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


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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


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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


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Exclusions

Meat Animal Research CenterClay Center, NE


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Excluded

Exclusions

Meat Animal Research CenterClay Center, NE


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Excluded

Excluded

Exclusions

Meat Animal Research CenterClay Center, NE


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Exclusions

Meat Animal Research CenterClay Center, NE


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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


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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


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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


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Factors Affecting ID Rate

  • # of potential sires – fewer is better

Meat Animal Research CenterClay Center, NE


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Meat Animal Research CenterClay Center, NE


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Meat Animal Research CenterClay Center, NE


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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


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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


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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


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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


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Meat Animal Research CenterClay Center, NE


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JP’s Sire Matching Program

Meat Animal Research CenterClay Center, NE


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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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Meat Animal Research CenterClay Center, NE


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Meat Animal Research CenterClay Center, NE


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Meat Animal Research CenterClay Center, NE


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Meat Animal Research CenterClay Center, NE


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Value of Dam Genotype ????

Meat Animal Research CenterClay Center, NE


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Meat Animal Research CenterClay Center, NE


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