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Wading through genomic data

Stewart Bauck Published on 31 December 2014

Today, many dairy producers are integrating genomic testing into their daily breeding and selection decisions or contemplating doing so. It is remarkable to think that a tissue sample collected from the ear, a hair pulled from the tail switch or a drop of blood spotted onto a card from a day-old calf can get you a genetic evaluation equal to progeny tests on many daughters of sires.

Built on the foundation of the database maintained over the years by the USDA Animal Improvement Programs Laboratory (USDA-AIPL), genomic testing uses the relationship between the single nucleotide polymorphism (SNP) markers on low-density to high-density chips and the phenotypic data collected on the farm to create an estimate for the animal’s genetic merit with high reliability.



The great news – and bad news – is that for every trait that the USDA does a genetic evaluation on (including production as well as type), you can now get both a traditional and a genomic predicted transmitting ability (PTA), along with the associated reliability. This is bad news only in the sense that it is a huge amount of information to deal with.

The genomic evaluation report produced by the USDA on a weekly (formerly monthly) basis contains 198 columns of data on every animal – not including the pedigree file – as well as a new report that gives the projected inbreeding if a tested female is bred to any one of more than 25,000 available A.I. sires. For the average dairyman, that amount of information is not something that is easily managed.

Fortunately for the dairyman, there are some shortcuts and solutions that can help them to use this information in a more comprehensive manner. To begin, the report contains a genomic estimate for several of the most important composite traits, recognized by the industry for their value in balanced selection. Composite traits include Net Merit, Cheese Merit, Fluid Merit and Grazing Merit (Table 1).

Transmitting ability

  • Net Merit. Net Merit is reported as a genomically enhanced index and contains the following traits in a new formula that was updated December 2014 with the addition of new fertility components, such as heifer conception rate and cow conception rates, and updated economic weightings.

    As a trait, Net Merit is frequently the singular index that producers will use to rank animals, and in most instances where samples are submitted to a commercial genotyping facility, the report received back will include the ranking of animals within the report based on Net Merit and will also include the ranking of the animal against the entire database of all animals within the USDA database on a percentile basis (Table 2).


    In addition to the actual Net Merit figure, the report contains an estimate of the reliability or accuracy of the prediction for Net Merit, and typically, with the parent average and a genomic test, that reliability is in the range of 70 percent, which for this trait means it has the equivalent accuracy to 20 daughter records.

  • Cheese Merit. If Net Merit is not the index that is most relevant for you, there are several others that are reported by the USDA. The first is Cheese Merit, and this index is targeted to those herds paid for components through their processor. In this instance, the weight is on fat and protein, along with Productive Life; in fact, there is a penalty for fluid production (Table 1).
  • Fluid Merit. If Cheese Merit is not applicable for your herd, there is a Fluid Merit index that puts weighting on milk yield and longevity and is designed for herds that have a focus on fluid milk production.
  • Grazing Merit. Recently, a new index has been introduced that caters to herds that use seasonal calving based around grass production, referred to as Grazing Merit. In this instance, the selection is around fertility and those traits that favor efficient milk production from grass.

Dairy net merits

In addition to composite traits, there are other combination measures available to dairymen. These include:

  • Holstein TPI and Jersey JPI indexes. For herds that nominate through the Holstein or Jersey Associations, then index traits such as Total Performance Index (TPI) or Jersey Performance Index (JPI) are available that, like Net Merit, rejoin a number of important component measures into an overall formula for balanced selection.
  • PTA Type. In addition to the index traits mentioned above, the USDA gathers the information provided from classifiers and produces PTAs for a wide variety of type traits that dairymen are familiar with and use on a routine basis.

    Among these, PTA Type is frequently used as the overall measure of body type, including feet and leg scores and udder composite, to describe the animal with the most appropriate physical traits that support efficient dairy production under a variety of management situations.

If the existing or commonly reported index traits are not appropriate for your individual circumstance, then the data reports commonly available allow you to design and implement your own custom index appropriate for your needs.

  • Custom indexes. With the report available in a worksheet format, you can apply whatever weighting you want to the traits of greatest interest to you and rank heifers from best to worst based on those selections.

    When you do this, it is important to remember that the production traits are on different scales, so you might need to use a multiplier or weighting for each trait to give it the appropriate amount of emphasis.


    For example, the trait of Productive Life is measured in months, and an average value might be 2. By contrast, milk yield might have an average value of 400, so to include those traits into a custom index and give them equal weight, you would need to multiply the Productive Life PTA by 200, or conversely, divide the milk yield PTA by 200 so they are on the same scale.

In the final analysis, there is a lot of important information reported from the USDA-AIPL genomic evaluations, and for those that like the details, there is plenty to play with.

On the other hand, if you are looking for some simple and proven tools that allow you to rank and compare animals, then the index traits of Net Merit, Cheese Merit, Fluid Merit or Grazing Merit are helpful. Breed association composite traits, such as TPI or JPI, are also a way to compile a lot of important traits into a single figure.

Many type traits are available, but the composite index of PTA Type, Feet and Legs Composite or Udder Composite give you some good tools that are easy to use. Finally, if you have a particular focus you are interested in, then get a copy of the report in a worksheet format and get to work on your own composite index that best meets your needs. PD

Stewart Bauck is a general manager with Neogen Corporation. He can be contacted by email.