The Value of Genomic Predictions

Jared DeckerAssistant Professor

Beef Genetics SpecialistComputational Genomics

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 DataDecker, 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

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

GE-EPDs

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.

Resources Available

Major Shift• Gene Tests vs Genomic Prediction

• Take all 20,000 genes into account

• Validation central to the process

Train Validate Use

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

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MBV2.2

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

Single-StepPedigree 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.

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Traditional EPDs

EPD

Own Performance

Pedigree

Progeny Performance

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Two-Step Genomic-Enhanced EPDs

GE-EPD

Own Performance

Pedigree Genomic Test Result

Progeny Performance

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One-Step Genomic-Enhanced EPDs

GE-EPD

Own Performance

Pedigree+

Genomic

Progeny Performance

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)

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.

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

Progeny Equivalent Value

• Ultrasound technicians charge between $15 and $25 per animal

• 6 progeny equivalents x $15-$25 = $90-$150

Selection IntensityeBEEF.org fact sheet“Decreasing Generation Interval to Increase Genetic Progress”

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

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

Jack Ward: Hereford Genetic Summit

Traditional GE-EPD$0 $1,000 $2,000 $3,000 $4,000 $5,000 $6,000 $7,000 $8,000

$5,325

$7,475

Spring 2014 Sales Data

The Missouri SHOW-ME-SELECT™

Replacement Heifer Program

The SHOW-ME-SELECT™ Programfor more information

Google “Show-Me-Select Replacement Heifers”

PBS Affiliates Friday, June 6, 2014 www.MarketToMarket.org “Better Beef Prices Through Improved Animal

Husbandry"

Show-Me-SelectService Sires

• Proven AI Sire• Natural Service Sire

Show-Me-SelectService Sires

• Proven AI Sire• Natural Service Sire• Genomic Enhanced Sire

– Value of increased reliability

Show-Me-SelectShow-Me-Plus Heifer

Premiums for heifers with various classifications

Tier PregnancyShow-

Me-Plus CountMedian

PriceMean Price

Premium/Discount

Genomic PredictionPremium

Tier I Natural Service No 66 2250 2223 Base Tier I Natural Service Yes 3 2700 2683 460.61 460.61Tier I Mix No 3 2200 2133 -89.39Tier I AI No 76 2350 2354 130.89Tier I AI Yes 20 2538 2696 473.52 342.63Tier II Natural Service No 3 2100 2100 -122.73Tier II Mix No 1 2400 2400 177.27Tier II AI No 4 2550 2538 314.77Tier 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.

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 Heifershttp://blog.steakgenomics.org/2016/02/genomic-roi-early-returns-suggest.htmlSee 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

Further Economic Analysis

Local Genetic Adaptation Grant

http://blog.steakgenomics.org/2016/05/local-genetic-adaptation-grant.html

Regions

Selection between regionsIf animal is adapted to a region:• It performs well• Produces progeny in that region

Selection between regionsIf animal is adapted to a region:• It performs well• Produces progeny in that regionIf animal is not adapted to a region:• It under performs• Culled, no progeny

Selection between regionsIf animal is adapted to a region:• It performs well• Produces progeny in that regionIf animal is not adapted to a region:• It under performs• Culled, no progenyThis selection changes frequency of DNA variants responsible for local adaptation

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

Region-Specific GE-EPDs and IndexesGene-by-environment interactions and local adaptation lead to re-ranking of animals between environments

Animal WW EPD Milk EPD MW EPD $WBull A 56 27 25 52Bull B 49 23 27 42

Environment 1

Region-Specific GE-EPDs and IndexesGene-by-environment interactions and local adaptation lead to re-ranking of animals between environments

Animal WW EPD Milk EPD MW EPD $WBull A 56 27 25 52Bull B 49 23 27 42

Environment 1

Animal WW EPD Milk EPD MW EPD $WBull A 47 22 21 40Bull B 48 23 27 43

Environment 2

http://eBEEF.org

A Steak in Genomicshttp://blog.steakgenomics.org/

https://www.facebook.com/SteakGenomics

Thanks!