# Presentation: 728751

## Benefits from Cooperation in Genomics 

## Topics

**Genomic cooperation**
**Simulation**** of very large population**
**Proposals for genotype sharing**
**Country border issues and North American experience**
**Genomic MACE equations**
**USA update**
**Actual**** HOL, JER, and BSW results**
**Database and implementation**

## Cooperative International Projects

**Traditional**** genetic evaluations**
**MACE instead of merging phenotypes**
**Small benefits expected from data merger**
**Proven bulls only, not cows or young bulls**
**Parentage testing, genetic recessives, pedigrees done by breed associations**
**Genomics****: what role for Interbull?**

## Sequencing of Genomes

| Species | Year |
| --- | --- |
| Human - $3 billion | 2000 |
| Cow - $53 million funded by: | 2004 |
|   50% Nat’l Human Genome Res Inst |  |
|   50% USA, CAN, AUS, NZL |  |
| Chicken | 2004 |
| Pig - < $20 million | 2009 |

## Human DNA Data Sharing

**"The highest priority of the International **
**Human Genome Sequencing Consortium **
**is ensuring that sequencing data from the **
**human genome is available to the world's **
**scientists rapidly, freely and without restriction." **
**National Human Genome Research Institute, **
**2008**** **
**"The principle of rapid pre-publication release **
**should apply to other types of data from other **
**large-scale production centers." **
**Wellcome Trust, 2003**** **

## Simulation ResultsWorld Holstein Population

**40,360**** older bulls to predict ****9,850 ****younger bulls in Interbull file**
**50,000**** or ****100,000 SNP****; 5,000 QTL **
**Reliability vs. parent average REL**
**Genomic REL = corr****2**** (EBV, true BV) **
**81% vs 30%**** observed using ****50K**
**83% vs 30%**** observed using ****100K**

## Genotype Exchange Options

**Give away for free (not likely)**
**Genotype own bulls, then trade?**
**Trade an equal number or all bulls?**
**Country A has ****5000 ****and B has ****1000**
**Proportional to population size?**
**Trade among organization pairs or create central genomic database?**
**Service fee for young animals to pay for ancestor genotyping?**

## Problems of Not Sharing

**Genetic progress ****not as fast**** as with full access to genotypes**
**Severe limits on researcher access to genotypes (****secrecy****)**
**Genomics may lead to natural ****monopoly****, similar to railroads**
**Small companies / countries can’t afford to buy sufficient genotypes**

## Share Young Bull, Cow Genotypes?

**May be marketed in >1 country**
**Exchange of young animals and females ****more important as their REL increases**** with genomics**
**Helps to synchronize databases**
**Could lead to joint evaluation**

## North American Cooperation 

**174 markers, 1068 ****USA and CAN**** bulls**
**Illinois, Israel, and USDA researchers**
**1991-1999**
**367 markers, 1415 ****USA and CAN**** bulls**
**USDA, Illinois, and Israel**
**1995-2004**
**38,416 markers, 19,464 animals**
**USDA, Missouri, Canada, and Illumina**
**Oct 2007- Dec 2008**

## Country Borders

**Most ****phenotypic**** data collected and stored within country**
**Genomic**** data allows simple, accurate prediction across borders**
**Need ****traditional**** EBV or PA for foreign animals, but not available for young bulls, cows, or heifers**
**May need full foreign pedigrees**
**Genomic**** evaluations official on USA scale for many foreign animals (not just CAN)**

## Foreign DNA in North American DataProven bulls, Young bulls, and Females

| Ctry | old | yng | fem | Ctry | old | yng | fem |
| --- | --- | --- | --- | --- | --- | --- | --- |
| NLD | 25 | 134 | 53 | GBR | 7 | 7 | 1 |
| DEU | 22 | 31 | 64 | DNK | 5 | 5 | 0 |
| ITA | 14 | 17 | 5 | LUX | 0 | 0 | 8 |
| AUS | 12 | 30 | 0 | BEL | 3 | 1 | 0 |
| HUN | 6 | 29 | 2 | CHE | 4 | 0 | 0 |
| FRA | 12 | 19 | 2 | NZL | 4 | 0 | 0 |
| CZE | 3 | 15 | 0 | FIN | 1 | 0 | 0 |

## USA Update

**Genomic PTAs ****official in January**
**Traditional PTAs sent to Interbull**
**MACE used if foreign dtrs included**
**Genomic info used for most bulls**
**Genomic PTA transferred to descendants (to ancestors in future)**
**Jersey results also are official**
**More Brown Swiss needed (CHE)**

## Genomic Methods

**Direct**** genomic evaluation**
**Sum of effects for 38,416 genetic markers**
**Not published**
**Combined**** genomic evaluation**
**Include phenotypes of non-genotyped ancestors by selection index**
**Transferred**** genomic evaluation**
**Propagate info from genotyped animals to non-genotyped relatives by selection index**

## Genotyped Animals (n=19,464)As of December 2008

## Experimental Design - UpdateHolstein, Jersey, and Brown Swiss breeds

|  | HOL | JER | BSW |
| --- | --- | --- | --- |
| Predictor: |  |  |  |
| Bulls born <2000 | 4,422 | 1,149 | 225 |
| Cows with data | 947 | 212 |  |
| Total | 5,369 | 1,361 | 225 |
| Predicted: |  |  |  |
| Bulls born >2000 | 2,035 | 388 | 118 |

**Data from ****2004 ****used to predict independent data from ****2009**

## Reliability Gain1 by BreedYield traits and NM$ of young bulls

| Trait | HO | JE | BS |
| --- | --- | --- | --- |
| Net merit | 24 | 8 | 3 |
| Milk | 26 | 6 | 0 |
| Fat | 32 | 11 | 5 |
| Protein | 24 | 2 | 1 |
| Fat % | 50 | 36 | 10 |
| Protein % | 38 | 29 | 5 |

**1****Gain above parent average reliability ~35%**

## Reliability Gain by BreedHealth and type traits of young bulls

| Trait | HO | JE | BS |
| --- | --- | --- | --- |
| Productive life | 32 | 7 | 2 |
| Somatic cell score | 23 | 3 | 16 |
| Dtr pregnancy rate | 28 | 7 | - |
| Final score | 20 | 1 | - |
| Udder depth | 37 | 18 | 3 |
| Foot angle | 25 | 8 | - |
| Trait average  | 29 | 11 | N/A |

## Value of Genotyping More AnimalsActual and predicted gains for 27 traits and for Net Merit

| Bulls |  | Reliability Gain |  |
| --- | --- | --- | --- |
| Predictor | Predicted | NM$ | 27 trait avg |
| 2130 | 261 | 13 | 17 |
| 2609 | 510 | 17 | 18 |
| 3576 | 1759 | 23 | 23 |
| 4422 | 2035 | 24 | 29 |
| 6184 | 7330 | 31 | 30 |

**Cows:**
**947**
**1916**

## Genomic MACEGenomics Task Force, Pete Sullivan

**Residuals correlated across countries**
**Repeated tests**** of the same major gene, or**
**SNP effects estimated from ****common bulls**
**Let c****ij ****= proportion of common bulls **
**Let g****i**** = DE****gen**** / (DE****dau**** + DE****gen****)**
**Corr(e****i****, e****j****) = c****ij ***** Corr(a****i****, a****j****) * ****√****(g****i**** * g****j****)**
**Avoids double counting genomic information from multiple countries i, j**
**New deregression formulas needed**

## Conclusions

**Reliability for young animals**
**30-38%**** for traditional parent averages**
**60-70%**** genomic REL for USA HOL traits**
**81% ****using 40,360 simulated bulls**
**83%**** using 100K instead of 50K markers**
**High reliability requires large numbers of genotyped animals**
**Gains much smaller for USA JER and BSW breeds**
**Trading, sharing, profit is needed**
**Revised MACE may include genomics**

## Acknowledgments

**Genotyping and DNA extraction:**
**USDA Bovine Functional Genomics Lab, U. Missouri, U. Alberta, GeneSeek, Genetics & IVF Institute, Genetic Visions, and Illumina**
**Computing:**** **
**AIPL staff (Mel Tooker, Leigh Walton, Jay Megonigal)**
**Funding:**** **
**National Research Initiative grants**
**2006-35205-16888, 2006-35205-16701**
**Agriculture Research Service**
**Holstein and Jersey breed associations**
**Contributors to Cooperative Dairy DNA Repository (CDDR)**

## CDDR Contributors

**National Association of Animal Breeders (NAAB, Columbia, MO)**
**ABS Global ****(DeForest, WI)**
**Accelerated Genetics ****(Baraboo, WI)**
**Alta ****(Balzac, AB, Canada)**
**Genex ****(Shawano, WI)**
**New Generation Genetics ****(Fort Atkinson, WI)**
**Select Sires ****(Plain City, OH)**
**Semex Alliance ****(Guelph, ON, Canada)**
**Taurus-Service ****(Mehoopany, PA)**