# Presentation: 468278

## Genetic evaluation using combined data from all breeds and crossbred cows

## Jersey  Holstein

**Jersey ******** Holstein**

| Cow # | Pounds of Milk | % Butterfat | Pounds of Butterfat |
| --- | --- | --- | --- |
|  X-1 |   9,784 | 4.85 | 475 |
|  X-3 | 13,065 | 4.71 | 615 |
| X-17 | 13,837 | 3.85 | 533 |

**From USDA research herd at Beltsville, MD**

**Notes:**
AVG:	13054lbs milk (5760kg) 
	4.57% fat
	546lbs protein (260kg)

## Crossbreds averaged 12,904 pounds of milk and 588 pounds of butterfat, outperforming dams by more than sire proof predictions (Fohrman,1947).
Advanced register Holsteins averaged 13,833 pounds of milk and 493 pounds of fat in 1945. 

**Advanced register Holsteins averaged ****13,833**** pounds of milk and ****493**** pounds of fat in 1945.**** **

***USDA Yearbook of Agriculture 1947***

**Red Dane ******** Jersey**

**Notes:**
5760kg milk
263kg fat

## Goals

**Evaluate crossbred animals without biasing purebred evaluations**
**Accurately estimate breed differences**
**Compare crossbreeding strategies**
**Compute national evaluations and examine changes**
**Display results without confusion**

## All-Breed Analyses

**Crossbred animals**
**Will have PTAs, only ****3%**** did before if in breed association grading-up programs**
**Reliable PTAs from both parents**
**Purebred animals**
**Information from crossbred relatives**
**More herdmates (other breeds, crossbreds)**
**Routinely used in other populations**
**New Zealand ****(1994),**** Netherlands ****(1997)**
**USA goats ****(1989),**** calving ease ****(2005)**

## Methods

**All-breed animal model**
**Purebreds and crossbreds together**
**Relationship matrix among all**
**Unknown parents grouped by breed**
**Variance adjustments by breed**
**Age adjust to 36 months, not mature**
**Within-breed-of-sire model examined but not used**

## Data

**Numbers of cows of all breeds**
**22.6 million**** for milk and fat **
**16.1 million**** for protein**
**22.5 million**** for productive life**
**19.9 million**** for daughter pregnancy rate**
**10.5 million**** for somatic cell score**
**Type traits are still collected and evaluated in separate breed files **

## Purebred and Crossbred DataUSA milk yield records

| Breed | % of total | Cows born 2003 |
| --- | --- | --- |
| Holstein | 90.5 | 642,354 |
| Jersey | 6.4 | 45,151 |
| Brown Swiss | .8 | 5,960 |
| Guernsey | .4 | 2,563 |
| Ayrshire | .3 | 1,926 |
| F1 Crossbred | 1.2 | 8,647 |

## Crossbred Cowswith 1st parity records

| Fresh year | F1    (%) | F1 cows | Back-cross | Het   > 0 | XX cows |
| --- | --- | --- | --- | --- | --- |
| 2006 | 1.4 | 10153 | 3422 | 15365 | 6099 |
| 2005 | 1.2 | 8647 | 2495 | 12621 | 4465 |
| 2004 | 1.1 | 7863 | 1983 | 11191 | 3947 |
| 2003 | .9 | 6248 | 1492 | 9051 | 3111 |
| 2002 | .7 | 4689 | 1467 | 7338 | 2564 |

## Number of Cows with Records (with > 50% heterosis; March 2007)

| Dam |  |  |  | Sire Breed |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| Breed |  | AY |  | BS | GU | JE | MS | XX | HO |
| AY |  | — |  | 29 | 29 | 221 | 48 | 43 | 1796 |
| BS |  | 20 |  | — | 50 | 294 | 42 | 13 | 2619 |
| GU |  | 46 |  | 96 | — | 288 | 32 | 16 | 3256 |
| JE |  | 181 |  | 357 | 155 | — | 116 | 56 | 3718 |
| MS |  | 281 |  | 52 | 10 | 71 | — | 5 | 965 |
| XX |  | 489 |  | 1544 | 308 | 3568 | 323 | — | 8859 |
| HO |  | 1843 |  | 13993 | 1721 | 35193 | 1858 | 675 | — |

## Number of Cows with Records (with > 50% heterosis; March 2007)

| Sire Breed |  | Dam Breed | # | Sire Breed |  | Dam Breed | # |
| --- | --- | --- | --- | --- | --- | --- | --- |
| BS |  | SM | 25 | HO |  | DL | 47 |
| DL |  | HO | 109 | HO |  | LD | 195 |
| MO |  | HO | 73 | HO |  | MI | 60 |
| NO |  | HO | 38 | HO |  | NR | 21 |
| NR |  | HO | 23 | HO |  | RE | 22 |
| SR |  | HO | 118 | HO |  | SM | 16 |

**Notes:**
MI = Mueserhineissel  RE = European Red Dairy  SM = Simmental   LD = American Lineback   DL = Dutch Belted   MO = Montbeliarde NO = Normande

## Crossbred Daughters Addedfor sires in top 10 NM$ within breed

|  | Sire
breed | Daughters |  |
| --- | --- | --- | --- |
| Sire Name |  | Feb ‘07 | Added |
| Legacy | AY | 157 | 33 |
| Agenda | BS | 35 | 21 |
| Excite | BS | 144 | 57 |
| Q Impuls | JE | 241 | 20 |
| Stetson | MS | 36 | 31 |

## Heterosis for Yield Traits Percent of Parent Breed Average

|  |  | Milk |  |  |  | Fat |  | Protein |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| Breed |  |  | HO Sire |  | HO Dam | HO Sire | HO Dam | HO Sire | HO Dam |
| Ayrshire |  |  |  | 2.4 | -2.0 | 2.7 | -1.8 | 2.9 | -2.4 |
| Brown Swiss |  |  |  | 5.6 |   3.2 | 4.8 |   4.5 | 4.7 |   3.8 |
| Guernsey |  |  |  | 5.2 |   2.4 | 7.1 |   4.4 | 5.5 |   4.0 |
| Jersey |  |  |  | 7.5 |   1.6 | 6.6 |   4.5 | 7.2 |   4.1 |
| M. Shorthrn  |  |  |  | 2.8 |   0.3 | 3.2 |   1.3 | 3.6 |   1.2 |
| Heterosis |  |  |  | 3.4 |  | 4.4 |  | 4.1 |  |

## Breed Effects and Heterosis

**Three estimates of breed differences: **
**From phenotypic breed differences**
**From herds containing crossbred cows**
**From all-breed model using all data**
**All three estimates were similar**
**Estimates of general heterosis from 2001 and 2003 studies were used in the current research and not re-estimated**

**Notes:**
Chose to use phenotypic breed means, should be no difference when new all breed means are used.

## Unknown Parent Groups

**Look up PTAs of known parents**
**Estimate averages for unknowns **
**Group unknown parents by**
**Birth year  **
**Breed **
**Path (dams of cows, sires of cows, parents of bulls)**
**Origin (domestic vs other countries)**

## 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**
**Convert all-breed base to within-breed bases (or vice versa)**
**PTA****brd**** = (PTA****all**** – mean****brd****) SD****brd****/SD****HO**
**PTA****all**** = PTA****brd**** (SD****HO****/SD****brd****) + mean****brd**
**Heterosis and inbreeding**
**Both effects removed in the animal model**
**Heterosis added to crossbred animal PTA**
**Expected Future Inbreeding (EFI) and merit differ with mate breed **

## Milk (kg)Genetic trend on all-breed base

## Fat (kg)Genetic trend on all-breed base

## Protein (kg)Genetic trend on all-breed base

## Somatic Cell ScoreGenetic trend on all-breed base

## Productive LifeGenetic trend on all-breed base

## Daughter Pregnancy RateGenetic trend on all-breed base

## EBV differences from Holstein estimated from an all-breed model

|  | Difference from Holstein (pounds) |  |  |
| --- | --- | --- | --- |
|  | Milk | Fat | Protein |
| AY | -5269 | -134 | -130 |
| BS | -4213 | -79 | -71 |
| GU | -6120 | -82 | -137 |
| JE | -6530 | -75 | -104 |
| MS | -7121 | -245 | -198 |

## Phenotypic breed differences from Holstein from an all-breed model

|  | Difference from Holstein (pounds) |  |  |
| --- | --- | --- | --- |
|  | Milk | Fat | Protein |
| AY | -6587 | -207 | -176 |
| BS | -4555 | -97 | -82 |
| GU | -7286 | -143 | -179 |
| JE | -6956 | -99 | -119 |
| MS | -8419 | -320 | -240 |
| HO | 23104 | 842 | 694 |

## EBV differences from Holstein estimated from an all-breed model

|  | Difference from Holstein |  |  |
| --- | --- | --- | --- |
|  |    SCS | PL (mo) | DPR (%) |
| AY | -0.16 | 0.3 | 2.4 |
| BS | -0.10 | 0.8 | 1.1 |
| GU | 0.07 | -8.5 | 0.8 |
| JE | 0.19 | 3.2 | 5.5 |
| MS | -0.07 | -2.2 | 4.5 |

## Phenotypic breed differences from Holstein from an all-breed model

|  | Difference from Holstein |  |  |
| --- | --- | --- | --- |
|  |    SCS | PL (mo) |    DPR |
| AY | -0.11 | 3.3 | 0.8 |
| BS | -0.15 | 1.9 | -0.6 |
| GU | 0.29 | -1.3 | -1.1 |
| JE | 0.26 | 4.9 | 5.0 |
| MS | 0.12 | 1.5 | 3.3 |
| HO | 3.07 | 28.1 | 25.5 |

## Net Merit Relative EmphasisIn cooperation with Dr. Tony Seykora et al.

| Trait | 2003 | 2006 | Trait | 2003 | 2006 |
| --- | --- | --- | --- | --- | --- |
| Protein | 33 | 23 | Udder | 7 | 6 |
| Fat | 22 | 23 | F&L | 4 | 3 |
| Milk | 0 | 0 | Size | 3 | 4 |
| PL | 11 | 17 | DPR | 7 | 9 |
| SCS | 9 | 9 | CA$ | 4 | 6 |

**DPR**** = daughter pregnancy rate (fertility), ****CA$**** is index of calving ease and stillbirth**

**Notes:**
My abstract reported NM$ and CM$ using 2003 formula.
The results presented today are using the updated 2006 formula.
CA$ values are actually CE values for 2003.
CA$ index is being implemented August 2006.

## NM$, FM$, CM$ Economic Values

|  | NM$ | FM$ | CM$ |
| --- | --- | --- | --- |
| Milk | 0.00 | 0.11 | −0.07 |
| Fat | 2.70  | 2.70 |   2.70 |
| Protein | 3.55 | 0.00 |   5.73 |

**Other values are same in each index:**
**PL**** 29, ****SCS**** -150, ****Size**** -14, ****Udder**** 28, ****F&L**** 13, ****DPR**** 21, ****CA$**** 1**

**Notes:**
Values are $/PTA unit

## Other Trait Estimates

**Calving ease and stillbirth estimated from breed means**
**7.3 million**** HO, ****37000**** JE, ****17000**** BS,       ****2000**** GU, ****2000**** AY, ****300**** MS**
**Body size composite estimated from mature weight**
**Udder composite, Feet / Leg composite extrapolated from regressions on other traits within Holsteins**
**Size, PL, milk, DPR, SCS**

## Correlations used in Predictions

| Corr with | Size | PL | SCS | DPR | Milk |
| --- | --- | --- | --- | --- | --- |
| Udder | .26 | .30 | −.33 | .03 | −.20 |
| F&L | .22 | .19 | −.02 | −.04 | −.02 |

**Canada now scores linear conformation traits of all breeds on the same scale**

**Notes:**
From 2006 proposed Net Merit document.  Generally, good udders correlated with increased size, longer PL, lower SCS, slightly lower milk.
Feet and Leg composites positively associated with larger, longer lived, milk yield, and slight DPR decrease.
Jersey is shown for comparison. More highly correlated with size and PL, Udders were correlated with lower SCS. 
Feet and Leg composite positively correlated with DPR.

## Assumed Effects – Other TraitsTransmitting ability differences from Holstein

|  | Size | Udder | F&L | Calving Difficulty |  | Still-birth |
| --- | --- | --- | --- | --- | --- | --- |
| Jersey | −10.4 | −1.4 | −2.1 | −7.1 | −1.5 |  |
| B. Swiss | 0.0 | 0.7 | 0.3 | −3.2 | −0.7 |  |
| Guernsey | −7.3 | −0.5 | −1.3 | −4.6 | 1.1 |  |
| Ayrshire | −5.8 | −1.6 | −0.9 | −3.5 | −1.2 |  |
| M. Short. | −4.2 | 0.1 | −0.6 | −0.1 | −2.4 |  |
| Heterosis | 0.9 | 0.0 | 0.0 | 0.0 | 0.0 |  |

**Notes:**
Udder and F & L were calculated from regressions using the correlations on the previous slide.
Calving Ease and stillbirths are breed means from June 2006.
Heterosis value for size is from New Zealand. 
Calving Ease heterosis was calculated in a crossbreeding presentation 2 years ago.  Slight positive CE heterosis for 1st lactation , and slight negative for 2nd and later lactations. 
Other heterosis values assumed to be zero.

## Merit of F1 Holstein Crossbreds

| Second Breed |  | NM$ |  | CM$ |  | FM$ |
| --- | --- | --- | --- | --- | --- | --- |
| Ayrshire |  −304 |  |  −261 |  | −364 |  |
| Brown Swiss |  55 |  |  139 |  | −78 |  |
| Guernsey | −408 |  | −405 |  | −503 |  |
| Jersey |  31 |  | 153 |  | −158 |  |
| M. Shorthorn | −498 |  | −461 |  | −547 |  |

**Compared to 2005 genetic base for Holstein**

**Notes:**
Jersey x Brown Swiss F1 were +76 CM$  better than purebred Holsteins.

## Later Generation Crosses

| Holstein backcross or multi-breed |  | NM$ |  | CM$ |  |     FM$ |
| --- | --- | --- | --- | --- | --- | --- |
| HO x (BS x HO) | +28 |  | +70 |  | −39 |  |
| HO x (JE x HO) | +16 |  | +77 |  | −79 |  |
| BS x (JE x HO) | −32  |  | +109 |  | −251 |  |
| JE x (BS x HO) | −44 |  | +116 |  | −292 |  |
| HO x (BS x JE) | +44 |  | +147 |  | −118 |  |

**Compared to 2005 genetic base for Holstein**

**Notes:**
Three way cross on the bottom line +147 CM$, is similar to F1 JE x HO.

## Butterfat yield of three breed crosses was greater than from their F1 crossbred dams.
Three breed crosses averaged 14,927 pounds of milk and 641 pounds of butterfat as 2-year-olds in 1947. 

**Three breed crosses averaged ****14,927**** pounds of milk and ****641**** pounds of butterfat as 2-year-olds in 1947. **

***USDA Yearbook of Agriculture 1947***

**Three-Breed Crosses**

**Notes:**
6660kg milk
290kg fat

No predictions based on f1 daus:dam so don’t know whether this can be attributed to ‘hybrid vigor’
This group was heavy on the Red Dane sire
These were 3 breed crosses, so more hybrid vigor should be maintained (~85% in 3 breed rotations), 
as opposed to rotating only 2 breeds (~65% in 2 breed rotations)

## Scandinavian and French Breeds

**AIPL has pedigree records for other breeds (NR, SR, MO);  but few production records yet**
**For further information:**
**Interbull conversions to Ayrshire base**
**U. Minnesota scientists (Heins et al.) **

**Notes:**
Exotic Breeds - -For example: Normande, Montbelliard, Nordic Red,  Breeds that are not routinely evaluated in the US.
US has pedigree data on these breeds of interest, from Interbull. 
The US has very little domestic production data. 
Currently, Interbull puts all “red” breeds on an Ayrshire basis. 
Proposal is to combine these breeds into a “Red Dairy Cattle” (RDC) breed, however, US would convert these back to an Ayrshire breed.
All-Breed animal model would allow for “all-breeds”, and crossbreds to be evaluated.
2 articles by Brad Heins in the July 2006 Journal of Dairy Science.

## Conclusions

**Conclusions**

## Conclusions (1)

**All-breed model accounts for:**
**Breed effects and general heterosis**
**Unequal variances within breed**
**May 2007 implementation expected**
**PTA converted back to within-breed bases, crossbreds to breed of sire**
**PTA changes larger in breeds with fewer animals**

## Conclusions (2)

**Breed effects were estimated**
**Yield, PL, SCS, DPR by all-breed model**
**Calving ease and stillbirth breed means**
**Udder, F&L composites from other traits**
**Lifetime Net Merit formula for August 2006 applied**
**Holsteins still superior for FM$**

**Notes:**
Breed effects for Yield, PL, SCS and DPR using an “all-breed” animal model, very similar to phenotypic breed means.

## Conclusions (3)

**BS x HO and JE x HO crosses had higher NM$ and CM$ than HO**
**BS x JE had higher CM$ than HO**
**Three-breed crosses (HO, BS, JE) are higher than HO backcrosses for CM$, similar for NM$**
**Use best bulls within each breed**

## Acknowledgments

**Several others at AIPL contributed greatly to this project, including Mel Tooker, George Wiggans, John Cole, Jay Megonigal, and Ashley Sanders**