# Presentation: 244973

## Quality of Data Included in Genetic Evaluations for Daughter Pregnancy Rate

**Notes:**
The Animal Improvement Programs Laboratory (AIPL) have provided genetic evaluations for daughter pregnancy rate (DPR) beginning February 2003. Over the last year, AIPL staff examined several methods to improve the quality of data used to calculate DPR.  Today I wish to present some of this information. 

## Evaluation Methods

**BLUP Animal Model**
**Same programs used for yield, PL, SCS**
**Adjust for regional, seasonal and parity differences.**
**Convert to preg rate = (233-DO) / 4**

**Notes:**
The national evaluations include up to five lactations for each cow (the same number as for yield traits). Cow fertility records are processed with the same animal model programs that AIPL uses for yield traits, productive life, and somatic cell score. Cows in the same herd and management group are compared directly, and the definition of management groups is the same as for yield traits except for cows that change herds during a lactation. For yield traits, the herd providing the most information is the herd of evaluation. For pregnancy rate, the herd in which the cow became pregnant or from which the cow was sold because of reproductive problems is the herd of evaluation.

Days Open are converted to pregnancy rate using this simple linear formula.
Before using the data, several adjustments to DO are made to the data. 

## Average breed effects across regions and time by calving month

**Notes:**
This summary is all the breeds, over all the regions over all times. The first set of adjustments are made to days open based upon the region of the country where the herd is located. Records are also adjusted for seasonal effects prior to analysis. Initial research indicated that for all breeds fertility is best with fall calvings and poorest with spring calvings because fewer cows express estrus or conceive during hot summer months. Some breeds have insufficient numbers of herds to obtain accurate adjustments in all five regions and five time periods. Thus, Jersey adjustments were applied to Guernsey data, and Holstein adjustments were applied to data from all other breeds.
Regional differences and seasonal differences were covered in greater detail by Ignacy Misztal from the University of Georgia

## Parity Pre-Adjustments Initiated May 2003

| Parity | Holstein | Jersey |
| --- | --- | --- |
| 1st |      0 |      0 |
| 2nd |    - 4.1 |    - 3.7 |
| 3rd |    - 7.1 |    - 5.6 |
| 4th |  - 11.7 |    - 9.4   |
| 5th |  - 16.7 |  - 13.4 |

**Notes:**
Parity has been adjusted in the animal model, however adjusting the data for parity before entering the animal model allows DPR to be the same as other traits.
Jersey values were applied to Guernsey data, and Holstein to the remaining breeds.  No adjustments are made for 1st parities with increasing adjustments as parities progress. 
All of this data flows to AIPL from the Regional Processing Centers. After adjustments are made to ‘raw’ days open,  a critical look is taken at the data.

## Pregnancy Rate Evaluation Data Sources

**Days open reported, verified calving interval.**
**No calving interval, days open reported.**
**No breeding date reported, next calf.**
**No breeding reported, no next calf.**
**Sold for reproductive reasons, days open set to 250.**
**Pregnancy verification codes have been available since 2002.**

**Notes:**
Date pregnant is determined from several information sources and is verified by the cow's calving interval when available. The best information on date pregnant is the date of last insemination verified by the next calf's birth date occurring within 15 days of the expected date. If no inseminations are reported through Dairy Herd Improvement records, the date pregnant is calculated by subtracting an average gestation length from the date of next calving. For lactations that do not have a date of next calving available (because the cow has been sold, the herd stopped testing, or the current date is less than the last breeding date plus the average gestation length), the date pregnant is assumed to be the date of last insemination but cannot be verified. The last reported breeding date is also used if the next lactation is initiated by abortion. The last insemination is assumed to have failed if no calving is reported within 295 days and the cow is still alive at that time.
A final source of information for some lactations occurs when the owner reports that a cow was sold because of reproductive problems. Such cows are assumed to be nonpregnant when sold, and the date of last insemination is disregarded. 
Since 2002 pregnancy verification codes have been available for use which allow earlier use of data.

## Pregnancy Rate Evaluation

**Records considered complete at 250 DIM**
**Lower limit set to 50 DO**
**5%**** of records**
**Upper limit set to 250 DO**
**14%**** of records**

**Notes:**
Records for pregnancy rate are considered to be complete at 250 days in milk (DIM), and pregnancy status after 250 DIM is used but set to 250 DO. Date pregnant is set equal to 50 for any cows that become pregnant before 50 DIM. Some extremely early pregnancy dates obtained by calculation from date of next calving are inaccurate because of short gestation lengths or unreported abortions. The lower and upper limits of 50 and 250 are applied after adjusting days open for region & season effects and affect 5% and 14% of records, respectively.

## Sources of Fertility Data 1998-1999

|  | AY | BS | GU | HO | JE | MS |
| --- | --- | --- | --- | --- | --- | --- |
| Breeding date verified    by next calving date | 55 | 54 | 48 | 57 | 64 | 53 |
| Breeding date disagrees with next calving date | 6 |  8 |  8 |  5 |  5 |  8 |
| Breeding date but no next calving date | 16 | 15 | 20 | 19 | 17 | 16 |
| Next calving date, but no breeding reported  |   7 |  9 |  8 |  6 |  6 | 11 |
| Cows sold for reproductive problems |   6 |  5 |  5 |  5 |  3 |  4 |
| No information for fertility | 10 |  9 | 11 |  8 |  5 |  8 |

**Sources of Fertility Data 1998-1999**

**Notes:**
This table gives the percentages of recent cows with each type of fertility information or with no information. For Holsteins and Jerseys, only 6% of lactations had a next calf born with no previously reported breeding date and another 5% had breeding dates inconsistent with birth date of the next calf. Thus, accurate breeding dates are reported by most farms, but many of the reported final breeding dates (19% for Holstein) cannot be verified because the cow was sold for reasons other than reproductive problems. Differences among breeds in percentages of lactations terminated by reproductive culling seem consistent with the smaller decline in fertility experienced by Jerseys.

## May 2003 Evaluation

**Holstein**** data from May 2003 evaluation**
**40 million**** lactations**
**16 million**** cows**
**Example evaluations: **
**Data for recent, well-sampled bulls **
**Actual bull evaluations**

**Notes:**
Data used by AIPL to calculate DPR include over 40 million lactation records from 16 million cows that calved since 1960. Having listened to other AIPL staff talk about the theory behind DPR, let’s look at actual bulls from the May 2003 evaluation:

## Older Bull Evaluations (May 2003)

| Bull | REL | DO | DPR | PL | NM$ |
| --- | --- | --- | --- | --- | --- |
| Duster | 99 | - 9.6 | +2.4 | +4.3 | +451 |
| Bellwood | 99 | - 0.8 | +0.2 | -0.5 | +353 |
| Mandel | 99 | +7.2 | - 1.8 | -0.7 | +244 |
| Luke | 99 | +9.2 | - 2.3 | -1.8 | +136 |
| Mountain | 99 | - 4.4 | +1.1 | +1.1 | +280 |
| Mascot | 99 | +3.2 | - 0.8 | -2.9 | +20 |

**Notes:**
These bulls ranked by NM are older well sampled bulls with hundreds of daughters.  These bulls were used by AIPL to introduce DPR to the public, and is a way to show the relationship between DO and DPR.  These values have been updated, but have not changed much since they were announced almost a year ago. 

## Bulls ranked by Net Merit May 2003

| Bull |  DPR |   PL | Net Merit $  |
| --- | --- | --- | --- |
| O Manfred Justice   |   0.4 |   3.1 | 759 |
| Vision-Gen Ozzie  | - 0.7 |   0.6 | 692 |
| Emerald Dawson | - 1.1 |   0.9 | 675 |
| Pagen-Ernwood | - 1.3 |   2.2 | 630 |
| Ricecrest Marshall | - 1.7 | - 0.1  | 625 |
| Carol Prel. Mtoto | - 1.5 |   2.0  | 607 |
| Windsor Machoman |   1.1 |   3.0 | 598 |
| C.-Corner Defense |   0.0 |   2.6 | 593 |

**Notes:**
When bulls are viewed based on Net Merit, we can see that high Net Merit does not necessarily mean low fertility.
High DPR appears correlated to higher PL.
But low DPR is not necessarily the same as Pagen / Mtoto show.

## Future Directions

**Pregnancy rate will be included in Net Merit.**
**Fertility records will be used earlier in lactation.**
**DPR can be used in multi-trait PL.**
**Fertility database and formats will be improved.**

**Notes:**
What lies ahead?
Pregnancy rate will be included in Net Merit
Fertility records will be used earlier in lactation
DPR can be used in multi-trait PL.
Fertility database and Formats will be improved...
What do I mean by formats?
Formats are simply viewed as the way in which data is passed to AIPL.  We are researching a new Reproductive format.

## Format 5 - Reproductive Records

**Animal ID, sire ID, dam ID, X-ref ID**
**Animal herd code information**
**Reproductive segments:**
**Date of event, code for actual or estimated date**
**Includes many events, service sire ID**

**Notes:**
AIPL has just asked the DRPC’s to begin sending us data in order to improve our ability to access reproductive data.
The first part of new reproductive format 5 is similar to out production format 4.  Includes ID’s and herd info.
Currently, AIPL is limited to using only the last breeding date.  Using the new format will allow much greater flexibility in accessing levels of fertility.

## Format 5 - Reproductive Event Codes

**H  Observed in estrus (heat) but   ****	**** not inseminated**
**S  Synchronized estrus event ****	****  ****	**** (injection or other methods)**
**A  Artificial insemination**
**N  Natural service breeding**
**E  Embryo donation**

**Notes:**
H = A concern is that the correlation of milk yield with fertility may be caused not only by estrus expression or conception problems in high-producing cows but also by the owner voluntarily waiting more days to begin breeding the high producers.( voluntary waiting period). These causes and effects are difficult to separate. 
S= Another concern is that rankings could differ for herds that synchronize estrus versus herds that rely on traditional estrus detection.
A/N = Keep track of service sires, and validate cow sires.
E= credit for donor cows

## Format 5 - Reproductive Event Codes . . .

**I****	****Embryo implantation**
**P****	****Confirmed pregnant**
**O****	****Confirmed not pregnant (open)**
**X****	****Cow given a “do not breed” ****	**** ****	****designation**
**D****	****Delete event(s) for this “date of   ****	****event”**

**Notes:**
P= Currently we can store this information, but it is not associated with any date. Using this new data will allow AIPL to associate a date with this event.
O= previous breeding date is not used.
X= do not breed, health reasons?
D= ability to correct errors

So using these ‘new’ event codes AIPL:

## Format 5 in the Future:

**Separate estrus expression and conception rate (female fertility)**
**Service sire fertility (male fertility)**
**Keep track of ****ALL**** service sires, number and type of services, not just the most recent**

## Conclusions

**Most herds are reporting accurate breeding dates.**
**Records currently used only if complete   (250  DIM).**
**More reproductive events will be obtained in the future.**
**More accurate and complete data will provide better fertility evaluations for farmers and industry.**

**Notes:**
Most herds are reporting ‘good’ data.
Currently records are used only if they have the opportunity to be complete so that selection bias can be avoided.
Methods to use actual pregnancy diagnoses and records in progress are being developed and used so that pregnancy rate can be evaluated earlier in lactation. Incomplete and unverified records should receive less weight in the evaluations but currently all records that are included get the same weight.
Information on each insemination may be used in the future, but currently only the date of successful or last insemination is stored at AIPL. Also, AIPL does not yet collect data on pregnancy rate for heifers. Age at first calving could possibly be evaluated, but heifer fertility traits are somewhat different genetically from cow fertility traits.
More accurate data = more accurate genetic evaluations.
Thank you!

## Acknowledgments

**All DHIA herds and processing centers contributed data**
**Lillian Bacheller for work on improving the fertility database**
**John Clay suggested expressing cow fertility as pregnancy rate**