26 Mar. 2004 Meat Animal Research CenterClay Center, NE

R.L.Quaas

26 Mar. 2004 Meat Animal Research CenterClay Center, NE

R.L.Quaas

Validating Genetic Tests for Quantitative Traits

Validating Genetic Tests for Quantitative Traits

Dick QuaasCornell

University

Dick QuaasCornell

University

26 Mar. 2004 Meat Animal Research CenterClay Center, NE

R.L.Quaas

QTL Project TeamQTL Project Team

Dick Quaas - Cornell

Mark Thallman – MARC

Rohan Luigi Fernando – Iowa State

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QTL Project Team Objectives QTL Project Team Objectives

Develop protocol for validation (or not) of gene

marker or test results with independent (field)

data

Develop & test methods for incorporating

markers into national cattle evaluation

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Today’s ObjectivesToday’s Objectives

NOT to present NBCEC protocol for validation Has been superceded

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BIF Molecular Technology Guidelines Committee Objectives

BIF Molecular Technology Guidelines Committee Objectives

Terminology and nomenclature,

Molecular sampling protocols,

Molecular test validation, and

Best use practices for incorporating molecular

testing into breed improvement programs and

ultimately National Cattle Evaluation.

26 Mar. 2004 Meat Animal Research CenterClay Center, NE

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BIF Molecular Technology Guidelines Committee

BIF Molecular Technology Guidelines Committee

Craig Huffhines - American Hereford Assoc.  Sally Dolezal - American Angus Assoc. Robert Williams - International Charolais Larry Cundiff - USDA Mark Thallman - USDA Mark Allan - USDA Keith Bertrand - UGA Dan Moser - KSU Dick Quaas - Cornell

26 Mar. 2004 Meat Animal Research CenterClay Center, NE

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Today’s ObjectivesToday’s Objectives

NOT to present NBCEC protocol for validation Discuss various studies of gene test data which

might be considered “validation” Share experience, not results

My analyses; input from Thallman & Fernando

Discuss how my notion of validation has changed

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QTL Tests – available & ‘near’QTL Tests – available & ‘near’

Genetic Solutions GeneStar Marbling* – Thyroglobulin promoter GeneStar Tenderness – Calpastatin GeneStar Tenderness II

Calpain 1 (exon 9) & Calpastatin Merial – Quantum Genetics

ingenity LLeptin* (U. Saskatchewan research)

** RLQ Analysis

26 Mar. 2004 Meat Animal Research CenterClay Center, NE

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QTL Tests (continued)QTL Tests (continued)

Frontier Beef Systems TenderGene

mu-Calpaincodon 316 (exon 9) & codon 530 (exon 14)

MARC & NZ research MMI – NCBA – ???

Several microsatellite markers from CMP proj. Bovigen

Ohio State markers

26 Mar. 2004 Meat Animal Research CenterClay Center, NE

R.L.Quaas

NBCEC Taurus dataNBCEC Taurus data

Carcass phenotypes including (WBSF) &

genotypes on Simmental-sired cattle (mostly

commercial Angus dams) Some progeny of Angus & Red Angus sires

(not included in analysis thus far) Some genotypes on Simmental sires Source of data

CMP ASA progeny testing program

26 Mar. 2004 Meat Animal Research CenterClay Center, NE

R.L.Quaas

NBCEC Indicus dataNBCEC Indicus data

King Ranch Santa Gertrudis Carcass phenotypes incl. WBSF Genotyped by both Frontier Beef (GeneSeek)

& Genetic Solutions

ASA Simbrah Calpain genotypes

13 sires226 CMP carcasses with WBSF

26 Mar. 2004 Meat Animal Research CenterClay Center, NE

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AnalysesAnalyses

Mixed Model

Y = Genotype + CG + Sire + e

‘Genotype' includes category for

ungenotyped contemporaries

Sire random: REML estimates of VCs

Fixed Model

Y = Genotype + CG + e

26 Mar. 2004 Meat Animal Research CenterClay Center, NE

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Validation: original viewValidation: original view

Genomic Company ready to market DNA test Data on test “published” in some form

Validation Test companies results/claims with

independent field dataGenotype effectsMode of action

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First AnalysisFirst Analysis

GeneSTAR® Marbling

“Validate” Genetic Solutions results found in US

calf-fed trial

Close to original vision

26 Mar. 2004 Meat Animal Research CenterClay Center, NE

R.L.Quaas

GenotypeGenetic

SolutionsNBCEC

2 star 370 527

1 star 369 517

0 star 358 516

2 vs. 0 star 12 11

NBCEC vs. Genetic SolutionsMarbling Score Least Squares MeansNBCEC vs. Genetic Solutions

Marbling Score Least Squares Means

26 Mar. 2004 Meat Animal Research CenterClay Center, NE

R.L.Quaas

mu-Calpainmu-Calpain

2 SNP in mu-calpain gene (also called calpain 1) SNP316 = exon 9

CC; CG; GG SNP530 = exon 14

AA; AG; GG Compared results to unpublished MARC results

from GPE-7 cattle

26 Mar. 2004 Meat Animal Research CenterClay Center, NE

R.L.Quaas

LS Means: 2 Additive Mu-Calpain Genotypes

LS Means: 2 Additive Mu-Calpain Genotypes

0

1

2

3

4

5

6

7

8

9

10

WB

Sh

ear

Fo

rce

(lb

s.)

316 CG 316 GG316 CC

530

AA

530

AA

530

AA

530

AG

530

AG

530

AG

530

GG

530

GG

530

GG

26 Mar. 2004 Meat Animal Research CenterClay Center, NE

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LeptinLeptin

Press Release Merial and Quantum Genetics, Inc. Sign Global Pact Wednesday July 23, 6:08 pm ET

SASKATOON, Sask., Canada; DULUTH, Ga., ... a Global Marketing Agreement ... provides Merial with exclusive rights to market Quantum's new patent-pending DNA test to determine an animal's leptin genotype, as well as the application of this knowledge.

The leptin protein is ... a major determinant of feed intake and energy balance in beef and dairy cattle. The test helps to

determine an animal's genetic propensity to "marble", ... helps

to determine an animal's genetic propensity for increased milk production.

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http://sask.usask.ca/~schmutz/meat.htmlhttp://sask.usask.ca/~schmutz/meat.html

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DGAT1DGAT1

Dairy cattle well documented for dairy production traits

Beef Cattle Thaller et al. (2003): K232A polymorphism of

DGAT1 has a significant effect on IMF. lysine polymorphism increases IMF in the

semitendinosus30 German Holsteins

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Types of TestsTypes of Tests

Previous (except for DGAT1 which is a DNP) SNPs in or close to a gene Probably not causal mutations

Very tightly linked marker

Next: Carcass Merit Project Microsatellites

Purely linked-markers

Combined Breed Analysis

+ (P<.10) ++ (P<.05) +++ (P<.01)

Level of Significance Quantitative Trait Locus

1 2 3 4 5 6 7 8 9 10 11Trait SF SF SF SF SF SF OT MB MB MB REAShear Force (SF) +++ ++Overall Tend.(OT) ++ ++Myofibrilar Tend. + ++Conn. Tiss. Tend. +++ +Juiciness + +++ ++ +Flavor + +Marbling (MB) +++Ribeye Area (REA) + ++ ++ +Fat Thick +++ ++Hot Carc Wt +++ +++KPH Fat + ++Yield Grade ++ +

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A Priori InformationA Priori Information

Can validate Estimates

From Genomics CoFrom research organization

Can follow up Reports of significant effects Qualitative statements of effects Qualitative statements of possible effects

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Real ValidationReal Validation

Statistical power Large nos. of animals

Multiple breeds Allele frequencies Breed differences in effects

Effects on as many other traits as available Additivity/Dominance Epistasis Duplicate samples for repeatability of test

26 Mar. 2004 Meat Animal Research CenterClay Center, NE

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Real WorldReal World

Few $$ for validation Phenotypes & DNA from breed associations

or breedersWBSF … limits data source

Genotypes from genomics company Consequences

Not many breeds ~300-400 genotyped carcasses Lack of power

26 Mar. 2004 Meat Animal Research CenterClay Center, NE

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Real WorldReal World

Lack of power Greatly exacerbated by unequal allele freq

Eg., one homozygote represented by a single carcass in DGAT1 sample of 271

Other traitsThallman suggests testing with very

stringent criterionMy concern that any ‘positive’ result will

appear in an ad

26 Mar. 2004 Meat Animal Research CenterClay Center, NE

R.L.Quaas