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Genomics
Finding True Genetic Merit
2
Dam EPD Sire EPD
Pedigree Estimate
EPD
TRUE Progeny
Difference
Mendelian Sampling
Effect
Adapted from Dr. Bob Weaber
Consider 3 Bulls
+3
-3
-4
+4
+5
+5
-2
+2
+3
-3
+4
+4
-5
-5
-2
-2
+3
+3
-4
-4
+5
-5
+2
+2
EPD= 5
EPD= -3
EPD= 1
Below-average bulls will have some above-average alleles and vice versa!Slide courtesy of Dr. Dorian Garrick
Full Sibling Simmental Example
• Four flush mates from 1976• Abricot, 0058311 x CKR Miss Cezon 044F, 0171845• Planned Mating gives the following expected EPDs
CE WW YW ADG MCE Milk Stay CW YG Mrb API TI
PM 0.1 50.15 64.5 0.09 4 25.0 2.00 14.2 -0.24 -0.11 48.9 48.5
Eagle 4.1 47.8 66.6 0.12 11.3 27.3 7.9 14.1 -0.25 -0.10 68.6 50.4
Mr Clean 1.6 65.0 87.0 0.14 2.4 16.4 7.4 30.8 -0.16 0.04 71.3 57.7
Polled Preference 3.7 43.5 50.5 0.04 1.3 18.2 -3.0 3.0 -0.27 -0.09 44.6 47.2
Northstar -3.0 43.4 56.3 0.08 8.3 25.0 -7.1 9.5 -0.25 -0.1 24.9 44.0
It took time and lots of data to achieve high accuracy EPDs
DNA Testing
What is it?
Why do it?
Who to test?
How to test?
When to test?
DNA in Cattle30 pairs of chromosomes in the nucleus of the cell.
Nucleotide = Building block
Adenine (A), Guanine (G), Thymine (T), Cytosine (C)
3 Billion Nucleotides (DNA)
Sequence of these nucleotides key to genetic variation
Bull A…ATTGACGTCGATAGAGTC...
Bull B…ATTGACTTCGATAGAGTC…
SNP, “snip”
Genome Structure – SNPs everywhere!
Arias et al., BMC Genet. (2009)Bovine Chromosome
Mar
ker
Pos
ition
(cM
)
Horizontal bars are marker locations Affymetrix 9,713 SNP
We use the 30K, 50K, 80K, and now 150K chips
Slide courtesy of Dr. Dorian Garrick
Translating SNPs into Molecular Breeding Value (MBV)
• Training - Acquire 50K SNP genotypes on discovery population– High accuracy, actively used animals
• Look for SNPs that affecting traits of interest– EPDs or phenotypes, independently for each trait
• Final result: Equation that translates SNPs into MBVs• MBVs blended with EPDs to have Genomically-
Enhanced EPDs (GE) • Validated
DNA Testing
What is it?
Why do it?
Who to test?
How to test?
When to test?
What can genomics do for you?
Make better selection decisions with higher accuracy EPDs
(in unproven animals)
Faster genetic change (progress)
Benefits of Genotyping
1. Increase accuracy of EPDs for young (unproven) animals. Trait Progeny
Equivalents
CE 5
BW 7
WW 8
YW 9
Mlk 8
MCE 3
Stay 28
Sh Force 6
Mrb 8
REA 4
BF 1
Accuracy in Predicting Genetic Merit
Pedigree Average
ACC = 0.10 (P)
Accuracy in Predicting Genetic Merit
Pedigree AverageOwn Performance
ACC = 0.23
Accuracy in Predicting Genetic Merit
Pedigree AverageOwn Performance13 Progeny
ACC = 0.40
Accuracy in Predicting Genetic Merit
Pedigree AverageOwn PerformanceMBV
ACC = 0.40
Accuracy in Predicting Genetic Merit
Pedigree AverageOwn PerformanceMBV13 Progeny
ACC = 0.46
Accuracy in Predicting Genetic Merit
Pedigree AverageOwn PerformanceMBV700 Progeny
ACC = 0.99
Benefits of Genotyping
1. Increase accuracy of EPDs for young (unproven) animals.
2. Parentage (5 to 10% of reported parents are wrong)!
– DNA on parents must be on file in order to confirm the parentage
DNA Testing
What is it?
Why do it?
Who to test?
How to test?
When to test?
Who should you test?
• AI sires and donor dams: Required– GGP-HD (High Density: 50K, 80K, 150K)– Maintain training population with high impact animals
• Replacement heifers/cows, bull calves (not considered for AI prospects)– GGP-LD (Low Density: 30K)– Nearly equivalent improvement in the accuracy of
EPDs – What would you pay to progeny test these animals?
DNA Testing
What is it?
Why do it?
Who to test?
How to test?
When to test?
Ordering a Kit
Call 406.587.4531 or email [email protected]
Supply ASA with the following information: ASA registration/on file number *animal must be in
the database to request GGP-HD or GGP-LD Tattoo, sex, sire and dam's registration numbers
Indicate whether a blood blotter or hair collector card needs to be sent. Hair cards are billed an additional $3.00/sample.
Tips: Make collecting DNA samples SOP
Double check the ID/Tattoo with animal when collecting
Remove dirt/manure before collection
Blood cards Let cards dry completelyDo not stack cards until dry
Hair cardsMust contain root bulbs(nucleus)Pencil thickness of hair
DNA Testing
What is it?
Why do it?
Who to test?
How to test?
When to test?
When
• Prior to making your selection decisions
• Takes 3 to 4 weeks for results
• If any problems with parentage, this will take even longer
• DO NOT WAIT UNTIL LAST MINUTE!
Take Home Points• Buys you time• Improve the accuracy of the EPDs
– Time testing so you use these higher accuracy EPDs in your selection decisions!
• Confirm parentage• Does not replace the need to collect actual
measurements• Future methods of using the DNA will be even better at
predicting breeding value• IGS has the largest total number of cattle (16 million) in
beef genetic evaluation. BUT, we are still well under AAA in numbers of genotyped animals and carcass records.
Questions?
American Simmental Assoc. DNA Department• [email protected]• 406-587-4531
• Reach me directly– [email protected]– 573-239-2436
When is DNA Testing Required? GGP-HD
AI Sires, includes in herd use. Donor Dams, even if you're not selling embryos.
Parent Verification(PV) Purchased embryos, owner of ET calf not associated with the
owner of the donor dam. Genetic Defect Testing
All sires and donor dams where TraitTrac shows Population Risk(PR), Carrier in Lineage(CL) or Documented Carrier in Lineage(DL) for any defects ASA currently tracks.
How do we know if MBV are reliable?
• Validation• Acquire 50K SNP genotypes on a population of
animals independent of discovery population• Evaluate how well the MBV predicts genetic merit
from traditional EPDs or phenotypes– Genetic correlation between MBV and the trait
GGP-HD/GGP-LD Report
CE BW WW YW MCE Milk MWW STAY Doc CW YG Marb BF REA Shr
Increase 0.11 0.16 0.13 0.15 0.04 0.05 0.08 0.22 0 0.12 0.09 0.27 0.02 0.16 0.15
Impact on Accuracy--%GV=50%Genetic correlation=0.7
Genomics will not improve the EPD accuracy of a high accuracy bull
Pedigree only
Pedigree and genomic
Slide courtesy of Dr. Dorian Garrick
