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The April 2020 genetic evaluation – a summary of the changes

Sophie Eaglen for Progressive Dairy Published on 17 April 2020

The April 2020 sire evaluation had more changes than usual. This is not coincidental. The most noticeable of changes was the genetic base change.

Every five years, the U.S. genetic evaluation updates its genetic base to keep it up-to-date with the current milking population. Our last genetic base change was in 2015, and it’s therefore time to adjust the base again.

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Because the genetic base change affects PTAs already, it’s beneficial to include others changes to models, traits and indices in the same evaluation. That way, the dairy industry isn’t hit with multiple large changes in a row but instead has one large “reset” and can then continue with a stable set of proofs. It can be confusing, however, to understand all the changes and how they affect the PTAs on familiar and new bulls.

Below is a summary of all the changes to the genetic evaluation that were implemented in April 2020. While it is impossible to calculate what change caused what PTA to shift, the list below may give you an idea of why a certain PTA on a specific bull changed the way it did.

Health traits
Jersey

U.S. Jersey producers can start breeding for disease resistance to common health disorders. The Jersey breed received six new health traits this sire evaluation. The traits are mastitis, displaced abomasum, milk fever, metritis, ketosis and retained placenta – the same traits launched for Holsteins in April 2018. The traits will be expressed in the same manner as the Holstein proofs, as a percentage of resistance above average. The average percent of mastitis resistance in the Jersey breed is 89.6%.

In a herd with average management conditions, daughters of a Jersey bull with a +3.0 for mastitis resistance are thereby expected to have an average resistance rate to clinical mastitis of 89.6 + 3 = 92.6%. The new CDCB health trait evaluations for Jerseys were derived from data recorded in Dairy Herd Information (DHI) herds. There has been a concerted industry effort to collect more Jersey health data for the national collaborators’ database managed by CDCB. Despite low heritabilities, the new traits are a great opportunity for the Jersey breed to select for even healthier animals.

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Holstein

As more health data is collected and we are getting used to the health traits on Holsteins, the CDCB is working hard to improve their predictability. In April 2020, new editing criteria were implemented to make both the Holstein and Jersey health predictions more accurate. Health records of cows that have lactation records up to 700 days are now included in the analyses. Herds that do a poor job in recording health data are excluded. And since the number of crossbred animals is increasing in the U.S., heterosis is now included in the model so that Holstein-Jersey crossbreds can contribute to the prediction models of their respective parent breeds as well.

Calving traits

Calving traits (calving ease and stillbirth) are not only difficult traits to improve, they are also notoriously difficult traits for which to calculate PTAs. A calving event is one observation, but it is affected by both the mother and calf and their underlying genetics. Every nation with a genetic evaluation struggles to accurately separate the genetics of that one observation into the part contributed by the mom and the part contributed by the calf. The CDCB has re-evaluated their statistical models for both calving traits and decided to implement changes that lead to considerable improvements in accuracy of prediction.

First, herds that have more than 95% easy calvings (category 1) will now be excluded from the evaluation, to minimize subjectivity of scoring.

However, the largest change made was the inclusion of a parity by sex of calf interaction effect in the models for calving ease and stillbirth. Until now, we always assumed a 50-50 ratio for male and female calves across all parities. Since the heavy use of sorted semen, however, this assumption does not hold true anymore.

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Sorted semen is most often used in first-lactation cows. We therefore get more female calves from our heifers. Females are born with more ease than males, thus they are less often stillborn. We need to take that into account when we estimate the PTAs of bulls. The easier calvings of their daughters may be due to their good genetics for calving ease, but it could also be due to their disproportionate number of female calves. How would these daughters perform if they would give birth to a 50-50 ratio of bull and heifer calves? The inclusion of a parity by sex of calf effect will accurately account for the recent trend of sorted semen usage, especially in first-lactation cows.

Because we did not account for the use of sorted semen until now, the calving performance of cows bred with sorted semen was previously overestimated. You may therefore see a considerable decrease in the PTA for Daughter Calving Ease at the April 2020 evaluation. Sire calving ease is also affected by the model change, but that change is much smaller. The new model is more representative of our industry today, and the resulting PTAs are thereby of higher accuracy and should better reflect reality.

Changes to total performance indices

Every breed association calibrates its total performance index every few years. Previous genetic progress, current and future milk markets and new data on traits allow each breed to carefully adjust their indices to lead the breed into the direction deemed most beneficial. Three of the breed associations introduced changes to their indices in April 2020. It’s clear that all indices aim to improve the bottom line in a difficult milk market, as all breeds move away from large, high-producing cows to more emphasis on components, health and efficiency.

Holstein TPI

Holstein USA has always kept up with changing times. In the early months of 2020, they reviewed recent genetic progress in the breed and future forecasted changes in milk pricing and decided to adjust their TPI formula accordingly. Upon evaluation, we see the TPI index changing to an index with increasing emphasis on health and efficiency traits as well as milk components. Health, fertility, Productive Life and calving traits and milkfat receive an increased weight. Valuable milk produced by healthy cows in an efficient way seems to be the objective of the TPI in 2020. Holstein USA states that dairy farmers using the TPI formula will be breeding for a more profitable herd of cattle.

The key changes to TPI are:

  • Fat and Protein are now equally represented, each at 19% of the index which means that selection on TPI will now lead to a slightly higher gain in butterfat, as Fat received lower emphasis compared to Protein (17% versus 21%).

  • The Feed Efficiency sub-index is updated to match the most recent economic assumptions for Cheese Merit $ (based on USDA research).

  • Health traits are now included at a 2% weighting through an overall Health sub-index. This allows selection for disease resistance through TPI, which will result in higher herd profitability through lowering on-farm incidences of economically important health disorders.

  • Early first calving has been added to the Fertility sub-index, which remains at 13% of the index.

  • Weighting for Productive Life has increased by 1%, which was taken from Dairy Form.

  • Feet & Legs Composite is modified to include Rear Legs – Side View.

Jersey JPI

USJersey went all out this April 2020 evaluation and decided to give their brand-new health traits an immediate placement in the Jersey Performance Index (JPI). With the changes to their total performance index, listed below, USJersey aims to increase production with high milk density by moderately sized, efficient cows. All this high-component milk must be produced while improving herd life, fertility, udder health and functional conformation. Udder composition, milk composition and health are the traits that get the spotlight in the new JPI.

The key changes to JPI are:

  • The inclusion of two new type traits: Rear Teat Placement Side View and Rear Teat Placement Rear View that receive a weighting of 0.8% and 0.6%, respectively

  • The inclusion of a health sub-index including all six new health traits. The heaviest weighting is reserved for mastitis (1.9%), milk fever (1%) and displaced abomasum (1%), followed by ketosis (0.4%), metritis (0.2% ) and retained placenta (0.1%).

  • Combined Fat and Protein (CFP) has been renamed and shall now be referred to as Milk Density. USJersey aims for a milk density of 9.0 pounds combined fat and protein per hundredweight.

  • A larger negative weighting for stature

Guernsey PTI

US Guernsey has embraced cow livability and included it into the PTI index with a 3% weighting, which was taken from Productive Life. Productive Life will have accounted for some of the value that cow livability brings. The inclusion of this trait to the index therefore naturally causes a reduction for Productive Life to not double count.

Changes to type traits of colored breeds

In addition to the base change, the colored breeds (all breeds other than Holstein) will likely see another considerable change to their type traits. This has to do with a change in the standard deviation of these traits, which is a mathematical term used to express the amount of variation (spread) in values. The type traits are expressed on a point scale where 95% of the values range between -3 and 3.

One single point represents a certain amount of observed change in the trait, and we call that the standard deviation. Previously, the standard deviation was calculated across all years of data. However, as animals change due to genetic progress, the measurements on very old cows are losing relevance. The new methodology only uses cows born between 2013-17 to set the new 2020 base standard deviation for the type traits of colored breeds. Standard deviations became larger for most traits, which means you will likely see more extreme values on both ends of the scale (positive and negative).

Conclusion

The U.S. genetic evaluation system is responsible to keep estimated PTAs realistic, accurate and relevant to the current state of the industry. In addition, the system is responsible to calculate values of traits that have economic value to the U.S. dairy producer. In order to not disturb our PTAs, every sire evaluation, changes to models and the introduction of new traits often come all at once. This is especially the case when we have genetic base change, such as this April 2020. All changes bring improvement and will continue to increase the genetic merit of our dairy cows. It may take a few months, but we shall soon be used to the new reality and once again move onward and upward as we always do: breeding cows for a profitable and sustainable future.  end mark

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