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How to meet your herd’s objectives with genomic testing

Stuart Bauck Published on 24 August 2015

Whether you concentrate on developing elite genetics or producing milk for the market, genomic data can be a valuable tool in achieving your goals. In this article, we will examine testing options and how both breeding herds and commercial herds might use those options differently.

To understand the testing options available to dairy producers, it is useful to remember that for the dairy industry, the basis for virtually all of the genetic evaluation is the USDA Agricultural Research Service (USDA-ARS).



The Animal Improvement Programs Laboratory and the Bovine Functional Genomics Laboratory were merged to form the Animal Genomics and Improvement Laboratory.

Together, they are responsible for maintaining the database of production records submitted via the dairy records companies, ensuring the integrity of the pedigree records for the animals in the database and merging it with genomic data to produce genomically enhanced predicted transmitting abilities (PTAs).

Within the scope of this evaluation are the production and type traits that define the modern genetic evaluation. The Council for Dairy Cattle Breeding (CDCB) now manages the interface between producers and the USDA-ARS and is responsible for collecting data and preparing reports.

So what are the practical implications of this? For breeder herds, participating in the official dairy genetic evaluation gives them access to a whole host of information relevant in selecting superior breeding stock to produce the next generation of elite cows and bulls. This includes:

  • High-accuracy genomic PTA for production and type traits
  • Parentage verification to the sire and the dam
  • Disease status for important lethal conditions such as fertility haplotypes and lethal recessives such as complex vertebral malformation and brachyspina, along with breeding status for horn poll, coat color and other traits

To access this information, there are several things the producer must choose to do. First, the producer has to agree to submit the information to the CDCB in the agreed-upon format, which means a formal nomination process (almost always undertaken by an A.I. company or genotyping service laboratory) that includes completing a number of mandatory information fields (approved identification, sex, breed, etc.), followed by submission of genotype data to the CDCB.


Second, the producer will select the appropriate genotyping product specific for their requirements. Since accuracy of the genomic PTA is critical, they will usually always select a higher-density genotyping product that includes “add-on” content. Products in this category range from 18,000 to 150,000 SNP chips and are typically priced at more than $45.

For these products, the animal’s nomination information, together with its genotype data, is submitted to the USDA, and there it is converted to a common genotype format and the genomic prediction is conducted.

Parentage is verified, PTAs are calculated, and status is determined for genetic conditions along with selection traits such as coat color. In some cases, the genotyping service provider will also make available the specific carrier status for traits such as A2 milk and horn poll based on causative mutations.

There is one further option in the category of CDCB-provided results, and that is an ultra-low-density solution. This product uses a low-density genotyping chip with limited add-on content, and while it does not have the same versatility in terms of reporting on lethal conditions and horn poll, it does have the benefit of important cost savings while still providing the same accuracy or reliability of PTA based on USDA genomic evaluations.

The price for this product is under $40, so for the seedstock breeder, this is an attractive option for accessing genomic predictions.

What about the commercial dairy producer? What are the options available for them? While a breeding herd places high value on the accuracy of the genomic prediction and the add-on content for lethal conditions and value-added traits such as horn poll, coat color and A2 milk, that is generally not the case for the commercial producer. For them, the focus is on three things:


  • Cost
  • Ability to rank heifers, with or without parentage
  • Turnaround time for availability of results

To address these items, the formal process of CDCB/USDA nomination may not be relevant for them, and genotyping solutions costs in excess of $40 per animal may be beyond their objectives. Plus, every day a calf spends in an operation before a management decision is made is another day of feed and overhead costs. To address this need, the commercial producer has several options available.

First, the previously mentioned, ultra-low-density solution will give a USDA evaluation at a price point that makes sense for a commercial operation. Since add-on content is not required by the commercial producer, this can be an attractive option.

In addition, it may make sense to look outside the USDA evaluation to other genotyping solutions. Today, additional solutions are available that will calculate a genomic value derived strictly from the genotype information – referred to as a direct genomic value or sometimes called a molecular breeding value.

It provides an accurate estimate of direct genetic merit, amenable to simple sorting of heifers for future potential, and results are usually available in two to three weeks from the time the sample is received in the lab.

It does not include parentage at the present time, and add-on traits such as horn poll, coat color and A2 milk are not provided. For the commercial dairy producer looking at a simple but effective sorting tool, this is an excellent option.

In this article, we have looked at solutions frequently used by breeding herds to get genomic predictions and key breeding traits, and for the commercial dairyman looking for access to low-cost, high-value sorting tools for real-time management under their conditions.

In the end, there is a solution appropriate for every application and the knowledge available for how to use it to their best advantage to remain competitive and at the forefront of production in the future. PD

  • Stuart Bauck

  • Veterinarian and Manager
  • GeneSeek
  • Email Stuart Bauck