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 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, x CKR Miss Cezon 044F, Planned Mating gives the following expected EPDs CEWWYWADGMCEMilkStayCWYGMrbAPITI PM Eagle Mr Clean Polled Preference Northstar 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 Cattle 30 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 Marker Position (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 CE5 BW7 WW8 YW9 Mlk8 MCE3 Stay28 Sh Force6 Mrb8 REA4 BF1

Accuracy in Predicting Genetic Merit

ACC = 0.23

Accuracy in Predicting Genetic Merit ACC = 0.40

Accuracy in Predicting Genetic Merit ACC = 0.40

Accuracy in Predicting Genetic Merit ACC = 0.46

Accuracy in Predicting Genetic Merit 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 or 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 completely Do not stack cards until dry Hair cards Must 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 Reach me directly –

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 CEBWWWYWMCEMilkMWWSTAYDocCWYGMarbBFREAShr Increase

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