# Presentation: 755999

## Predicting Genetic Interactions Within and Across Breeds

## Modeling Genetic Interactions

**Crossbreeding and heterosis in an all-breed animal model**
**Estimate breed differences routinely **
**Recommend mating strategies**
**Inbreeding depression adjustments in genetic evaluations**
**Within-breed interactions predicted using dominance relationships**

## All-Breed Analyses

**Crossbred animals**
**Will have EBVs, most did not before**
**Reliable EBVs from both parents**
**Purebred animals**
**Information from crossbred relatives**
**More contemporaries**
**Routinely used in other populations**
**New Zealand (1994), Netherlands (1997)**
**USA goats (1989)**

## Purebred and Crossbred DataUSA milk yield records

| Breed | Cows born 2002 | % of total |
| --- | --- | --- |
| Holstein | 632,659 | 90.9 |
| Jersey | 43,333 | 6.2 |
| Brown Swiss | 5,884 | .8 |
| Guernsey | 2,851 | .4 |
| Ayrshire | 2,101 | .3 |
| F1 Crossbred | 7,863 | 1.1 |

## Across-Breed Methods

**All-breed animal model**
**Purebreds and crossbreds together**
**Age adjust to 36 months, not mature **
**Variance adjustments by breed**
**Unknown parents grouped by breed**
**Westell groups instead of regressing on breed fractions**
**General heterosis subtracted**

## Unknown Parent Groups

**Groups formed based on**
**Birth year  **
**Breed **
**Path (dams of cows, sires of cows, parents of bulls)**
**Origin (domestic vs other countries)**
**Paths have >1000 in last 15 years **
**Groups each have >500 animals**

## All- vs Within-Breed EvaluationsCorrelations of PTA Milk

| Breed | 99% REL bulls | Recent bulls | Recent cows |
| --- | --- | --- | --- |
| Holstein | >.999 | .994 | .989 |
| Jersey |   .997 | .988 | .972 |
| Brown Swiss |   .990 | .960 | .942 |
| Guernsey |   .991 | .988 | .969 |
| Ayrshire |   .990 | .963 | .943 |
| Milking Shorthorn |   .997 | .986 | .947 |

## Display of PTAs

**Genetic base**
**Compute on all-breed base **
**Convert back to within-breed-of-sire bases for ease of comparing to previous PTA**
**Heterosis and inbreeding**
**Both effects removed in the animal model**
**Heterosis added to crossbred animal PTA**
**Expected Future Inbreeding (EFI) and genetic merit differ with mate breed **

## Within-Breed Methods

**Adjust for inbreeding depression**
**Remove past F, include future F**
**Expected future F (EFI) = .5 mean A****ij**
**EBV****0**** vs EBV****EFI**** vs unadjusted EBV**
**Optimal selection theory**
**Maximize w’ EBV****0**** + b****y.F**** w’ A w**
**Use of EBV****0**** avoids double-counting**

## Effect of Inbreeding AdjustmentsUsed in USA since 2005

**Protein genetic trend estimates**
**3% more for EBV****0**** than EBV**
**6% less for EBV****EFI**** than EBV**
**Correlations of EBVs within breed**
**.993 corr(EBV****EFI****, EBV) for cows**
**.998 corr(EBV****EFI****, EBV) for bulls**
**Select on EBV****0**** for crossbreeding?**

## Within-Breed Interactions

**Dominance relationship matrix**
**5.5 million Holstein cows with data**
**1.6 million interactions among 4263 sires and maternal grandsires**
**30 minutes for D****-1****, 16 hours to solve**
**Dominance variance**
**Assumed 5% of phenotypic variance **
**Estimate from Van Tassell et al, 2000 **

## Predicted Sire-MGS Interactions305-d milk kg (heterosis = 318 kg) 

| Bulls | Duster | Man-fred | Durham | BW Mar-shall | Garter |
| --- | --- | --- | --- | --- | --- |
| Duster |  | +86 | -35 | +125 | -11 |
| Manfred | 200 |  | +39 | +69 | -22 |
| Durham | 245 | 46 |  | -90 | +7 |
| BW Mar-shall | 183 | 123 | 161 |  | +71 |
| Garter | 51 | 60 | 18 | 15 |  |

**Numbers of observations below diagonal**

## Conclusions

**Can predict genetic interactions**
**Inbreeding adjustments since 2005 **
**All-breed animal model expected 2007**
**Sire-MGS dominance effects within breed mostly smaller than heterosis**
**Future research on interactions**
**Specific heterosis and epistasis**
**Delivery of information to breeders**