Genomics in the dairy industry

Genomic evaluation highlights young bulls with higher-reliability proofs compared with traditional genetic indexes and gives dairy farmers greater confidence when selecting youngstock for breeding.

Genomic evaluations produce estimates of genetic merit based on an animal’s DNA information and are available for the following breeds:

• Holstein
• Friesian
• Guernsey
• Ayrshire
• Jersey

Genomic evaluations have a number of benefits for your herd:

• Provide young bulls with higher-reliability proofs compared with pedigree index proofs
• Higher-reliability genomic proof compared with the traditional pedigree index calculation for female youngstock
• Give you greater confidence in selecting youngstock from which to breed your next batch of replacement heifers
• Allow you to serve the genetically superior animals with sexed semen and put the rest to beef to increase your calf value (or, in the case of excess replacement heifers, to sell the less-superior genetics)

Genomic indexes are calculated using a young animal’s own DNA or genetic material, rather than being estimated from the performance of its parents and ancestors.

Genomically testing youngstock has an advantage over pedigree index calculations as it evaluates the mixture of genes that have been passed down from both parents. For example, in traditional pedigree index calculations, non-identical twins or full siblings would have the same proof. However, genomics can identify which is superior or help you spot a poor trait that you would not want to breed into your herd.

The first step in the genomic testing process is to build up a reference population for the breed, which contains the DNA information of bulls with a high-reliability daughter-based proof.

Any animal with a high-reliability proof can be used, whether they have poor or excellent genetics. This wide spectrum of genetics allows geneticists to identify markers (SNPs) in the DNA that are related to poor or favourable traits shown in the animal’s genetic proof. 

These associations are used to create a ‘SNP-key’, which can then be used to evaluate young animals without daughter or production information, based only on the DNA present in a tissue or hair sample. 

To achieve a large enough reference population, genotype sharing agreements may need to be created between countries with similar genetics for breeds with a small population size. Holstein, Guernsey, Jersey and Ayrshire genotypes are shared between the UK, Canada, USA and Italy.

• Step 1: A sample of the animal’s hair or tissue goes to the laboratory
• Step 2: Lab scientists extract the DNA
• Step 3: The DNA is put onto a ‘SNP-chip’ and the sequence of bases that make up the DNA is read at various locations along its length
• Step 4: A computer file showing this sequence is sent to geneticists working at Edinburgh Genetic Evaluation Services (EGENES) on behalf of AHDB Dairy
• Step 5: Geneticists develop a ‘SNP-key’, which unlocks or translates the sequences to turn them into a genomic index that can be understood by farmers and cattle breeders
• Step 6: In the UK, the genomic index will be expressed as a Predicted Transmitting Ability (PTA). All official PTAs carry the AHDB Dairy logo

The set-up of genomic evaluations by AHDB Dairy is funded by farmers’ levy; however, it’s up to the breeding companies and breed society to collect genotypes to create a reference population. Fees for this fall to users of the service.

Several companies now provide genomic testing in the UK for breeds with established genomic evaluations. Genomic evaluations for females are free, after the initial lab test fee. However, bulls will incur a small charge to make their genomic proofs official.