26 Mar. 2004
Meat Animal Research Center
Clay Center, NE
R.L.Quaas
Validating Genetic Tests
for Quantitative Traits
Dick Quaas
Cornell
University
26 Mar. 2004
Meat Animal Research Center
Clay Center, NE
R.L.Quaas
QTL Project Team

Dick Quaas - Cornell

Mark Thallman – MARC

Rohan Luigi Fernando – Iowa State
26 Mar. 2004
Meat Animal Research Center
Clay Center, NE
R.L.Quaas
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
26 Mar. 2004
Meat Animal Research Center
Clay Center, NE
R.L.Quaas
Today’s Objectives

NOT to present NBCEC protocol for validation

Has been superceded
26 Mar. 2004
Meat Animal Research Center
Clay Center, NE
R.L.Quaas
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 Center
Clay Center, NE
R.L.Quaas
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 Center
Clay Center, NE
R.L.Quaas
Today’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
26 Mar. 2004
Meat Animal Research Center
Clay Center, NE
R.L.Quaas
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 L
 Leptin* (U. Saskatchewan research)

* RLQ Analysis
26 Mar. 2004
Meat Animal Research Center
Clay Center, NE
R.L.Quaas
QTL Tests (continued)

Frontier Beef Systems
 TenderGene
 mu-Calpain
 codon
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 Center
Clay Center, NE
R.L.Quaas
NBCEC 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 Center
Clay Center, NE
R.L.Quaas
NBCEC Indicus data

King Ranch Santa Gertrudis
 Carcass phenotypes incl. WBSF
 Genotyped by both Frontier Beef (GeneSeek)
& Genetic Solutions

ASA Simbrah
 Calpain genotypes
 13 sires
 226 CMP carcasses with WBSF
26 Mar. 2004
Meat Animal Research Center
Clay Center, NE
R.L.Quaas
Analyses

Mixed Model
Y
= Genotype + CG + Sire + e
 ‘Genotype'
includes category for
ungenotyped contemporaries
 Sire

random: REML estimates of VCs
Fixed Model
Y
26 Mar. 2004
= Genotype + CG + e
Meat Animal Research Center
Clay Center, NE
R.L.Quaas
Validation: original view

Genomic Company ready to market DNA test
 Data

on test “published” in some form
Validation
 Test companies results/claims with
independent field data
 Genotype effects
 Mode of action
26 Mar. 2004
Meat Animal Research Center
Clay Center, NE
R.L.Quaas
First Analysis

GeneSTAR® Marbling

“Validate” Genetic Solutions results found in US
calf-fed trial

Close to original vision
26 Mar. 2004
Meat Animal Research Center
Clay Center, NE
R.L.Quaas
NBCEC vs. Genetic Solutions
Marbling Score Least Squares Means
Genotype
Genetic
Solutions
NBCEC
2 star
370
527
1 star
369
517
0 star
358
516
2 vs. 0 star
12
11
26 Mar. 2004
Meat Animal Research Center
Clay Center, NE
R.L.Quaas
mu-Calpain

2 SNP in mu-calpain gene (also called calpain 1)
 SNP316

CC; CG; GG
 SNP530


= exon 9
= exon 14
AA; AG; GG
Compared results to unpublished MARC results
from GPE-7 cattle
26 Mar. 2004
Meat Animal Research Center
Clay Center, NE
R.L.Quaas
LS Means: 2 Additive Mu-Calpain
Genotypes
530 GG
530 AG
530 AA
530 GG
530 AG
530 GG
7
530 AG
WB Shear Force (lbs.)
8
530 AA
9
530 AA
10
6
5
4
3
2
1
0
316 CC
26 Mar. 2004
316 CG
Meat Animal Research Center
Clay Center, NE
316 GG
R.L.Quaas
Leptin
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.
26 Mar. 2004
Meat Animal Research Center
Clay Center, NE
R.L.Quaas
http://sask.usask.ca/~schmutz/meat.html
26 Mar. 2004
Meat Animal Research Center
Clay Center, NE
R.L.Quaas
DGAT1

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
semitendinosus
 30 German Holsteins
26 Mar. 2004
Meat Animal Research Center
Clay Center, NE
R.L.Quaas
Types 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
26 Mar. 2004
Meat Animal Research Center
Clay Center, NE
R.L.Quaas
Combined Breed Analysis
Level of Significance
Trait
Shear 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
+ (P<.10)
Quantitative Trait Locus
1 2 3 4 5 6 7 8 9 10 11
SF SF SF SF SF SF OT MB MB MB REA
+++
++
++
++
+
++
+++
+
+
+++ ++
+
+ +
+++
+
++ ++
+
+++
++
+++ +++
+
++
++
+
++ (P<.05)
+++ (P<.01)
A Priori Information

Can validate
 Estimates
 From
Genomics Co
 From research organization
 Can follow up
 Reports of significant effects
 Qualitative statements of effects
 Qualitative statements of possible effects
26 Mar. 2004
Meat Animal Research Center
Clay Center, NE
R.L.Quaas
Real 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 Center
Clay Center, NE
R.L.Quaas
Real World
Few $$ for validation
 Phenotypes & DNA from breed associations
or breeders
 WBSF … limits data source
 Genotypes from genomics company
 Consequences
 Not many breeds
 ~300-400 genotyped carcasses
 Lack of power

26 Mar. 2004
Meat Animal Research Center
Clay Center, NE
R.L.Quaas
Real World

Lack of power
 Greatly
exacerbated by unequal allele freq
 Eg., one homozygote represented by a
single carcass in DGAT1 sample of 271
 Other traits
 Thallman suggests testing with very
stringent criterion
 My concern that any ‘positive’ result will
appear in an ad
26 Mar. 2004
Meat Animal Research Center
Clay Center, NE
R.L.Quaas
26 Mar. 2004
Meat Animal Research Center
Clay Center, NE
R.L.Quaas