A Genomic outlook for sheep genetic evaluations

What is a Genomic Evaluation?

Genomic information enables predictions of genetic merit to be made using measures of an animal’s DNA, rather than being solely reliant on data derived from measurements taken on them and their relatives.

Genomic approaches do not replace our current genetic analyses but build on them – introducing an additional genomic step that greatly increases the accuracy of our predictions.

Genomic breeding evaluations have been the backbone of dairy genetic improvement for more than 20 years. They deliver faster rates of genetic gain and enable the use of younger sires within the breeding programme rather than waiting for sires to become proven.

The process of genomic testing and analysis

Step 1: A sample (nasal swab, blood, or tissue) from the animal goes to a laboratory to be genotyped.

Step 2: The laboratory extracts DNA from the sample.

Step 3: The DNA is put onto a ‘50K SNP-chip’ and the variation in the DNA is recorded at 50,000 different points along the DNA strand.

Step 4: Breeders can receive information on major genes / parentage.

Step 5: A file containing the DNA sequence is sent to the team of geneticists working for EGENES (based at SRUC).

Step 6: Records are validated to check parentage and genotype quality.

Step 7: Geneticists develop a ‘SNP-key’, which unravels the relationship between the DNA sequence and the known genetic merit of performance recorded animals, taking into account their current EBVs.

Step 8: Genomic Breeding Values (GBVs) are produced for use by farmers/breeders.

Step 9: GBVs are published on the Signet website with an indicator showing which animals: -

• have a genotype used in the genetic evaluation.
• have been sire or dam verified using their DNA.

How close are we to using this information?

A major first for UK sheep genetics was the launch of genomic breeding values for hill sheep in June 2023. Delivered as part of Signet’s National Hill Sheep Evaluation, the new genomic breeding values were implemented following research by Dr Samir Id Lahoucine at SRUC using funding from the Hybu Cig Cymru (HCC)-led Hill Ram Scheme and Farming Connects Welsh Sheep Genetics Programme. The new approach incorporates genomic information (that was being collected in hill flocks for DNA parentage assignment) into breeding values that are more accurate, informative, and reliable.

This work shows we can deliver genomic breeding values for Terminal Sire breeders in the future as part of a mixed breed evaluation, we just need to collate enough genotypes.

What is next?

The next stage will involve the sharing of genotypes from terminal breeds to create a base population that can be used to produce genomic breeding values. AHDB currently have data sharing agreements with the Suffolk, Charollais and Hampshire Down Sheep Societies to enable this to happen. AHDB and QMS are funding additional genotype collecting with further genotypes coming from both research projects and individual breeders.

Signet will continue to collect and store phenotypes and genotypes from breeders; this is essential for the future development of genomics breeding values.

Why the excitement about genomics?

We are still learning about the many benefits associated with the storage of DNA and its use in genetic evaluations, these include: -

• The correction of parentage errors.
• The identification of major genes (like Scrapie and Myostatin), as well as reporting potentially harmful recessive traits.
• A more accurate way to compare recorded sheep in flocks that may have little pedigree linkage between them.
• A more accurate way to introduce new, unrecorded genetics into a breeding programme. Encouraging new breeders to get involved and find useful outcrosses.

 

Faster rates of genetic gain will be realised across the population, with breeding values becoming more accurate (particularly for hard to measure traits such as those derived from CT scanning) and the use of superior young rams in the breeding programme.