Genomic testing: where is the greatest value?
Download as PPTX, PDF1 like432 views
The document discusses the economic value of genomic testing in dairy farming, highlighting its potential for improving genetic progress, reproduction, and overall profitability. Key strategies include the use of sexed and conventional semen, selling surplus calves, and optimizing breeding practices. The findings suggest that genomic testing can be beneficial and its value is expected to increase as the industry learns to leverage the technology effectively.
Genomic testing: where is the greatest value?
- 1. Albert De Vries Department of Animal Sciences University of Florida Gainesville, FL 32608 devries@ufl.edu Genomic Testing: Where is the Greatest Economic Value? USDA-NIFA Dairy Genomics Workshop, Okeechobee, FL, December 7, 2016
- 2. Genomic test predicts future performance Must have a plan Plan may be profitable
- 3. Acknowledgments • Dairy farmers • Allied industry • University/USDA colleagues, students • Funding: This work is financially supported by USDA-NIFA AFRI grant award 2013-68004- 20365 titled “Improving Fertility of Dairy Cattle Using Translational Genomics”.
- 4. Outline 1. Genetics 101 2. Genomic testing: where is the value? Avoid inbreeding Sell surplus calves/heifers Use sexed and/or beef semen Genetic progress and culling Better reproduction Optimization What is next? 3. Take home messages
- 5. AGIL meeting with BARC and NEA management, November 5 2014 (5) Paul VanRaden Trait Relative emphasis in USDA index (%) PD$ 1971 MFP$ 1976 NM$ 1994 NM$ 2000 NM$ 2003 NM$ 2006 NM$ 2010 NM$ 2014 Milk 52 27 6 5 0 0 0 -1 Fat 48 46 25 21 22 23 19 22 Protein … 27 43 36 33 23 16 20 Longevity … … 20 14 11 17 22 19 SCS … … –6 –9 –9 –9 –10 –7 Udder … … … 7 7 6 7 8 Feet/Leg … … … 4 4 3 4 3 Body Size … … … –4 –3 –4 –6 –5 Preg Rate … … … … 7 9 11 7 Calving … … … … 4 6 5 5 Heifer CR … … … … … … … 2 Cow CR … … … … … … … 1 Changes in trait selection across time Net Merit (NM$) = USDA genetic selection index 2014 revision: 12 traits Lifetime value of genetic worth ($) compared to cow born in 2010 Variation: $194 standard deviation of true transmitting ability $388 standard deviation of true breeding value
- 6. University of Florida genomic testing Clarifide Plus and Igenity Essential Net Merit 9 calves PTA EBV=2xPTA Worst: $253 $506 Best: $530 $1060 Difference: $227 $554 Best calf is expected to be $554 more profitable than worst calf ($185 per lactation)
- 7. “Identify top genetics IVF/ET sell top genetics” “Identify low genetics sell, or use as ET recipients” No IVF/ET? “Genomic test the heifers, identify the elite individuals and breed those heifers to sexed semen”
- 9. • Genetic progress = genetic variation x selection intensity x √(reliability of test) • Genetic progress per year = genetic progress between generations / generation interval How good the ranking is: • Pedigree info. • Genomic test info. Natural genetic differences How picky we can be Genetic progress 101 Breeders equation
- 10. -300 -200 -100 0 100 200 300 400 500 600 700 0 500 1000 1500 2000 2500 3000 3500 4000 PTAnetmerit($) Age (days) Heifers Cows PTA Net Merit distribution FL farm, 539 heifers, 1058 cows (no genomic testing) Standard deviation PTA ≈ $125 Standard deviation EBV ≈ $250 True genetic variation > Estimated genetic variation
- 11. Dr. Kent Weigel UW (2011)
- 12. True breeding value of selected animals ($) $350 genetic standard deviation Net Merit 10% 30% 50% 70% 90% 10% 194 128 88 55 22 30% 336 222 153 95 37 50% 434 287 197 123 48 70% 514 339 234 145 57 90% 583 385 265 165 65 Animals selected Reliability of test
- 13. How to calculate value of genomic testing? • Try to include all important factors: – Genetic age trend, genetic variation, inseminations, milk production, feed, prices, reproduction, culling, stillbirth, cost of testing, … – Sell surplus worst heifer calves – Not included: inbreeding, bad matings – Reliabilities: 0%, “some”, “a lot” ($0), genomic ($50) • Do math … • Bottom line: profit per milking cow per year – And many other results
- 14. Scenario 1: Only conventional semen reference +$14 +$26 +$15 = $42 - $27 • Only conventional semen • 12% surplus heifer calves sold • “genomic” profit per milking cow per year: $431 reliability
- 15. Scenario 1: Only conventional semen reference +$26 +$47 +$26 = $76 - $50 • Per dairy calf: reliability
- 16. Scenario 2: top 50% heifers sexed semen reference +$22 +$41 +$37 • Top 50% heifers with sexed semen, remainder conventional • 18% surplus heifer calves sold • “genomic” profit per milking cow per year: $449 reliability
- 17. Genetic variation matters sexed semen on top 50% heifers (Scenario 2) EBV (PTA)Standard deviation Reliability
- 18. Sire matters too • Increase in sire PTA to break-even with genomic profit/milking cow per year • Net Merit, $350 breeding value • Top 50% heifers with sexed semen (Scenario 2) +$50 +$20 -$6 Reliability
- 19. Genetic progress and culling • Increase cow cull rate instead of selling surplus heifers?
- 20. Net Merit genetic trends (PTA) https://www.cdcb.us/eval/summary/trend.cfm 2010 – 2014: Sire of cow PTA: $58/year Cow PTA: $47/year Dam of cow PTA: $35/year
- 21. Conclusion culling - genetics • After review of existing work: Increased genetic progress in sires should increase cow cull rates by a few percent at most. But • Selective breeding within the herd, and selection of calves, may capture some additional genetic progress, depending on level of reproduction.
- 22. Pregnancy rate (%) 6,795 Holstein dairy herds Mostly eastern USA November 2016 DairyMetrics, www.drms.org 19.1%
- 23. Source: Overton and Cabrera (2017). Figure 1 Value of increased pregnancy rates ($/cow/year) 6 model studies
- 24. Valuing change in reproduction • Herd budget spreadsheet – …, calves, heifers, cows, milk, feed, repro, culling, insemination, prices, genetics, … • 3 x 2 = 6 policies: – 3: “Traditional”, constant cull rate, no surplus calves – 2: Conventional semen only, sexed semen + genomic testing – Sell surplus calves, vary cull rate (if needed) • Change reproduction: – Vary probability of estrus detection and/or probability of conception for free – Calculate results: …, cull rate, surplus calves, profit, …
- 25. Surplus female dairy calves 6 policies:
- 26. Profit per milking cow per year 6 policies:
- 27. Optimization • Best breeding mix (sexed, conventional, beef) – Increase in pregnancy rate – Increase in crossbred calf price
- 28. Effect of beef price: User • Crossbred calf $225, $300, or $375 (Purebred: $150) • Genetics: traditional or genomic test • Breeding mix: User-defined (sexed, conventional, beef) $225 $300 $375 Profit/milking cow/year
- 29. Effect of beef price: Optimal • Crossbred calf $225, $300, or $375 (Purebred: $150) • Genetics: traditional or genomic test • Breeding mix: Optimal (sexed, conventional, beef) $225 $300 $375 Profit/milking cow/year
- 30. Effect of better repro: User • Pregnancy rate: 14%, 20%, or 28% • Genetics: traditional or genomic test • Breeding mix: User-defined (sexed, conventional, beef) 14% 20% 28% Profit/milking cow/year
- 31. Effect of better repro: Optimal • Pregnancy rate: 14%, 20%, or 28% • Genetics: traditional or genomic test • Breeding mix: Optimal (sexed, conventional, beef) ≈14% ≈20% ≈28% Profit/milking cow/year
- 32. Timing of costs and returns • Pregnancy rate: 28% • Genetics: traditional vs. genomic test • Breeding mix: Optimal (sexed, conventional, beef) • Δ Profit/milking cow/year = $57 (genomic – traditional) Profit/milking cow/year
- 33. What is next? • All shown results preliminary • Many factors, prices play a role • Results on your farm will be different • It is complicated, need professional advice • Best strategies emerging
- 34. Take home messages • Genomic testing is here to stay • Genomic testing of females on the farm can be profitable, maybe • Better reproduction makes testing more profitable • Value of testing will likely increase when we learn how to best use the information devries@ufl.edu
Editor's Notes
- #6: 5
- #10: Genetic progress in selected population vs. population at large Accuracy = sq
- #11: Is it an ok graph?
- #12: Table from Dr. Kent Weigel from the University of Wisconsin (2011) Age of the animal on the left On top, 3 types of genetic information With (genomic) and without (traditional) genomic testing Focus on heifers See how reliability increases