# Presentation: 662259

## Genomic Selection in Dairy Cattle

## Simulated ResultsWorld Bull Population

**15,197 older and 5,987 younger bulls in Interbull file**
**40,000 SNPs and 10,000 QTLs **
**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**

## Current Genotyped Animals (n=6005)

## Genomic Methods

**Direct**** genomic evaluation**
**Inversion for linear prediction, REL**
**Iteration for nonlinear prediction**
**Combined**** genomic evaluation**
**Traditional PA or PTA, subset PA or PTA, and direct genomic combined by REL in 3 x 3 selection index**
**Nonlinear genomic predictions used**

## Nonlinear and Linear Regressions for marker allele effects 

## Experimental DesignActual North American Data

**August 2003 PTAs for ****3,576**** older bulls to predict January 2008 daughter deviations for ****1,759**** younger bulls  (total = ****5,335**** bulls)**
**Results computed for ****27 traits****: 5 yield, 5 health, 16 conformation, and Net Merit**
**Nonlinear A used, B didn’t work**

## Marker P-Values for Net Merit

## Marker Effects for Net Merit

## Marker Effects for Milk

## R2 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 |

## R2 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 (mast) | 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 |

## SNP Density Comparison

|  | REL of PA | Genomic REL |  |  |
| --- | --- | --- | --- | --- |
| Trait |  | 10K | 20K | 40K |
| Net Merit $ | 30 | 48 | 50 | 53 |
| Milk yield | 35 | 53 | 56 | 58 |
| Fat yield | 35 | 64 | 66 | 68 |
| Protein yield | 35 | 54 | 56 | 57 |
| Productive Life | 27 | 38 | 41 | 45 |
| SCS (mastitis) | 30 | 45 | 47 | 51 |
| Dtr Preg Rate | 25 | 37 | 39 | 41 |

## X, Y, Pseudo-autosomal SNPs

**487 SNPs**

**35 SNPs**

**0 SNPs**

**35 SNPs**

## Conclusions

**Genomic predictions significantly better than parent average (P < .0001) for all 26 traits tested**
**Gains in reliability equivalent on average to ****11**** daughters with records **
**Analysis used ****3,576**** historical bulls **
**Current data includes ****5,285**** proven bulls**
**Larger populations require more SNPs**

## Acknowledgments

**Funding:**** **
**NRI grants 2006-35205-16888, 16701**
**CDDR Contributors (NAAB, Semex)**
**Genotyping and DNA extraction:**
**BFGL, U. Missouri, U. Alberta, GeneSeek, GIFV, and Illumina**
**Computing**** from AIPL staff**