# Presentation: 379419

## Genomic Data and Cooperation Result in Faster Progress 

## Experimental Design

**Predict April 2008 daughter deviations from August 2003 PTAs**
**Similar to Interbull trend test 3 **
**3576**** older Holstein bulls**
**1759**** younger bulls  (total = ****5335****)**
**Genomic predictions computed for ****27 traits****: 5 yield, 5 health, 16 conformation, and Net Merit**

## Genotyped Animals (n=6005)As of April 2008

## Genomic Data and Methods

**38,416 ****markers for each bull**
**Direct**** genomic evaluation**
**Inversion for linear prediction, REL**
**Iteration for nonlinear prediction**
**Combined**** genomic evaluation**
**3 x 3 selection index combining direct genomic PTA, traditional PA or PTA, and subset PA or PTA by REL**

## R-square values and Reliabilities comparing traditional to genomic predictions

|  | Squared corr (x100) |  | Reliability |  |  |
| --- | --- | --- | --- | --- | --- |
|  |  |  | Traditional | Genomic | Genomic |
| Trait | PA | Genomic | PA | Realized | Gain |
| Net Merit | 11 | 28 | 30 | 53 | 23 |
| Milk | 28 | 49 | 35 | 58 | 23 |
| Fat | 15 | 44 | 35 | 68 | 33 |
| Protein | 27 | 47 | 35 | 57 | 22 |
| Fat %  | 25 | 63 | 35 | 78 | 43 |
| Protein % | 28 | 58 | 35 | 69 | 34 |

## R-square values and Reliabilities comparing traditional to genomic predictions

|  | Squared corr (x100) |  | Reliability |  |  |
| --- | --- | --- | --- | --- | --- |
|  |  |  | Traditional | Genomic | Genomic |
| Trait | PA | Genomic | PA | Realized | Gain |
| Longevity | 17 | 27 | 27 | 45 | 18 |
| SCS | 23 | 38 | 30 | 51 | 21 |
| Fertility | 20 | 29 | 25 | 41 | 16 |
| S.calf ease | 27 | 29 | 28 | 31 | 3 |
| D.calf ease | 14 | 22 | 25 | 40 | 15 |
| Final score | 23 | 36 | 24 | 42 | 18 |

## Value of Genotyping More SNP9,604 (10K), 19,208 (20K), and 38,416 (40K) SNP

|  | R2 of PA | Genomic R2 |  |  |
| --- | --- | --- | --- | --- |
| Trait |  | 10K | 20K | 40K |
| Net Merit $ | 11 | 25 | 26 | 28 |
| Milk yield | 28 | 45 | 47 | 49 |
| Fat yield | 15 | 41 | 43 | 44 |
| Protein yield | 27 | 45 | 46 | 47 |
| Longevity | 17 | 24 | 25 | 27 |
| SCS  | 23 | 34 | 36 | 38 |
| Fertility | 20 | 27 | 28 | 29 |

## Value of Genotyping More Bulls

| Bulls |  | R2 for Net Merit |  |  |
| --- | --- | --- | --- | --- |
| Predictor | Predictee | PA | Genomic | Gain |
| 1151 | 251 | 8 | 12 | 4 |
| 2130 | 261 | 8 | 17 | 9 |
| 2609 | 510 | 8 | 21 | 13 |
| 3576 | 1759 | 11 | 28 | 17 |

## Expected vs Observed Reliability

**Reliability for predictee bulls **
**Traditional PA: ****27%**** average across traits**
**Genomic: ****63%**** expected vs. ****50%**** observed**
**Observed range ****78%**** (fat pct) to ****31% ****(SCE)**
**PTA regressions ****.8**** to ****.9**** of expected**
**REL and PTA adjustments**
**Multiply genomic daughter equivalents by ****.7**** to make expected closer to observed **
**For example, 16 * .7 = ****11**
**Include polygenic effect, less than 5% **

## Simulated ResultsWorld Bull Population

**15,197**** older and ****5,987**** younger bulls from all countries in Interbull file**
**40,000 SNP and 10,000 QTL (heavy tail) **
**Provided timing, memory test**
**Reliability vs parent average REL**
**REL = corr****2**** (EBV, true BV) **
**80% vs 34%**** expected for young bulls**
**72% vs 30%**** observed in simulation**

## Genetic Progress

**Assume 60% REL for net merit**
**Sires mostly ****2**** instead of ****6**** years old**
**Dams of sons mostly heifers with 60% REL instead of cows with phenotype and genotype (66% REL)**
**Progress could increase by ****>50%**
**0.37 vs. 0.23 genetic SD per year**
**Reduce generation interval more than accuracy**

## Conclusions

**Genomic predictions significantly better than parent average (P < .0001) for all 27 traits tested**
**Gains in reliability equivalent on average to ****11**** daughters with records **
**Analysis used ****3576**** historical bulls **
**April data included ****5285**** proven bulls**
**R****2**** increases with more bulls and SNPs**

## Acknowledgments

**Funding:**** **
**National Research Initiative grants**
**CDDR Contributors (NAAB, Semex)**
**Genotyping and DNA extraction:**
**BFGL, U. Missouri, U. Alberta, GeneSeek, GIFV, and Illumina**
**Computing**** from AIPL staff**