1. Quaas, Thallman & Van Eenennaam 20 April 2006 Choctaw, MS Beef Improvement Federation (NBCEC Validation Update) Commercial DNA Tests NBCEC Validations Dick Quaas, Cornell University Mark Thallman, USMARC Alison Van Eenennaam, UC-Davis

2. Quaas, Thallman & Van Eenennaam 20 April 2006 Choctaw, MS Beef Improvement Federation (NBCEC Validation Update) Home Background Sample Populations Marker Assisted Selection Ancillary Results Glossary The purpose of the NBCEC commercial DNA test validation is to independently verify associations between genetic tests and traits as claimed by the commercial genotyping company using phenotypes and DNA from reference cattle populations. The validation process is a partnership of the owners of DNA and phenotypes (e.g., breed associations) and genomics companies, facilitated by the NBCEC Commercial genetic test validations IGENITY TenderGene TM GeneSTAR ® Quality Grade GeneSTAR ® Tenderness www.nbcec.org validation

3. Quaas, Thallman & Van Eenennaam 20 April 2006 Choctaw, MS Beef Improvement Federation (NBCEC Validation Update) Marker Assisted ??? Marker Assisted Selection (MAS) Select Breeding Stock NBCEC validation is for MAS Marker Assisted Management (MAM) Sort cattle for management purposes, e.g., Feedlot cattle  optimal endpoint Feedlot cattle  implant regime NBCEC does not validate MAM tools

4. Quaas, Thallman & Van Eenennaam 20 April 2006 Choctaw, MS Beef Improvement Federation (NBCEC Validation Update) Bovigen Marker Validation: Done GeneSTAR Quality Grade (reported @ ‘05 BIF) TG5 (original GeneSTAR Marbling) + M2 CMP Charolais only (CMP Herefords 99:1 M2 allele freq.) GeneSTAR Tenderness (reported @ ‘05 BIF) T1 = CAST & T2 = CAPN1 316 CMP Charolais & Herefords

5. Quaas, Thallman & Van Eenennaam 20 April 2006 Choctaw, MS Beef Improvement Federation (NBCEC Validation Update) Merial Marker Validation: Done Igenity TenderGENE UoG-Cast1 + CAPN1 316 + CAPN1 4751 CMP Charolais, Red Angus, Brangus & Brahmans

6. Quaas, Thallman & Van Eenennaam 20 April 2006 Choctaw, MS Beef Improvement Federation (NBCEC Validation Update) Bovigen Marker Validation: Near Done GeneSTAR Tenderness T1 = CAST & T2 = CAPN1 316 T3 = CAPN1 4751 & “Tx” CMP Charolais & Herefords + LSU Brahmans CMP Brahmans Tx is almost fixed in (European) Taurus No association in Brahmans; Bovigen will not include in GeneSTAR Tenderness New

7. Quaas, Thallman & Van Eenennaam 20 April 2006 Choctaw, MS Beef Improvement Federation (NBCEC Validation Update) Quality/Fatness Marker Summary Bovigen: GeneSTAR Quality Grade Results Small, nonsignificant effect on marbling Significant effect on % Choice or better Similar findings w/ TG5 in Simm-Angus Conclusion Modestly effective, primarily due to TG5, Stars aren’t equal; TG5 >>>M2

8. Quaas, Thallman & Van Eenennaam 20 April 2006 Choctaw, MS Beef Improvement Federation (NBCEC Validation Update) Quality/Fatness Marker Summary Merial submitted 4 leptin SNP + GHR UASM1, UASM2, exon2fb, A252T Traits analyzed: Carcass wt, REA, Fat thick., YG, Marbling score Results: Leptin SNP not associated with traits; (A252T not polymorphic) GHR associated with REA & YG but favorable allele rare

9. Quaas, Thallman & Van Eenennaam 20 April 2006 Choctaw, MS Beef Improvement Federation (NBCEC Validation Update) Quality/Leanness Marker Summary Merial (leptin SNP) Not for seedstock selection for carcass traits Possibly for “marker assisted management” Results to be included under Ancillary Analyses on website Future leptin studies of other traits, e.g. female fertility

10. Quaas, Thallman & Van Eenennaam 20 April 2006 Choctaw, MS Beef Improvement Federation (NBCEC Validation Update) Tenderness Marker Summary Bovigen & Merial each market 3 tenderness SNP 2 identical calpain SNP: CAPN1 316 & 4751 from MARC 1 calpastatin SNP Bovigen: CAST-T1 (Genetic Solutions) Merial: UoG-CAST1 (U. of Guelph) Current NBCEC Consensus 3-SNP Tenderness Panels are effective & equally so

11. Quaas, Thallman & Van Eenennaam 20 April 2006 Choctaw, MS Beef Improvement Federation (NBCEC Validation Update) Tenderness Marker Summary Calpastatin SNP (UoG-CAST1 or T1) Taurus: 60-90% favorable alleles Brahmans: ~40-60% favorable Calpain 316 (T2) Taurus: ~20 % favorable Brahmans: ~2% favorable Calpain 4751 (T3) Taurus: ~50 % favorable Brahmans: ~5-10% favorable

12. Quaas, Thallman & Van Eenennaam 20 April 2006 Choctaw, MS Beef Improvement Federation (NBCEC Validation Update) Tenderness Marker Summary Current NBCEC Consensus 3-SNP Tenderness Panels are effective & equally so About 2.25 lbs difference between “best” & ”worst” genotypes Should expect.75-1.5 lb. by making herd homozygous depending on breed

13. Quaas, Thallman & Van Eenennaam 20 April 2006 Choctaw, MS Beef Improvement Federation (NBCEC Validation Update) Current Test Conundrum Tenderness: Phenotypes not available for EPDs Tests are effective What’s the economic return? Quality/Yield Grade: Huge economic return Tests are ‘modestly’ effective Ultrasound EPDs available and very effective

14. Quaas, Thallman & Van Eenennaam 20 April 2006 Choctaw, MS Beef Improvement Federation (NBCEC Validation Update) www.nbcec.org (validation tab)