Use of DNA information in Genetic Programs.

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Use of DNA information in Genetic Programs.
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Next Four Seminars

• John Pollak DNA Tests and genetic Evaluations
  and sorting on genotypes.
• John Pollak Parent Identification With DNA
• Rob Templeman Parent Uncertainty Models
• Bob Weaber Application to Commercial Bull
  Evaluations

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Outline

• DNA Information in Genetic Evaluation
• DNA Tests
• Inclusion in Genetic Evaluations
• Commercial Ranch Genetic Evaluations
• Sorting Bulls on DNA Genotyping
• DNA Parent identification

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DNA Tests
One use of DNA test information is to incorporate
that information into genetic evaluation systems.
We view ourselves as the gate keepers to what
information should go into evaluations.
The process of validation is a means to insure
DNA test results going into our genetic
evaluations are reproducible.
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Terminology
Discovery, Validation, Assessment and Application
Discovery Process of identifying QTL
Validation Process of replicating results in
independent data through blind testing
Assessment Process of evaluating the effect of
the QTL in a broader context (other traits and
environments)
Application Process of using the DNA
information in genetic decisions
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DNA Tests for Carcass Merit Traits

• Thyroglobulin
• Calpain (MARC Discovery)
• Calpistatin
• Leptin
• Three QTL from NCBA Carcass Merit Project (genes
  unknown)
• DGAT1

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SNPs in Calpain1 Gene

• CAPN1 gene
• ?-Calpain enzyme ? post-mortem tenderness
• MARC 2 SNP that alter amino acid at positions
  (codons) 316 and 530 of µ-calpain
• Public domain marker
• Genotyping performed as a service by GeneSeek
  Incorporated (Lincoln, NE)

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Calpain Commercial Tests

• Frontier Beef Systems ? Merial
• Igenity TenderGENE
• Calpain codons/SNPs/markers 316 530
• Bovigen Solutions (Genetic Solutions products)
• GeneStar Tenderness II
• Calpain1 (exon 9codon316) Calpastatin
• MMI Genomics
• Calpain codons 316 530

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NBCEC Taurus Data

• 14d post-mortem WBSF measurements on 362 AI-sired
  cattle
• 23 Simmental sires
• Predominately commercial Angus dams
• 19 CG same source, sex, days on feed and
  harvest date

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Initial MARC Results
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Calpain Marker Genotype Counts
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Frequency at SNP 316
f(C allele) .18 f(G allele) .82
Equilibrium Genotype Frequencies CC .032
CG .296 GG .672
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Frequency at SNP 530
f(A allele) .23 f(G allele) .77
Equilibrium Genotype Frequencies AA .053
AG .354 GG .593
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Calpain 2 Additive Genotypes
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Indicus-influenced Cattle

• 297 King Ranch Santa Gertrudis carcasses
• 226 Simbrah carcasses from CMP (10 sires)
• Separate analyses by breed similar results
• Highly significant genotype effect, either
  individually or jointly
• No interaction between SNP316 SNP530
• SNP530 NOT significant after fitting SNP316,
  i.e., SNP 530 provides no additional information
  if you know the SNP316 genotype.

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Indicus-influenced Cattle
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Outline

• DNA Information in Genetic Evaluation
• DNA Tests
• Inclusion in Genetic Evaluations
• Commercial Ranch Genetic Evaluations
• Sorting Bulls on DNA Genotyping
• DNA Parent identification

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Marker Assisted EPDs
The evolution of the use of marker data for
traits where EPDs are available will be to
include that DNA data in genetic evaluation.
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Test Case Marker Assisted EPD

• WBSF measurements
• Calpain genotypes
• Small data set
• Relatively large fraction of WBSF measurements on
  progeny of genotyped sires

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Progeny Genotype vs. Sire Genotype
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Haplotype

• Marker allele make-up of a sperm or egg
• Examples (316 alleles C G, 530 alleles A
  G)
• CCGG ? only CG gametes
• CCGA ? CG CA gametes
• CGGA ? CG, CA, GA GG gametes (without knowing
  phase)

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Marker Assisted EPDs

• EPD
• Expected Haplotype Effect given sire genotype
• Polygenic effect

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EPD data

• SF data in current WBSF sire evaluation
• 1833 WBSF records
• 120 Simmental sires
• 93 Contemporary Groups
• Genotypes (only sires used in EPD analysis)
• 1/2 of sires were genotyped
• 2/3 of animals had genotyped sire

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ASA Simmental Sire Genotype
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WBSF EPD vs MA-EPD
Genotype
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WBSF EPD vs MA-EPD
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Outline

• DNA Information in Genetic Evaluation
• DNA Tests
• Inclusion in Genetic Evaluations
• Commercial Ranch Genetic Evaluations
• Sorting Bulls on DNA Genotyping
• DNA Parent identification

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Progeny Testing Commercial Bulls
The commercial ranch project centers on the
progeny test of yearling bulls brought into a
commercial ranch each year.
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Economic Genetic Programs
We can treat genetic programs as economic
enterprises with costs and returns.
Process Define current genetic program then
assess changes to that program relative to costs
and returns.
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Progeny Test Costs
Individual identification Data recording Multiple
sire pastures (calf sire identification)
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Progeny Test Revenues
Increased revenue that results from increase
product generated by bull selection.
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Progeny Test Costs
Multiple sire pastures (Tool DNA)
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DNA Panels
Typically use microsatellites Anomalies in the
genome where DNA sequences of two (or more) base
pairs are repeated.
Alleles at the microsatellite loci are the number
of repeats. Example of a genotype at one
microsatellite locus 110/116
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Exclusions
A mismatch between the genotype of the putative
sire and the calf in question.
Sire 110/110
Calf 112/114
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Panel Exclusion Rate
Measure of the effectiveness of a DNA panel to
exclude an animal as a parent.
Probability of excluding as the parent any animal
drawn at random from the population.
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Sire Identification
The probability of uniquely identifying the sire
in a group of N bulls is ( Exclusion rate ) N
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Bull Sorting
We use the DNA genotypes to create the breeding
groups of bulls.
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Create genetically diverse groups. Objective is
to maximize the probability of uniquely
identifying one sire to a calf.
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Sire Sorting
Pasture 1
Pasture 2
Criteria Minimize the probability that both
bulls would qualify as the sire of a calf
produced by either bull.
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Sire Sorting
Pasture 1
N(N-1) 2
Pasture 2
Randomly assign one bull to each pasture.
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Sire Sorting
Pasture 1
110/110
112/114
112/116
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Sire Sorting
Pasture 1
110/110
112/114
112/116
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Sire Sorting
Pasture 1
112/114
112/114
112/116
Not this one
P(not excluded)0.65
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P (Excluded)
P(excluded) 1 - ? P(not excluded)i Across
all marker loci
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Sire Sorting
Produces calf
Pasture 1
112/114
110/110
112/116
P(not excluded)0.5
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Sire Sorting
Pasture 1
Produces calf
112/114
110/110
112/116
P(not excluded)0.4