The Value Of Genomic Predictions in Beef Cattle
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What is the value of a genomic prediction? Why should beef producers invest in this technology?
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The Value Of Genomic Predictions in Beef Cattle
- 1. The Value of Genomic Predictions Jared Decker Assistant Professor Beef Genetics Specialist Computational Genomics
- 2. March 2021 Prediction: 3,003,901 (80% CI 2,276,103 to 3,731,699; 95% CI 1,890,830 to 4,116,972) July 2015 Data Decker, J. E. (2015). Agricultural Genomics: Commercial Applications Bring Increased Basic Research Power. PLoS Genetics, 11(11), 3. http://doi.org/10.1371/journal.pgen.1005621
- 3. March 2021 Prediction: 3,405,056 (80% CI 2,765,474 to 4,044,637; 95% CI 2,426,900 to 4,383,211) June 2016 Data
- 4. GE-EPDs
- 7. Messages • Trust and effectiveness of beef breeding strategies and technologies. • Simplicity of using selection indexes and genomic technologies. • The profit and sustainability outcomes of using correct strategies and technologies.
- 9. Major Shift • Gene Tests vs Genomic Prediction • Take all 20,000 genes into account • Validation central to the process Train Validate Use
- 10. Major Shift • Gene Tests vs Genomic Prediction – An effect for each DNA variant is estimated – Animals molecular breeding value is sum of DNA variant effects A B B B A A B B B A A B A A A A B B MBV 2.2 0.1 0.2 -0.1 0 0.1 -0.2 0.8 0.1 0.1 -0.1 0.2 -0.1 0 -0.1 0.2 0.8 0.1 0.1
- 11. Single-Step Pedigree Relationship table uses averages On average, a bull shares 25% of its DNA with its grandsires. Genomic Relationship table uses actual relationships. Bull shares 25.8% of his genes with his paternal grandsire and 15.4% with his maternal grandsire.
- 14. One-Step Genomic-Enhanced EPDs 14 GE- EPD Own Performance Pedigree + Genomic Progeny Performance
- 15. Genomic-Enhanced EPD Products • American Angus Association • American Simmental Association • American Hereford Association • Red Angus Association of America • American Gelbvieh Association • North American Limousin Foundation • American International Charolais Association • Santa Gertrudis Breeders International • The International Brangus Breeders Association • Others in development (Maine-Anjou, Shorthorn, others)
- 16. Commercial Heifer Products • $17 to $40 • Maternal Edge Female Profile • Herd Navigator • Igenity Gold Profile • Igenity Silver Profile • Many others… • If sire has GE-EPDs, parentage often included.
- 17. Implement Genomic Predictions • Sell bulls with GE-EPDs – Increases EPD precision/reliability – Identify genetic differences between flush mates – Reduces risk – Equivalent to 10 to 20 progeny
- 18. Progeny Equivalent Value • Ultrasound technicians charge between $15 and $25 per animal • 6 progeny equivalents x $15-$25 = $90-$150
- 19. Selection Intensity eBEEF.org fact sheet “Decreasing Generation Interval to Increase Genetic Progress” ∆𝐺 = 𝒓 ∗ 𝜎𝑔 ∗ 𝑖 𝑳
- 20. Value of Genetically Superior Commercial Sires van Eenennaam, A. L., van der Werf, J. H. J., & Goddard, M. E. (2011). The value of using DNA markers for beef bull selection in the seedstock sector. Journal of Animal Science, 89(2), 307–320. http://doi.org/10.2527/jas.2010- 3223
- 21. Value of Genomics: Simulation Study • Additional income of genetically superior commercial bulls – $89 to $565 • Additional income of genetically superior seedstock bulls – $5,331 to $27,910 • Total value of genetic improvement from genomic testing – $204 to $1,119 van Eenennaam, A. L., van der Werf, J. H. J., & Goddard, M. E. (2011). The value of using DNA markers for beef bull selection in the seedstock sector. Journal of Animal Science, 89(2), 307–320. http://doi.org/10.2527/jas.2010-3223
- 22. Jack Ward: Hereford Genetic Summit $5,325 $7,475 $0 $1,000 $2,000 $3,000 $4,000 $5,000 $6,000 $7,000 $8,000 Traditional GE-EPD Spring 2014 Sales Data
- 23. The Missouri SHOW-ME-SELECT™ Replacement Heifer Program
- 24. The SHOW-ME-SELECT™ Program for more information Google “Show-Me-Select Replacement Heifers” PBS Affiliates Friday, June 6, 2014 www.MarketToMarket.org “Better Beef Prices Through Improved Animal Husbandry"
- 25. Show-Me-Select Service Sires • Proven AI Sire • Natural Service Sire
- 26. Show-Me-Select Service Sires • Proven AI Sire • Natural Service Sire • Genomic Enhanced Sire – Value of increased reliability
- 28. Premiums for heifers with various classifications Tier Pregnancy Show- Me-Plus Count Median Price Mean Price Premium/ Discount Genomic Prediction Premium Tier I Natural Service No 66 2250 2223 Base Tier I Natural Service Yes 3 2700 2683 460.61 460.61 Tier I Mix No 3 2200 2133 -89.39 Tier I AI No 76 2350 2354 130.89 Tier I AI Yes 20 2538 2696 473.52 342.63 Tier II Natural Service No 3 2100 2100 -122.73 Tier II Mix No 1 2400 2400 177.27 Tier II AI No 4 2550 2538 314.77 Tier II AI Yes 10 2500 2598 374.77 60.00 Show-Me-Select™ Show-Me-Plus heifers have been tested with a heifer genomic prediction panel, including commercial heifer tests or breed association GE-EPDs. See http://agebb.missouri.edu/select/prgmreq.htm for more information.
- 29. Predicted premiums for heifers with various classifications, based on mixed model analysis of 2014 and 2015 sale reports. Genomic ROI: Early Returns Suggest Premium for Show-Me-Plus Heifers http://blog.steakgenomics.org/2016/02/genomic-roi-early-returns-suggest.html See http://agebb.missouri.edu/select/prgmreq.htm for more information. Classification Premium ROI Artificial Insemination Pregnancy $130 Show-Me-Plus (Genomic Prediction) $204 326% to 700% Premiums for heifers with various classifications
- 31. Local Genetic Adaptation Grant http://blog.steakgenomics.org/2016/05/local-genetic-adaptation-grant.html
- 32. Regions
- 33. Selection between regions If animal is adapted to a region: • It performs well • Produces progeny in that region
- 34. Selection between regions If animal is adapted to a region: • It performs well • Produces progeny in that region If animal is not adapted to a region: • It under performs • Culled, no progeny
- 35. Selection between regions If animal is adapted to a region: • It performs well • Produces progeny in that region If animal is not adapted to a region: • It under performs • Culled, no progeny This selection changes frequency of DNA variants responsible for local adaptation
- 36. Selection between regions • Identify variants associated with differences in many traits • Use multiple methods with significance tests • Utilizes history of cattle in regions across the US – Heat – Cold – Altitude – Humid – Arid – Parasite – Hair Shedding – Immunity – Water Intake – Feed Intake – Others we can’t measure or wouldn’t think to measure
- 37. Region-Specific GE-EPDs and Indexes Gene-by-environment interactions and local adaptation lead to re-ranking of animals between environments Animal WW EPD Milk EPD MW EPD $W Bull A 56 27 25 52 Bull B 49 23 27 42 Environment 1
- 38. Region-Specific GE-EPDs and Indexes Gene-by-environment interactions and local adaptation lead to re-ranking of animals between environments Animal WW EPD Milk EPD MW EPD $W Bull A 56 27 25 52 Bull B 49 23 27 42 Environment 1 Animal WW EPD Milk EPD MW EPD $W Bull A 47 22 21 40 Bull B 48 23 27 43 Environment 2
- 39. http://eBEEF.org A Steak in Genomics http://blog.steakgenomics.org/ https://www.facebook.com/SteakGenomics Thanks!
Editor's Notes
- Holsteins are the genomic selection poster cows! Rate of technology use appears to be increasing!
- How many of you use GE-EPDs? How many of you buy genomic tests? How many of you have never used GE-EPDs?
- “Seedstock producers need to be educators.” MAY NEED TO DELETE THIS SLIDE.
- Cell phone How many of you have cell phones? Who can explain to me how a cell phone works?
- One step genomic prediction used in registered cattle for which we have pedigree information.
- Genomic-enhanced EPDs Combine information from traditional EPDs with genomic predictions The tool (EPDs) that the farmer uses has not changed, just become more accurate
- Genomic-enhanced EPDs Combine information from traditional EPDs with genomic predictions The tool (EPDs) that the farmer uses has not changed, just become more accurate
- Genomic-enhanced EPDs Combine information from traditional EPDs with genomic predictions The tool (EPDs) that the farmer uses has not changed, just become more accurate
- Grey – cow calf sector Black – processing sector Grass feed vs Grain feed. Figure 4. Breakdown of beef industry sector benefits resulting from the use of a genetically superior commercial sire sourced from a seedstock breeding program using performance records in the absence of DNA testing (none), or performance records in addition to intermediate- or high-accuracy DNA test information. Results are reported for indexes developed for terminal or self-replacing (maternal) herds targeting either the domestic Australian market, where steers are finished on pasture (grass), or a high-value market, where steers are finished on concentrate rations in feedlots (feedlot). Breeding objective traits of direct benefit to the processing sector (black) were assumed to be dressing percentage, salable meat percentage, rump fat depth, and marbling score, whereas those of direct benefit to the production sector (gray) were assumed to be sale BW–direct, sale BW–maternal, cow weaning rate, cow survival rate, cow BW, calving ease–direct, and calving ease–maternal. van Eenennaam, A. L., van der Werf, J. H. J., & Goddard, M. E. (2011). The value of using DNA markers for beef bull selection in the seedstock sector. Journal of Animal Science, 89(2), 307–320. http://doi.org/10.2527/jas.2010-3223
- Summary data from the Southeast Missouri Show-Me-Select™ Bred Heifer Sale held at Fruitland Livestock Sales,
- Analyzing data from the Southeast Missouri Show-Me-Select™ Bred Heifer Sale held at Fruitland Livestock Sales, I also assessed the sales price impact of Show-Me-Plus heifer designation. I analyzed data from 2014 and 2015 to remove the effect of reputation purchases for specific consignors. I fit a mixed model of price per HEIFER in which number of heifers per lot and average weight of the heifers were fit as fixed effects and consignor, heifer pregnancy type nested within date, and Show-Me-Plus nested within date were fit as random effects. Including the effect of Show-Me-Plus designation was not statistically significant (p = 0.44). The nested mixed model predicts that in 2015, a Show-Me-Plus heifer received a $154 premium. For comparison, in 2015, AI bred heifers received a predicted $222 premium and Tier II heifers received a $58 premium. Return on investment to the seller.
- Regions from Leighton, Willham, and Berger (1982) Test different methods to assign animals to a regions. Animal born in a region. Animal, sire, and dam born in a region. Animal, parents, and grandparent born in a region.