Meeting Consumer Demands through Genetic Selection: The NCBA Carcass Merit Project

2. Meeting Consumer Demands through Genetic Selection:The NCBA Carcass Merit Project Dan W. Moser on behalf of the CMP Team

3. Project Team Principal Investigators: Dr. Michael Dikeman, Kansas State University Shear Force Measurement, Sensory Panel Dr. John Pollak, Cornell University Database Management Dr. Dan Moser, Kansas State University Breed Association Liaison Dr. Clare Gill, Texas A&M University DNA Marker Validation Dr. Mark Thallman, US Meat Animal Research Center DNA Marker Validation Dr. Steve Koontz, Colorado State University Economic Analyses

4. Project Team Collaborators: Dr. Tom Holm, MMI Genomics Marker Genotyping/DNA Analyses Project Coordinators (NCBA): Ms. Elizabeth Dressler, NCBA Project Coordinator Dr. Bo Reagan, NCBA Executive Director of Science & Technology

5. Project Team Steering Committee: James Bennett, Virginia Jim Bradford, Iowa Rob Brown, TexasJohn Grande, Montana Kathleen Hawkins, Michigan David Nichols,Iowa

7. CMP Goals • To collect data for calculation of tenderness and other carcass EPD • To validate previously identified genetic markers for tenderness and other carcass traits

8. CMP Procedures • Project began in 1998, completed in 2004 • All US beef breed associations were invited to participate • Costs in the project were shared by the breed associations and the $1 per head beef checkoff

9. Participating Breeds Angus Brahman Brangus Charolais Gelbvieh Hereford Limousin Maine-Anjou Red Angus Salers Shorthorn Simmental Simbrah South Devon

10. CMP Bulls • Each breed selected: • 10 DNA sires • 50 progeny each • 5 sires also had sensory data collected • Additional EPD sires • Number based on registrations • About 25 progeny each

11. CMP Procedures • Cattle were generated or identified by breed associations • Fed in commercial feedlots • DNA sampled at first processing • Associations determined management, days on feed, implants, etc. • Harvested in commercial packing facilities

12. Participating Packers Caldwell Packing (MN) Central Packing (FL) ConAgra Excel Greater Omaha IBP Moyer Packing (PA) Sam Kane (TX) Washington Beef

13. CMP Procedures • Carcass data collected, steaks retrieved • Steaks sent to K-State meats laboratory • Shear steaks were aged 14 days • Sensory panel steaks were frozen after aging

14. CMP Procedures • DNA samples from sires, progeny on feed and carcasses were used to confirm identity and paternity • A significant number of identity and paternity errors were detected

24. CMP Procedures • The project was designed to allow comparison of sires within each breed, but not sires across breeds, or breed means • The average shear force of each breed in this study is as much the result of management as it is genetics

25. Project Results • 7200 progeny of 279 sires measured for shear force • 2400 progeny evaluated by sensory panel • 70 sires generated enough progeny for marker analysis • 2500 progeny used in marker analysis

26. Phenotypic Results • Carcass traits were representative of the industry • 26% of the progeny exceeded 11 lb. for WBSF • 20% were rated less than “slightly tender” by sensory panel • Sire progeny means within a breed varied by 1.90 to 6.62 lb.

27. Genetic Parameters • Shear force is: • Highly heritable in most breeds • Strongly correlated with sensory panel tenderness • The genetic correlation of shear force and marbling is: • Moderate to low, but favorable • Breed dependent?

28. Shear Force EPD • Currently published by: • Simmental • Simbrah • Shorthorn • Hereford • Over 200 sires in all • All breeds have received data

29. Evaluation of Marker Data • Eleven QTL discovered in previous checkoff funded research • Initial evaluation was simple and conducted on an individual sire basis • Significant collaborative efforts by a number of scientists led to a “state of the art” project-wide analysis of these data

30. Evaluation of Genetic Markers 1 2 3 4

31. Marker Evaluation Results • All eleven QTL were evaluated for effects on nine carcass and meat quality traits • Five QTL had highly significant (P < .01) effects on at least one trait • Two other QTL had significant (P < .05) effects on at least one trait

32. QTL 6 • Highly significant for shear force and overall tenderness • Accounts for 12 and 13% of phenotypic variance (VP), respectively • Significant for ribeye area • Accounts for 7% of VP • Significant for shear force and overall tenderness in previous research

33. QTL 7 • Highly significant for ribeye area and carcass weight • Accounts for 7 and 6% of VP, respectively • Significant for juiciness • Accounts for 7% of VP

34. QTL 8 • Highly significant for carcass weight • Accounts for 10% of VP • Significant for shear force, tenderness, ribeye area and flavor • Accounts for 6, 9, 3 and 4% of VP, respectively • Effects among all five traits are favorably correlated

35. QTL 10 • Highly significant for overall tenderness • Accounts for 4% of VP • Significant for juiciness • Accounts for 5% of VP

36. QTL 11 • Highly significant for marbling • Accounts for 8% of VP

37. Other Promising QTL • QTL 4, significant for fat thickness • Accounts for 5% of VP • QTL 5, significant for fat thickness • Accounts for 6% of VP • Significant for fat thickness in previous research

38. QTL Effects by Trait

39. Further Details • Dr. Mark Thallman will lead a discussion of the CMP marker analysis in the Emerging Technologies subcommittee, this afternoon

40. Economic Considerations • USDA Quality Grade does not adequately segregate steaks by level of tenderness • Economic impacts of improving tenderness vary by grade

41. Impact of Tenderness on Retail Price* *Impact of a 10% improvement in tenderness

42. How Can Producers Use These Results? • Use Shear Force EPD in selection • Use of the marker results requires commercialization by a partner company • Commercial tests could be in the form of linked markers (now) and/or direct tests (later)

43. Implementing Marker-Assisted Selection • Collect DNA on sire • Collect DNA and phenotypes on (50?) progeny • Determine markers that have significant effects for that sire • Select future progeny of sire based on marker results • Currently used in dairy and swine

44. QTL Effects by Trait

45. Disadvantages ofLinked Markers • Need some phenotypes on progeny of sire before selection • Only progeny of heterozygous sires are testable • Identify progeny that received favorable allele from sire, but does not identify homozygous favorable animals

46. Direct Tests • Data from CMP and previous research could be useful in further development of these linked QTL into direct tests • Time? • Cost? • Linked markers could be used until direct tests are available

47. Other Benefits of CMP

48. Other Benefits of CMP • Cooperation among breed associations • Raised awareness and visibility of marker-assisted selection • Advancement of statistical approaches to marker analysis

49. Other Benefits of CMP • Multi-breed database of DNA and phenotypes • For validation of genetic tests • For further discovery and development • Quite possibly the greatest benefit of all