Use of DNA information in Genetic Programs.

1
Use of DNA information in Genetic Programs.
2
Outline

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

3
DNA Test 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
4
DNA Tests for Carcass Merit Traits

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

5
Marker Assisted EPDs

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

6
Progeny Genotype vs. Sire Genotype
7
(No Transcript)
8
WBSF EPD vs MA-EPD
9
Commercial Ranch Project and the need for using
DNA in sire assignments.
10
Bull Sorting
11
Create genetically diverse groups. Objective is
to maximize the probability of uniquely
identifying one sire to a calf.
12
Outline

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

13
Verification
Verification Verifying that the putative parent
is the real parent.
In the seedstock industry, pedigree integrity is
the primary reason for DNA testing for parent
verification AI sires, ET cows and calves,
random checks.
14
Identification
Identification Identifying a parent from a
group of potential parents (e.g., multiple-sire
breeding pastures).
15
Practical Application
We are currently developing a program for genetic
evaluation for the commercial sector.
A problem is that the large commercial ranches
use multiple-sire pastures so DNA testing for
identification becomes necessary.
16
Perfect World
Begin by assuming that genotypes are scored
without error. Process of excluding bulls.
17
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.
18
Sire Identification
The probability of uniquely identifying the sire
in a group of N bulls is ( Exclusion rate ) N
19
(No Transcript)
20
Multiple Qualifying Sires
Could run more markers (a second panel). If this
was a seedstock problem probably would.
In the commercial program however this is not
cost effective, so we compute the probability
that each qualifying sire is the true sire.
21
Commercial Genetic Evaluation
Using probabilities then requires a system for
genetic evaluation that models sire uncertainty.
Under a sire uncertainty model do not need to
uniquely identify the sire. We will use the
probability associated with each bull of being
the sire.
22
Probabilities
Competing sires
Bull 1 110/110
Bull 2 110/112
Calf 110/114
If Bull 1 P(110) 1
If Bull 2 P(110) 0.5
23
Probabilities
Competing sires
Bull 1 220/222
Bull 2 224/228
Dam genotype 224/224
Calf 220/224
Bull 1 P(220)0.5
Bull 1 P(224)0.5
24
Two Qualifying Bulls
Bull 1 P(locus one) 1.0 P(locus two)
0.5 0.5 of his calves will have the calf genotype
in question.
Locus 1 110/114 Locus 2 220/224
25
Two Qualifying Bulls
Bull 2 P(locus one) 0.5 P(locus two)
0.5 0.25 of his calves will have the calf
genotype in question.
Locus 1 110/114 Locus 2 220/224
26
Two Qualifying Bulls
Bull 1 0.50 Bull 2 0.25 Bull 1 is twice as
likely as bull 2 to be the sire so the
probability of each bull is then Bull 1
2/3 Bull 2 1/3
27
Example Bell Ranch Data
AID Sire Prob Excl
Sire Prob Excl
28
Real World
Scoring genotypes is NOT a process without error.

29
Types of Scoring Errors
Independent of genotype (2-base pair
repeats) Base pair mis-reads (usually two bases
off) More likely in large DNA repeat segments
Dependent of genotype (2-base pair
repeats) Heterozygotes for alleles differing by
two bases are read as a homozygote for the
smaller allele genotype 110/112 gt scored as
110/110
30
Real World
Experience 10 - 15 chance he still qualifies
31
The Phenotypic Representation of a Sire
Identification Problem
Animal Scored Genotype
Animal Genotype
Will use a four allele locus as an example.
32
The Phenotypic Representation of a Sire
Identification Problem
Animal Scored Genotype
Animal Genotype
P(A1) 0.5-E P(A2) 0.5-E P(A3) E P(A4)
E E simple independent error rate
Bull 1 A1/A2
33
Population Frequencies
Possible Alleles 108 (.4) 110 (.3) 112
(.2) 114 (.1)
34
Genotyping Errors
Sire Scored Genotype 108/110
35
Progeny Probabilities
36
Progeny Probabilities
37
The Phenotypic Representation of a Sire
Identification Problem
Animal Scored Genotype
Animal Genotype
P(A1) 0.5-E P(A2) E P(A3) E P(A4)
0.5-E E simple independent error rate
Calf A1/A4
38
Progeny Probabilities
39
Progeny Probabilities
40
Bell Ranch
41
Progeny Exclusions
42
(No Transcript)
43
(No Transcript)