1. R.L.Quaas26 Mar. 2004 Meat Animal Research Center Clay Center, NE

2. R.L.Quaas26 Mar. 2004 Meat Animal Research Center Clay Center, NE Validating Genetic Tests for Quantitative Traits Dick Quaas Cornell University

3. R.L.Quaas26 Mar. 2004 Meat Animal Research Center Clay Center, NE QTL Project Team  Dick Q uaas - Cornell  Mark T hallman – MARC  Rohan L uigi Fernando – Iowa State

4. R.L.Quaas26 Mar. 2004 Meat Animal Research Center Clay Center, NE 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

5. R.L.Quaas26 Mar. 2004 Meat Animal Research Center Clay Center, NE Today’s Objectives  NOT to present NBCEC protocol for validation  Has been superceded

6. R.L.Quaas26 Mar. 2004 Meat Animal Research Center Clay Center, NE 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.

7. R.L.Quaas26 Mar. 2004 Meat Animal Research Center Clay Center, NE 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

8. R.L.Quaas26 Mar. 2004 Meat Animal Research Center Clay Center, NE 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

9. R.L.Quaas26 Mar. 2004 Meat Animal Research Center Clay Center, NE 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

10. R.L.Quaas26 Mar. 2004 Meat Animal Research Center Clay Center, NE 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

11. R.L.Quaas26 Mar. 2004 Meat Animal Research Center Clay Center, NE 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

12. R.L.Quaas26 Mar. 2004 Meat Animal Research Center Clay Center, NE 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

13. R.L.Quaas26 Mar. 2004 Meat Animal Research Center Clay Center, NE Analyses  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

14. R.L.Quaas26 Mar. 2004 Meat Animal Research Center Clay Center, NE 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

15. R.L.Quaas26 Mar. 2004 Meat Animal Research Center Clay Center, NE First Analysis  GeneSTAR ® Marbling  “Validate” Genetic Solutions results found in US calf-fed trial  Close to original vision

16. R.L.Quaas26 Mar. 2004 Meat Animal Research Center Clay Center, NE Genotype Genetic Solutions NBCEC 2 star370527 1 star369517 0 star358516 2 vs. 0 star1211 NBCEC vs. Genetic Solutions Marbling Score Least Squares Means

17. R.L.Quaas26 Mar. 2004 Meat Animal Research Center Clay Center, NE mu-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

18. R.L.Quaas26 Mar. 2004 Meat Animal Research Center Clay Center, NE LS Means: 2 Additive Mu-Calpain Genotypes

19. R.L.Quaas26 Mar. 2004 Meat Animal Research Center Clay Center, NE 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.

20. R.L.Quaas26 Mar. 2004 Meat Animal Research Center Clay Center, NE http://sask.usask.ca/~schmutz/meat.html

21. R.L.Quaas26 Mar. 2004 Meat Animal Research Center Clay Center, NE 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

22. R.L.Quaas26 Mar. 2004 Meat Animal Research Center Clay Center, NE 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

23. Combined Breed Analysis + (P<.10)++ (P<.05)+++ (P<.01) Level of Significance Quantitative Trait Locus 1234567891011 Trait SF OTMB REA 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 +++

24. R.L.Quaas26 Mar. 2004 Meat Animal Research Center Clay Center, NE 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

25. R.L.Quaas26 Mar. 2004 Meat Animal Research Center Clay Center, NE 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. R.L.Quaas26 Mar. 2004 Meat Animal Research Center Clay Center, NE 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

27. R.L.Quaas26 Mar. 2004 Meat Animal Research Center Clay Center, NE 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

28. R.L.Quaas26 Mar. 2004 Meat Animal Research Center Clay Center, NE