Fro Farm end of project report: The Reliability of Genomic Testing in Holstein Dairy Heifers

Introduction:

This project sets out to review the reliability of genomically testing Holstein Friesian dairy heifers against traditional parent average breeding data (PTA). The aim was to decide if genomic testing is financial worth investing in on a commercial dairy farm. Genomic testing for heifers has been widely available in the UK for around 8 years now and is presented in the same format as genomically tested bulls with very similar levels of reliability if reviewed within breed.

The Young family at Fro Farm, Abergavenny run a herd of 220+ Autumn Calving Holstein Friesian cows, rearing approximately 70 replacement heifers. Their milk contract includes some emphasis on constituents although volume is also important.  The family have taken a keen interest in breeding for many years, however, their breeding criteria has changed to take more account of Profitable Lifetime Index (£PLI), while ensuring they still use Type traits to breed a functional cow but with less angularity and less stature.

Method:

There are various options for Genomic testing in Wales, through the milk recording organisations, vets, breeding companies and some breed societies. At Fro Farm, the heifers were tested through CIS/Holstein UK, using a tissue DNA sample that was sent off for analysis. The results take 6 – 8 weeks to come back so it is important the sampling is carried out well in advance of any breeding decisions being made so the genomic information can be used to its full potential. 

In 2019, 63 dairy heifers under 1 year of age were genomically tested, prior to their first service to identify their strengths and weaknesses and to compare any differences between PTA data and the genomic information. This information was then to be used to see if the Young families breeding criteria would change as a result of this new information.  

Once the results we received the results, we carried out a parent check and processed the data through the company that carried out the testing and also on the farms AHDB Herd Genetic Report (HGR) through AHDB Dairy. This information would be overwritten once the genomic data was released, due to its increase reliability.  

Previously, the family had a clear breeding policy which included the following criteria:

• £PLI higher than best animal 
• Positive selection for health traits, fat % protein 
• Stop any further increase in stature 
• Improve strength 
• Positive selection for fore udder 
• Calving ease 
• Sire conception rate if available 
• Minimise any inbreeding

Results:

The key differences across the group of heifers are as follows:

Table 1 – Average PTA data (unless indicated) compared to genomic results for 63 heifers at Fro Farm.

Overall, the results show that there is variation in an animal’s genetic potential between PTA and genomic data and importantly, the genomic £PLI figure is 20% more accurate allowing a more strategic breeding policy to be implemented to maximise returns. As can be seen in the table, the genomic production data shows slower improvement than indicated in the PTA data. The initial findings indicate that a change in breeding criteria, with additional emphasis on fat and protein especially, will result in a financial gain if the genomic data is used instead of the traditional PTA data. 

Genomic testing would be a benefit on many farms where more accurate data can be used to improve herd performance as well as allowing farms to sell surplus heifers that don’t fit a farms requirement. The Young family already had a very focused breeding policy and strong herd management, which results in less variation between PTA and genomic data, but target areas can still be identified with the genomic results.

Unfortunately, at this time, the heifers are only part way through their first lactation so  comparing genomic projections with actual performance is not possible. However, anecdotally,  the heifers with predicted higher milk fat and protein potential, have performed better but on  many other traits, such as SCC there are no real outliers, so difference are hard to evaluate.  Having said this, on other farms already using genomics as part of their breeding programme,  we do see animals with a predicted high SCC routinely run higher SCC figures when milk  recorded and visa versa with those with low SCC predictions. 

An evaluation of actual performance V genomic predictions will be carried out in the Autumn  of 2021 when all first lactations are complete.

Inbreeding:

As part of the project, the AHDB HGR data was used to carry out the initial evaluation of the heifers, pre genomic testing. Within this review, one of the key areas highlighted as needing more attention was inbreeding. The HGR data was showing the average inbreeding for the 63 heifers to be 6.6%, when the industry recommendation is to avoid the level going above 6.25%. In the case of inbreeding, this can include: 

• reduced animal fertility
• reduced production
• potential health issues 
• long-term challenge of correcting these issues 

Further investigation found that the current programme the family had been using to calculate inbreeding had not been calculating properly. is now a major concern at Fro  Farm with several replacement heifers being over 12% inbred with the R2’s at 6.8% as an  average and the R1’s now at 7%.  

The table below shows the significant risk posed by not having accurate data when looking at  inbreeding levels for two heifers, randomly chosen at Fro Farm.  

Table 2 – Inbreeding figures for 2 heifers at Fro Farm in spring 2020. 

This difference in figures would not have been found if the project at Fro Farm had not used  the AHDB HGR report as an initial screen of the data. From the  whole project, these unexpected results have had the biggest impact on breeding decision  making at Fro Farm.

Conclusion:

Overall, the results show that there is variation in an animal’s genetic potential between PTA  and genomic data and importantly, the genomic £PLI figure is 20% more accurate allowing a  more strategic breeding policy to be implemented to maximise returns.

Genomic testing would be a benefit on many farms where more accurate data can be used to  improve herd performance as well as allowing farms to sell surplus heifers that don’t fit a farms  requirement. The Young family already had a very focused breeding policy and strong herd management, which results in less variation between PTA and genomic data, but target areas  can still be identified with the genomic results.

The main conclusion from this study is the importance of reliable, accurate data and the need to ensure any information you use can be trusted. Wrong data can have huge implications in the future, if not identified.