Using DNA on your farm to select more profitable cattle
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EPD basics, genomic prediction, planning for a return on investment in genomics, and new research in local adaptation in cattle.
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Using DNA on your farm to select more profitable cattle
- 1. Using DNA on your farm to select more profitable cattle Jared E. Decker Beef Genetics Specialist
- 5. Phenotypic Selection From www.critterzone.com Does NOT account for environmental differences! Less accurate
- 6. EPDs Defined Expected Future, average, mean Progeny Offspring Difference Implies comparison between animals NOT phenotypic performance 6
- 7. Relatedness Use pedigree or DNA data to estimate relatedness between all animals in data set Separate genetic variation from other sources of variation 7
- 8. EPDs in Practice Weaning Weight EPD = 50 Weaning Weight EPD = 70 Average Weaning Weight = 495 Average Weaning Weight = 515
- 9. DNA technology has changed cattle breeding
- 11. Genetic gain per year estimates from four paths of selection (Four Paths) and segmented regressions of trait PBV on birth year for all cows (All Cows) or the subset of cows registered in the national herdbook (Reg Cows) for six traits (milk, fat, and protein yields; SCS; PL; and DPR). Adriana García-Ruiz et al. PNAS 2016;113:E3995-E4004©2016 by National Academy of Sciences
- 13. Two-Step Genomic-Enhanced EPDs 13 GE-EPD Own Performance Pedigree Genomic Test Result Progeny Performance
- 14. Major Shift Gene Tests vs Genomic Prediction Take all 20,000 genes into account Validation central to the process Train Validate Use
- 15. Genomic Prediction 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
- 16. Single-Step Genomic-Enhanced EPDs 16 GE-EPD Own Performance Pedigree + Genomic Progeny Performance
- 17. 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.
- 18. Pedigree Relationship Matrix Paternal Grandsire Paternal Granddam Maternal Grandsire Maternal Granddam Sire Dam Animal Paternal Grandsire 1 0 0 0 0 0 0.25 Paternal Granddam 0 1 0 0 0 0 0.25 Maternal Grandsire 0 0 1 0 0 0 0.25 Maternal Granddam 0 0 0 1 0 0 0.25 Sire 0 0 0 0 1 0 0.5 Dam 0 0 0 0 0 1 0.5 Animal 0.25 0.25 0.25 0.25 0.5 0.5 1
- 19. Genomic Relationship Matrix Paternal Grandsire Paternal Granddam Maternal Grandsire Maternal Granddam Sire Dam Animal Paternal Grandsire 1 0 0.17 0 0 0 0.20 Paternal Granddam 0 1 0 0 0 0 0.30 Maternal Grandsire 0.17 0 1 0 0 0 0.33 Maternal Granddam 0 0 0 1 0 0 0.17 Sire 0 0 0 0 1 0.11 0.5 Dam 0 0 0 0 0.11 1 0.5 Animal 0.20 0.30 0.33 0.17 0.5 0.5 1.07
- 20. Pedigree Matrix
- 21. Pedigree and Genomic Matrix
- 22. Implement Genomic Predictions BUY BULLS WITH GE-EPDS • Increases EPD precision/reliability • Identify genetic differences between flush mates • Equivalent to 10 to 20 progeny • Reduces risk
- 23. Heifer Genomic Predictions • Have to use the information to see return on investment! • Test many more heifers than you plan to keep • Genomics provides additional information for ranking • Increased precision of genomics re-ranks heifers
- 24. Pick the right test! If testing a registered animal, use the breed association’s genomic prediction to produce GE-EPDs! If testing commercial straightbred cattle, if a breed specific test is available, USE IT! Breed-specific test is going to outperform multiple-breed test
- 28. Ask Questions Approximately how many DNA markers are included in the test? If it is a quantitative or complex trait, most likely, the more the better. Fewer than several hundred DNA markers, buyer beware
- 29. Ask Questions Jared Decker 573-882-2504 DeckerJE@missouri.edu Extension Livestock Specialists Breed Association Field Reps
- 31. Selection Intensity eBEEF.org fact sheet “Decreasing Generation Interval to Increase Genetic Progress” ∆𝐺 = 𝒓 ∗ 𝜎𝑔 ∗ 𝑖 𝑳
- 32. Progeny Equivalent Value Ultrasound technicians charge between $15 and $25 per animal 6 progeny equivalents x $15 to $25 = $90 to $150
- 33. Mike MacNeil at BIF Value of genomics ranged from $159 to $169 based on breeding objective
- 34. 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
- 35. 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
- 36. Get Paid For What They Are Worth Average of heifer crop = Average of steer crop
- 37. The Missouri SHOW-ME-SELECT™ Replacement Heifer Program
- 39. 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.
- 40. 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
- 41. Select on Genetics Reliable EPDs for Young Animals Match Cattle to Environment
- 42. USDA Grant Identifying Local Adaptation And Creating Region-Specific Genomic Predictions In Beef Cattle http://blog.steakgenomics.org/2016/05/local- genetic-adaptation-grant.html Producers invited to participate in research to identify cows that match their environment http://blog.steakgenomics.org/2016/04/producer s-invited-to-participate-in.html
- 43. 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
- 44. 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
- 45. Hair Score 5 Hair Score 4 Hair Score 3 Hair Score 2 Hair Score 1 Fact Sheet: Hair shedding scores: A tool to select heat tolerant cattle
- 46. Did She Stay or Did She Go? EPD T-statistic P-value Birth Weight 4.29 <.0001 Milk -5.37 <.0001 Fat Thickness -3.69 0.0002 Calving Ease Direct -3.49 0.0005 Teat Size -3.44 0.0006 Calving Ease Maternal -3.35 0.0008 Udder Attachment -3.15 0.0017 Milk+Gain -2.93 0.0035 Mature Cow Weight 2.5 0.0128 Weaning Weight 1.52 0.1277 Yearling Weight 1.3 0.1938 Carcass Weight 1.04 0.2974 Marbling -0.87 0.3873 Scrotal Circumference 0.45 0.6522 Ribeye Area 0.16 0.876 VERY Preliminary DataMichael MacNeil
- 48. http://eBEEF.org A Steak in Genomics http://blog.steakgenomics.org/ https://www.facebook.com/SteakGenomics Thanks!
Editor's Notes
- 2/25/2017
- Genetic gain per year estimates from four paths of selection (Four Paths) and segmented regressions of trait PBV on birth year for all cows (All Cows) or the subset of cows registered in the national herdbook (Reg Cows) for six traits (milk, fat, and protein yields; SCS; PL; and DPR).
- 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
- One step genomic prediction used in registered cattle for which we have pedigree information.
- Genomic selection, like all tools, has certain short comings. Genomic Selection works well if designed in one breed and used in the same breed. Does not work well if it is designed in one breed and used in a different breed.
- Genomic selection, like all tools, has certain short comings. Genomic Selection works well if designed in one breed and used in the same breed. Does not work well if it is designed in one breed and used in a different breed.
- If we design in both breeds and use in both breeds and their crossbreds, it works the same as, but not better than, designing in a single breed.
- 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.