Single Step - new method in genomic selection

About the job

Genomic selection has been applied in Switzerland for over 10 years. It has led to profound changes in breeding and to higher breeding progress. Soon, the multi-step method will be replaced by a single-step method (Single-Step).

In April 2011, the first genomically optimised breeding values (GOZW) were published. At that time, GOZW were available for milk production traits, cell count, conformation and a few fitness traits for the populations Brown Swiss, Holstein and Swiss Fleckvieh based on traditional breeding values of genotyped and tested bulls. Today, GOZW are estimated for six populations (Brown Swiss, Original Braunvieh, Holstein, Fleckvieh, Simmental and Limousin) and 86 traits. The multi-step method has made genomic selection a success story, but it has also become a victim of its own success.

The successes of genomic selection

Over the years, genomic selection has established itself as an important component of Swiss cattle breeding and is now indispensable. The proportion of inseminations with young bulls is steadily increasing and the proven second-use bulls, which were still common a few years ago, are almost a thing of the past. The prices for genomic selection have fallen with the steadily increasing number of genotypings. The change from a monthly publication of GOZW for newly genotyped animals to a fortnightly rhythm was implemented at the end of 2015. This has led to more and more breeders opting for the data-supported breeding programmes of their breeding associations and having all their female animals genotyped. They use the more reliable GOZW to make better breeding decisions.

The multi-step method reaches its limits

The summer months are generally already hotter than the rest of the year. With climate change, the problem becomes even more pronounced because temperatures are rising on average. Looking back a little more than 15 years and considering, for example, the next official meteorological station for Zug in Lucerne, an upward trend is generally visible for the whole year, but also for the summer (Figure 1). Furthermore, there are increasingly more temperature and weather fluctuations. From these facts, it can be deduced that our dairy cows are increasingly exposed to heat stress situations. In addition, production performance has increased in recent years. The resulting increased metabolic performance is associated with the production of more body heat. Furthermore, age and, of course, stage of pregnancy also influence metabolic performance.

Larger data sets mean greater challenges

The project team at Qualitas AG has been working with increased priority since early 2020 on the development of the Single-Step method for Swiss cattle breeding, with initial work already carried out from 2018. The switch to the Single-Step method means a complete reorganisation of routine processes and therefore progresses only step by step despite its great importance. Examples of these challenges are efficient evaluation models and software programmes adapted to the computer structure of Qualitas AG, automated processes for the fortnightly calculation of GOZW for newly typed animals, the integration of international information sources such as Interbull BV and ensuring that Single-Step BV (ssBV) only change over time due to new data bases. In addition to these challenges, necessary adjustments to the previous traditional evaluations, which are no longer up to date in times of Single-Step, are required. Since 2021, the project team has been in regular exchange with the Single-Step research team of LUKE, the counterpart to Agroscope in Finland and the world’s leading institution in the development of Single-Step methods. This collaboration enables Qualitas AG to access the latest developments. The first ssBV were distributed to the breeding associations in April this year and the ultimate goal of the project is to switch all genomic evaluations to Single-Step in the coming years. The introduction of Single-Step will be carried out trait by trait.

Results of development work for rearing losses

For these stress situations, not only the ambient temperature is responsible, but humidity also plays a role. To consider both factors simultaneously, temperature and humidity are converted into an index. This is called the THI (Temperature-Humidity Index). Various calculation formulas exist in the literature. In the present calculations, a THI application (NRC, 1971) was chosen, which is often used for genetic evaluations. The interaction of temperature and humidity and the resulting effects on the THI or on the cow are shown in Figure 2.

The methods of genomic selection briefly explained

Today’s genomic selection takes place in four steps (Figure 3):

• Traditional breeding values (BV) are estimated based on phenotypes and pedigree.
• The traditional BV are back-transformed to the phenotypic scale. This step is called "deregression" and is evaluated with the genotypes of the reference bulls (mostly tested bulls). In this way, the effects of certain genome locations on the traits are estimated.
• These effects are transferred to all available genotypes and direct genomic BV (DGZW) are estimated.
• The DGZW are combined with the traditional BV. From this, the genomically optimised BV (GOZW) are calculated.

The Single-Step method integrates the genotype information directly into the estimation system previously used for traditional BV.