Marker Assisted Selection Where, When, and Hownitro.biosci.arizona.edu/Nordicpdf/lecture18.pdf•...
Transcript of Marker Assisted Selection Where, When, and Hownitro.biosci.arizona.edu/Nordicpdf/lecture18.pdf•...
2Lecture 18
IntroductionQuantitative Genetics
– Selection Based on Phenotype and Relatives Information
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3Lecture 18
Introduction• Molecular Genetics
– Direct Selection on the Genotype Via Markers or Candidate Genes
Hans
A Better Mouse Trap
4Lecture 18
Introduction
• Combined (MAS)– Selection Based on
Phenotype, Relatives Information, and Markers
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5Lecture 18
HowLinked Markers
• Marker Assisted– Recombination an Issue– Must use IBD methods
• Single Marker-– Fernando and Grossman (1989)
• Multiple Marker– Goddard (1992), – Meuwissen and Goddard (1996)
• Multi-Marker, Multi-Stage– Xie and Xu (1998)
6Lecture 18
HowCandidate Genes
• Direct Selection on Candidate Genes (group)– Recombination Not an Issue– Selection Index
• Two Trait– Phenotype– Candidate Gene
• Lande and Thompson (1990)
8Lecture 18
Phenotype
Polygenes Candidate gene
Correlated Trait MethodLande and Thompson (1990)
Yp
Yc
ccPp YbYbI +=
11Lecture 18
Phenotype
Polygenes Candidate gene
AlternativeIndependent Trait Method: Gibson (1994)
Yp’ Yc
ccPp YbYbI += ''
14Lecture 18
When Will These Advances Cause
Animal Breeding To Become A Biotechnology Or Will It Just Be
A Passing Fad?Bulfield (1998)
15Lecture 18
Quest of Commercial Breeders
• Maximize Long And Short Term Response For All Traits Of Economic Importance – Selection Intensity– Accuracy Of Selection– Initial Genetic Variation– Effective Population Size
• How Does Molecular Genetic Impact Each of These?
16Lecture 18
Fixation
Loss
IntensityGene Pool
Selection
DriftInbreeding
Accuracy
RelativesSelected
Number Measured
Number Bred
Mutations
17Lecture 18
Selection Intensity• Function of Number of
Animals Tested– Costs and Space Limit
Numbers• Egg Production In The Dam
Line Of Broilers– Multi-stage Selection
• First Stage– Chicks– MAS Selection
• Second Stage– Hens– Phenotypic Selection
18Lecture 18
Lost Selection Intensity• Males In Poultry
Layer Programs– Usually Only One Or
Two Roosters Are Kept From Each Full Sib Family And Those Are Chosen At Random
19Lecture 18
BLUP Cannot Help– Selection Using
Ancestors Information Cannot Distinguish EBV’s Between Full Sibs
– Must Progeny Test: Too Costly
– MAS To The Rescue– Tremendous Increase
in Selection Intensity Within Family
20Lecture 18
Fixation
Loss
IntensityGene Pool
Selection
DriftInbreeding
Accuracy
RelativesSelected
Number Measured
Number Bred
Mutations
MAS
21Lecture 18
Accuracy of Selection• Factors
– Heritability of the Trait – Amount of Information
Available From The Individual And Relatives
• Sex Limited Traits– Egg Production
22Lecture 18
Accuracy of Selection• Cannot Be Measured
Directly In Either Sex – Disease Resistance– Meat Quality– Aspects Of Well-being
Environment of Selection
Environment of Production
23Lecture 18
Fixation
Loss
IntensityGene Pool
Selection
DriftInbreeding
Accuracy
RelativesSelected
Number Measured
Number Bred
Mutations
MAS
24Lecture 18
Initial Genetic Variation• Start With Elite
Populations– Highly Selected
• Favorable Alleles – May Have Been Lost
in Selection Program– Never Had
25Lecture 18
Initial Genetic Variation• Introgression
– MAS• Select Against
Undesirable Background
• Requires Fewer Generations
MAS
26Lecture 18
Fixation
Loss
IntensityGene Pool
Selection
DriftInbreeding
Accuracy
RelativesSelected
Number Measured
Number Bred
Mutations
MAS
27Lecture 18
Complex Issues
• Require Simulations• See Dekkers and Hospital (2002) for Review• Impact of Selecting for Single QTL
– Gibson (1994)– Ruane Colleau (1995, 1996)– Dekkers (1998, 1999)– Meuwissen and Goddard (1996)
29Lecture 18
Due to Polygenic Drag (Dekkers (1998, 1999))
OptimumShort TermWeights
Relative Polygenic ResponseNegative
30Lecture 18
Fixation
Loss
IntensityGene Pool
Selection
DriftInbreeding
Accuracy
RelativesSelected
Number Measured
Number Bred
Mutations
QTLPolygenes
MAS
31Lecture 18
Optimize The Short Term
• Meuwissen and Goddard (1996)– There Will Be a Series of New QTL
Found Sequentially, Concentrate on the Short Term
– Tandem Selection on QTL’s + Phenotype
32Lecture 18
Generation
Where: Additional Response (%) From MAS
Meuwissen and Goddard, 1996
0
20
40
60
80
100
1 2 3 5
Phen BeforePhen After
Sex-limitedCarcass
2459152530
3838 37 31 21
64 62 5539
6 wk wtFertility
Broilers
Egg Production% Fat
39Lecture 18
Fixation
Loss
IntensityGene Pool
Selection
DriftInbreeding
Accuracy
RelativesSelected
Number Measured
Number Bred
Mutations
BLUP
40Lecture 18
What Is the Impact of Genotypic Selection on Rate of Inbreeding, Loss of Genetic Variance, Long Term Response?
• Assume all Alleles at All Loci Are Known• Cannot Fix All Alleles in One Generation• Select on Index of All QTL’s at All Loci
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iiQTLbI ∑
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43Lecture 18
Fixation
Loss
IntensityGene Pool
Selection
DriftInbreeding
Accuracy
RelativesSelected
Number Measured
Number Bred
Mutations
Genotypic
44Lecture 18
Selection Goals Change
“In Real Life Selection Objectives - Especially In An Industry Like
Ours - Change. So Do The Best You Can In The Short Run”
Max Rothschild
45Lecture 18
Changing Selection Goals
Changes Problem From Multi-trait Single Stage to Multi-trait Multi-
Stage (Tandem) Selection Where Traits of Future Stages Are
Unknown
49Lecture 18Loss
Intensity
Gene Pool
DriftInbreeding
Accuracy
RelativesSelected
Mutations
Genotypic
Negatively Correlated Traits
Selection
MAS
50Lecture 18Loss
Gene Pool
DriftInbreeding
Accuracy
RelativesSelected
Mutations
Genotypic
Uncorrelated Traits
51Lecture 18
Optimal Selection Program
• Any Selection Program That Does Not Also Attempt to Minimize Rate of Inbreeding is Suboptimal
• Minimize Mating With Relatives
53Lecture 18
Expand Operation
Increase Selection IntensityMeasure More Animals
Keep Number of Breeders the Same
54Lecture 18
Generation 3
Response of Phenotypic Selection Relative to MAS With Selection Intensity
MAS Better
Phenotypic Better
Additional Proportion Measured
55Lecture 18
Generation 8
Response of Phenotypic Selection Relative to MAS With Selection Intensity
Phenotypic Better
Additional Proportion Measured
57Lecture 18
Lab Problem 1• Each Group Chose A Different Commodity
Group from below.– Fish, Shellfish, Dairy, Beef, Swine, Sheep (wool),
Sheep (meat), Horse, Broiler, Layer, Swine– What are the critical traits for each commodity group?– Subdivide Traits into categories where you feel MAS
will be Highly, Moderate, or Minor effective in improving the trait. Give Reason for putting into each category.