Council on Dairy Cattle Breeding
April 28, 2010

The Animal Improvement Programs Laboratory staff presented various research updates on current projects and future projects on the day before the meeting convened. They went into detail on the changes from the last genetic evaluation run and explained the theories that created some of the confusion to the general public. The research helped answer some of the questions that were raised over the last several weeks. They indicated with confidence that the current values for sires and cows are the most accurate to date.

The Council meeting was convened by Chairman Kendall. Several reports were given to the Council. Jay Mattison gave the QCS report on assessments of DHIA organizations which was approved.

Marj Faust gave a report on the Interbull meeting in Paris. She reported that the Interbull staff has completed its new database format. There was a discussion of creating an ad hoc committee of experts to advise the Interbull group on areas of technical expertise. Names will be solicited from each country. Interbull is working on implementing genomics in the future. They have done a preliminary validation run and plan on more research runs in the near future. The Council approved the sending of US genomic data by AIPL for a research run but not for general distribution. The next Interbull meeting will be in Riga, Latvia.

The NAAB reported that they have funded a post doctoral associate at AIPL to help develop more research for genetic improvement. They also asked for everyone to support the allocation of funds for the AIPL staff that have been included in the current budget.

Then a discussion on the changes of cow evaluations and its confusion to the breeder was held. This was described as one of the most significant changes in the last 15 years and was done to improve accuracy. The staff did not perceive the end results being as controversial as they turned out to be. The biggest issue is the two different bases for females currently. AIPL is working on five possible solutions to the multiple base problems. The next discussion was on imputed cow genomic values. The solution would be to label genomic values as to which are true genomic values and which are imputed. A motion from the Holstein Association was made to remove the female component of the genomic prediction equation until more research is completed. This motion failed. A motion was made that in the future all adjustments should be approved by an industry advisory committee before they are implemented. Motion passed.

With the potential of a new, cheaper, smaller SNP chip becoming available this summer for genomic evaluation, the discussion followed as to how to use this new data. Since no evaluation data is currently available a motion was made to delay the implementation of this new data for the August evaluation run. Then, that the research would be reviewed in October for possible inclusion in the December evaluations. Motion passed.

A report from the US Database committee outlined the current situations and identified potential threats and challenges to the future enhancement of a dairy database for the United States. Ongoing discussions will be held to develop more concrete proposals for future meetings.

A report on the National Animal Identification system was given. Because of populist pressure the government has abandoned the previous system which was being used by the majority of dairy breeds to identify animals. The movement to an electronic ID system has been derailed for the time being. The current feeling from government sources is that they will probably go back to a metal ear tag system that can only be administered by veterinarians as the solution. This is a huge step backward for our industry and one that will be expressed to government officials at two listening sessions in May.

The next meeting of the Council will be in Milwaukee, Wisconsin on October 27, 2010. With no other business the meeting was adjourned.

Reported by David Selner

Fertility Data
By Duane Norman

The numbers of new records included in evaluations for sire, cow and heifer conception rates are considerably lower than in past evaluations. As of January 2010, fertility data in format-5 (reproductive) records were provided for most herds by three dairy records processing centers (DRPCs: AgriTech Analytic, AgSource and Dairy Records Management Systems) and for six herds by a fourth DRPC (DHI-Provo). For April 2010 evaluations, records from AgriTech Analytics continued to be provided for most herds, but records from Dairy Records Management Systems and AgSource were provided only for herds requested by Genex/CRI. The reduction in additional numbers of format-5 records had a small limited effect on daughter pregnancy rate evaluations because current days open are reported in format-4 (lactation) records.

However, April genetic evaluations for cow and heifer conception rates are expected to have lower reliabilities than in January for most bulls. Likewise, the average number of inseminations per bull is expected to decline for phenotypic evaluations of sire conception rate. When genetic evaluations for conception rate are released in the future (possibly August 2010) for cows, any cow without a breeding record will not receive an evaluation.

Stay tuned to holsteinworld.com next week for all the latest in sire summary news as it happens!

AIPL Changes to Evaluation System (April 2010)
Beltsville \ BARC Animal & Natural Resources Animal Improvement Programs

Cow adjustments in genomic evaluation of yield traits
By George Wiggans, Tabatha Cooper, and Paul VanRaden

Traditional predicted transmitting abilities (PTAs) are inputs for genomic evaluation, but cows with high traditional PTAs for yield traits may be over evaluated. Adjustments were developed to rescale cow PTAs for yield traits to be more comparable to bull PTAs. Resulting genomic evaluations were more accurate when the rescaled cow PTAs were included in estimation of marker effects.

Genomic evaluations for the top cows, top young bulls, and top heifers decreased by about 250 pounds for milk, 8 pounds for fat, and 5 pounds for protein, whereas genomic evaluations for the top bulls with daughters decreased only by about 70 pounds for milk, 3 pounds for fat and 2 pounds for protein. Adjustments were largest for foreign bulls with a high proportion of genotyped daughters.

The population average of all bulls with daughters decreased slightly
by 40 pounds for milk, 1.5 pounds for fat, and 1.5 pounds for protein; standard deviations also decreased slightly by about 1%.

Correlations between genomic evaluations before and after the adjustment were 0.997 for bulls with daughters and 0.990 for cows and young animals. Net merit decreased by as much as $40 for many of the top cows and young animals because of the yield trait adjustments.

Only yield and component percentage traits were adjusted because non-yield traits had less variance in females than males and did not benefit from applying these same methods for PTA adjustment. [See Wiggans et al. (2010) for further documentation of methods.]

Haplotypes used for imputing genotypes
By Paul VanRaden, George Wiggans, and Jeff O’Connell

New methods were used for imputing missing genotypes in genomic evaluation. About 1% of marker genotypes are missing in initial data, and previously about half of those were imputed using gene content of relatives and an algorithm that did not use neighboring markers or map location on the chromosome. Program findhap.f90 was developed to determine the paternal and maternal haplotypes that sum to the animal’s genotype.

Simulation results indicated that the initial rate of 99.0% for correct
genotypes was increased to 99.95% after imputing the missing values with haplotypes. The same methods will allow imputing the much higher proportions of missing data that will result when lower or higher density marker sets are mixed with current data containing 50,000 markers. More than 1,000 nongenotyped cows had at least 90% of their single nucleotide polymorphisms (SNPs) correctly imputed using genotypes from multiple progeny (usually 5 or more). Those imputed genotypes are included in SNP estimation, and such cows will be listed in evaluation files with the genomic indicator set to 1 and will have a sample identification of “inputed” in the XML file. [See VanRaden (2010) and VanRaden et al. (2010) for further documentation of haplotyping methods.]

Improved reliability for genomic evaluations
By George Wiggans and Paul VanRaden

The contribution to reliability from genomics was modified to consider the sum of genomic relationships of the animal with each animal in the predictor population weighted by the reliability of that predictor animal’s evaluation. Previously, the contribution to accuracy from genomics was assumed to be the same for each animal within a breed. The standard deviation of the change in reliability was about 2 for young bulls and heifers and 1 for bulls that had daughters included in their traditional evaluations. [For more information on the genomic reliability approximation, see Wiggans and VanRaden (2010).]

LEADER TAKES UK NATIONAL HOLSTEIN CROWN
RESULTS FOR THE 2009 UK NATIONAL HOLSTEIN SHOW

SUPREME CHAMPION (and BEST UDDER)
Wills Brothers, Bassingthorpe Leader Dilys 10

RESERVE SUPREME CHAMPION (and EXHIBITOR BRED)
Seaton Farms, Styche Lyster Sally PI

HONOURABLE MENTION
Wills Brothers, Riverdane Outside Hazel

Monday 16th February 2009
Holstein UK celebrated 100 years of cattle breeding history as part of its centennial year celebrations with the 28th hosting of the National Holstein Show at The National Agricultural Centre, Stoneleigh, Warwickshire.

Judge Brian Carscadden placed the sixth lactation Bassingthorpe Leader Dilys as his Mature, Best Udder and Supreme Champion. Seaton Farms split Wills Brothers from a Champion and Reserve double with Styche Lyster Sally edging out Riverdane Outside Hazel into the Honourable Mention placing. ~Bruce Jobson reporting

A full report on the 2009 UK National Show will appear in an upcoming issue of Holstein World.

Update from The Centennial Celebration of the Animal Improvement Programs Laboratory (AIPL) – Oct. 28, 2008 – Baltimore, MD
By David Selner

The Animal Improvement Program Laboratory (AIPL) recently celebrated their 100th anniversary of helping United States dairy producers. At the general session of this event, scientists presented the research data that describes how genomic information can be utilized to increase the accuracy and the reliability of current genetic evaluations. Genomic research by the USDA laboratory has been ongoing for many years, but was only made possible by the cooperation of the major National Association of Animal Breeders members and Semex, who are Cooperative Dairy DNA Repository (CDDR) Contributors.

Questions have been raised as to who has access to this research data and over what time period. At this meeting, USDA scientists explained the specifics behind this research project. In the early 1980s breeding companies were approached to provide straws of semen from popular sires and all young sire progeny test sires. All of the major companies did provide this DNA material to create the DNA library at no cost to USDA. Genomic research continued through the 1980s and 1990s but no substantial marketable products were developed during this time frame. In the last few years the development of more sophisticated equipment and techniques to examine DNA in greater detail has allowed more progress. Suddenly the research became more focused on increasing genetic merit predictions with gene level data.

To avoid getting risky experimental data out in the public domain, and yet to help determine if this experimental data was truly useful a limited amount of information was shared with industry experts from the original CDDR collaborators. To formalize this process, an agreement was developed to further fund more research at USDA by the original collaborators. More DNA material and funding was provided by CDDR members and USDA granted exclusive access (one of USDA’s technology transfer mechanisms) to receive male genetic predictions during a five-year research period. USDA scientists justified this action by explaining all of the time, money and DNA material that had been provided over the last 20 years with no expectations from the original collaborators. In addition this research is still ongoing and will take several more years to complete. Even today with the January public release of genomic enhanced genetic evaluations, more research is being done to refine techniques and provide greater accuracy and reliability.

Segments of the industry, not CDDR contributors, have asked for clarification on this agreement. USDA’s simple answer was to cover the initial investment of the cooperators, to allow further investigation without misleading the whole breeding industry and to allow a reasonable transition phase into a different method of evaluating dairy genetics. No intent to slight certain segments of the industry or put them at a disadvantage was ever implied.

All genomic data completed in this first phase of research on currently marketable sires will be provided to the public in January 2009. Additional research is ongoing and will take time. The final timeline is to release all of the research genomic data on all sires in the DNA library in the spring of 2014. The genomic evaluations on females tested in approved laboratories and submitted to USDA will be made public in January 2009 by the respective breed associations as part of their normal products and services.

The concerns of some people about secrecy and exclusivity appear to be overly sensitive to their real importance. It appears to be a function of timing of the experimental data, its limited release to gain invaluable data to confirm research results and the fact that the research is still ongoing. No intent was made to keep people uninformed. Rest assured that by 2014, everyone will have access to hopefully the most accurate system of genetic evaluation in the world.

Dr. Ray Nebel has been visiting with DairyLine Radio over the past few weeks about things that can derail a herd`s reproductive success. To recap, the things he has touched on so far are:
-Transition
-Nutrition
-Disease
-Lack of systems

But the constant behind all of these things is people! Working with good people translates into a good team that will work hard to make things better. They are the ones working with the transition cows, mixing the ration, treating sick cows, etc. There must be strong compliance to set protocals and communicaton within the team. Schedule monthly team meetings as a time to have question & answer for everyone on the team.

Audio clip: Adobe Flash Player (version 9 or above) is required to play this audio clip. Download the latest version here. You also need to have JavaScript enabled in your browser.

In DairyLine`s continuing segment on what will derail reproduction in a herd, Dr. Ray Nebel of Select Sires cites disease as the third most important. Proper transition cow management and nutrition were the first two areas producers should be concerned with.

In regards to disease, the big three that you should screen for are BVD, Neospora & Leptospirosis. BVD is a disease that can mutate easily so you need to be vigilant in your testing, which can be done with a milk sample. Neospora can result in abortion in the second trimester and testing should be performed on the aborted fetus to see if that was the cause. Lepto results in lower conception rates and can be screened for with a urine sample. Work closely with your vet to stay on top of prevention of these 3 diseases that can cause problems with your herd`s reproductive health.

Audio clip: Adobe Flash Player (version 9 or above) is required to play this audio clip. Download the latest version here. You also need to have JavaScript enabled in your browser.

Dr. Ray Nebel of Select Sires shares important nutrition elements all producers should be aware of and continue to monitor in order to ensure a reproductively healthy herd.

1. Dry Matter Intake
2. Bunk Management
3. Energy Density
4. Protein Type & Level
5. Minerals
6. Toxins

Utilize the expertise and experience of your nutritionist. Make sure to make daily “walk throughs” a part of your routine – too much or too little feed, clean water, comfort of cows. Also, monitor the Milk Urea Nitrogren (MUN) of the herd as it is an indicator of nitrogen not utlized by the cow.

Audio clip: Adobe Flash Player (version 9 or above) is required to play this audio clip. Download the latest version here. You also need to have JavaScript enabled in your browser.

Knowing and being able to recognize the warning signs that might derail reproduction is very important. In the weeks ahead DairyLine Radio and Dr. Ray Nebel of Select Sires will be visiting about this topic. To start this series, Thursday`s Reproductive Moment focused on proper care of transition cows.

The transition period is the most important time in a cow`s reproductive cycle. Proper care during this time is the key to getting off to a good start as the cow enters the milking herd. The primary concerns are problems calving, metritis, metabolic disorders and excessive weight loss. Close monitoring of close-up cows (2-3 weeks prior to calving) is important. Of special concern is overcrowding.

To listen to Dr. Nebel`s full segment on DairyLine Radio, click the play button below:

Audio clip: Adobe Flash Player (version 9 or above) is required to play this audio clip. Download the latest version here. You also need to have JavaScript enabled in your browser.

Dr. Ray Nebel shares information in Thursdays Reproductive Moment regarding identifying your herds early problem cows. The entire DairyLine Radio segment can be heard by clicking the play button below. Here are a few of his key points.

It used to be that in order to identify problem cows in the herd, the only tool dairy producers needed was “cow sense.” This ability to recognize and understand when cows are uncomfortable or just arent doing their best, is becoming more and more of a lost art. Instead, dairies have come to rely on tools such as internal body temperature monitors and locomotion scoring. By identifying the problem cows early on, producers will avoid investing the time, money and labor to get her pregnant.

Audio clip: Adobe Flash Player (version 9 or above) is required to play this audio clip. Download the latest version here. You also need to have JavaScript enabled in your browser.