# Presentation: 379420

## Genomic Prediction Results

## Measuring Genetic Similarity

**Cattle genome sequenced in 2004**
**30**** chromosome pairs (including X,Y)**
**3 billion**** letters from each parent**
**Illumina Bovine SNP50****TM**** Chip**
**58,000**** genetic markers in 2007**
**39,835**** used in genomic predictions**
**Cost about ****$200**** per animal**

## How Related are Relatives?

**Example: Full sibs **
**are ****expected**** to share ****50%**** of their DNA on average, with SD of ****5%**** **
**may ****actually**** share ****40%**** to ****60%**** of their DNA because each inherits a different mixture of chromosome segments from the two parents.**
**SD ****3.5%**** reported previously was low**

## Simulated Results (Apr 2007)

**1777 older and 500 younger bulls**
**10,000 SNPs and 100 QTLs **
**Reliability vs parent average REL **
**58% vs 36%**** for young bulls**
**Higher REL if major loci and Bayesian methods used, lower if many loci (>100) affect trait**

## Simulated Results (2008)

**8271 older and 1984 younger bulls**
**40,000 SNPs and 500 QTLs **
**Provided timing, memory test**
**Reliability vs parent average REL **
**79% vs 37%**** expected for young bulls**
**76% vs 37%**** observed in simulation**

## Genotyped Bulls (Feb 2007)from Cooperative Dairy DNA Repository

**DNA of bulls stored in Beltsville (BFGL)**
**2560**** proven bulls used to computed predictions**
**Bulls born 1994-1996 with >75% reliability of Net Merit**
**Plus ancestor bulls born 1952-1993**
**659**** later bulls used to test predictions**
**Born 2001 with >75% reliability of Net Merit**

## Proposed Genotyping (Apr 2007)

**Data cutoff**

## Current Genotyped Animals (n=6005)

## 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**

## 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 

## Actual Results (Feb 2007 data)

**August 2003 PTAs for ****2650**** older bulls to predict January 2008 daughter deviations for ****569**** younger bulls  (total = ****3119**** 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

## Marker Effects for Final Score

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

|  | Squared corr (x100) |  | Reliability |  |  |
| --- | --- | --- | --- | --- | --- |
|  |  |  | Traditional | Genomic | Genomic |
| Trait | PA | Genomic | PA | Realized | Gain |
| Net Merit | 8 | 21 | 36 | 54 | 18 |
| Milk | 30 | 44 | 38 | 54 | 16 |
| Fat | 15 | 39 | 38 | 65 | 27 |
| Protein | 31 | 43 | 38 | 51 | 13 |
| Fat %  | 28 | 58 | 38 | 72 | 34 |
| Protein % | 32 | 51 | 38 | 66 | 28 |

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

|  | Squared corr (x100) |  | Reliability |  |  |
| --- | --- | --- | --- | --- | --- |
|  |  |  | Traditional | Genomic | Genomic |
| Trait | PA | Genomic | PA | Realized | Gain |
| Prod Life | 9 | 19 | 28 | 47 | 19 |
| SCS | 7 | 23 | 32 | 54 | 22 |
| DPR | 15 | 23 | 25 | 40 | 15 |
| SCE | 19 | 23 | 31 | 36 | 5 |
| DCE | 24 | 27 | 31 | 36 | 5 |
| Final Score | 24 | 32 | 28 | 37 | 9 |

## Expected vs Observed Reliability

**Reliability for predictee bulls **
**Average across traits: ****57%**** expected vs. ****48%**** observed vs. ****30%**** PA**
**Observed range ****72%**** (fat pct) to ****36%**
**PTA regressions ****.8**** to ****.9**** of expected**
**Redo 2003 cutoff using April data**
**Develop REL and PTA adjustments**

## Clones and Identical Twins21HO2121, 21HO2125, 21HO2100, CAN6139300, CAN6139303

|  | Traditional |  |  | Genomic |  |
| --- | --- | --- | --- | --- | --- |
| Bull | Dtrs | NM$ | REL | NM$ | REL |
| Triton - ETN | 98 | -363 | 82 | -371 | 91 |
| Triad - ETN | 26 | -306 | 68 | -370 | 91 |
| Trey - ETN | 108 | -395 | 83 | -371 | 91 |
| Loyalty | 108 | -185 | 78 | -196 | 87 |
| Lauriet | 83 | -203 | 76 | -196 | 87 |

## X, Y, Pseudo-autosomal SNPs

**487 SNPs**

**35 SNPs**

**0 SNPs**

**35 SNPs**

## SNPs on X Chromosome

**Each animal has two evaluations**
**Expected genetic merit of daughters**
**Expected genetic merit of sons**
**Difference is sum of effects on X**
**SD = .1 ****σ****G****, smaller than expected**
**Correlation with sire’s daughter vs. son PTA difference was significant (P<.0001), regression close to 1.0 **

## SNP Density Comparison2130 older and 261 younger bulls

|  | REL of PA | Genomic REL |  |  |
| --- | --- | --- | --- | --- |
| Trait |  | 10K | 20K | 40K |
| Net Merit | 35 | 45 | 49 | 48 |
| Milk | 37 | 49 | 52 | 51 |
| Fat | 37 | 52 | 55 | 57 |
| Protein | 37 | 52 | 54 | 53 |
| Productive Life | 28 | 44 | 45 | 42 |
| SCS | 31 | 44 | 45 | 47 |
| Dtr Preg Rate | 21 | 44 | 49 | 46 |

## Genetic Evaluation Advancesand increases in genetic progress

| Year | Advance | % Gain |
| --- | --- | --- |
| 1935 | Daughter-dam comparison | 100 |
| 1962 | Herdmate comparison | 50 |
| 1974 | Modified cont. comparison | 5 |
| 1977 | Protein evaluated | 4 |
| 1973 | Records in progress | 10 |
| 1989 | Animal model | 4 |
| 1994 | Net merit, PL, and SCS | 50 |
| 2008 | Genomic selection | >40 |

## Conclusions

**Genomic predictions significantly better than parent average (P < .0001) for all 26 traits tested**
**Gains in reliability from ****2650**** bulls (Feb data) equivalent on average to ****9**** daughters with records **
**April data included ****5285**** proven bulls, more analysis needed**