Genomics helps speed up genetic progress in dairy herd

Genomically testing cows could be a justifiable spending decision even at the current low milk price in order to save long-term costs and secure herd performance.

The Allwood family have taken such an approach in their commercial herd of Holsteins. In August they genomically tested 96 of their heifer calves as a means of selecting the best replacements as part of their ongoing herd expansion.

Lotty Allwood explains that the plan is to put the poorest animals to beef, which will save on rearing costs and create an added income stream.

See also: UK dairy farmers benefiting from using genomics

“We are expanding at a difficult time [in terms of milk price], so we don’t want to waste resources on animals that are not worth it,” she says.

In recent years, the cost of genomically testing females has come down and the technology improved. With heifer -earing costs quoted at about £1,800 an animal, and genomic testing now costing about £30 an animal, not rearing two heifers could cover testing costs on 100 animals, while also driving genetic improvements.

The Allwoods farm at Huntington Hall Farm, Chester, milking 590 cows that average 11,000 litres a cow a year. They are on target to hit 650 animals in milk by the end of the year.

See also: How to guide to using genomic indices

Genomic aim

The aim is to use genomics to breed the best females. By doing so they will increase the genetic value of their replacements and gradually reduce the number of lower-genetic-merit animals coming in.

Genomically testing females works on the same principle as genomically testing young bulls. By taking a DNA sample from a young heifer, it is possible to get an immediate indication of genetic merit, rather than having to wait for that animal to calve and start milking. Specific animals can then be selected to produce replacements depending on individual farm breeding requirements.

The Allwood family chose to genomically test heifers using NMR’s GeneTracker service. An ear tissue sample was taken from heifers aged between two weeks and 12 months.

It is crucial to take  samples before bulling age to enable breeding decisions to be made off the back of genomic results.

The results were received in September, with each heifer’s own breeding values displayed in the same way as bull proofs.

The Allwoods are now working with their breeding adviser to formulate a plan. However, all breeding decisions will be made with the aim of producing high-yielding, healthy, fertile, long-lived animals.

With this in mind, heifers will initially be screened for milk, somatic cell count and fertility. The aim is also to protect the herd’s strong profitable lifetime index (PLI), with some of the herd’s top heifers achieving a PLI of £450.

Miss Allwood says the fact genomic testing has an accuracy rate of 55-70%, depending on the trait, also provides the confidence to make specific management decisions.

Lotty Allwood taking a tissue sample for genomic testing.

“It’s a really secure investment. The amount you save not rearing a poor cow means the decision is a no-brainer. It is a way to look into the future and use technology to expand in a really positive way,” she concludes.

Using PLI to choose replacements

Sussex producer Tim Gue has been genomically testing all his heifers for the past four years and uses PLI as the primary means of selecting replacements. Heifers are then screened for type, fertility and longevity. The bottom one-third of cows and heifers are put to beef.

“Finding the worst animals is more important to me. My herd is improving at a much faster rate now as I’m not breeding from the bottom end. I am driving the top forward and bringing the bottom up faster,” he says.

Mr Gue believes PLI is an “absolute measure of profitability” and by only selecting the best females, PLI score has increased substantially in the herd of 400 pedigree Holsteins, which is run commercially.

The herd has an average PLI of £155 and the average of heifers due for service this year is £325. Four heifers with a PLI below £150 will be served to beef.

Fertility index has also improved and herd average classification score has increased by two points from 84 to 86 during the past five years.

Mr Gue says genomically testing females has enabled him to make the most of the best heifers, which may have gone undetected in the past.

“Several times, our best heifer on genomic testing has not ranked the best on parental average. Genomics finds them and lets you focus on them,” he says.

Heifer Huddlestone Glenton Cinderalla is one such animal. Having “never noticed” her in the herd, her genomic breeding values gave her a PLI of £529 and a fertility index of 7.2. As a result, AI companies have expressed interest in any bull calf she produces.

Genomic testing is also more reliable than pedigree indexes. For Mr Gue, genomics has specifically highlighted the variation between full siblings, with some showing as much as a 150-point difference in PLI between them – something that wouldn’t have been identified by looking at their pedigree index.

How to genomically test females

At present, only milk-recorded Holstein herds can genomically screen females, with several companies offering a genomic testing service for individual animals.

A lab will read an animal’s DNA to produce a genotype. Regardless of company used, this information is then fed to AHDB Dairy. It then uses an “SNP key” based on historic data for 26,000 bulls and their daughter performance to convert this into useable data. The genomic breeding values produced can then be used to make management and breeding decisions.

Compared with the use of genomic young sires, the industry has been much slower to embrace this technology for testing females. However, Marco Winters, head of genetics at AHDB Dairy, says all farmers can benefit from genotyping their heifers.

“Testing strategy will ultimately depend on cashflow. But the most important thing is that farmers plan to use the information effectively and ideally test animals before breeding age so decisions can be made in advance,” he says.

He suggests one of the following strategies:

• Test all heifers – this enables confident breeding decisions to be made as you can accurately identify all of the best and worst animals.
• Test the bottom 50% of heifers based on their pedigree index and cull out the worst – this may be relevant in herds that have to run a bull, but only want to breed their best.
• Test the top 50% of heifers based on pedigree index and breed the best to sexed semen – this may be relevant in expanding herds with not enough surplus heifers.

“Testing 50% of heifers may be a good starting point for farmers before making the leap to test everything, But it is important to realise you may be missing out on the very best animals by using this strategy,” says Mr Winters.

Genomic testing: Genetracker system explained

Genomically testing heifers is an effective way to identify the best and worst females in your herd and make strategic breeding decisions that could drive down costs and improve genetic progress.

Several companies offer a genotyping service, with all genomic breeding values then generated by AHDB Dairy. As an example, genomics and genetics adviser to NMR, Lucy Andrews-Noden from Priestcliffe Consulting, talks through how NMR’s GeneTracker service works. This service can be used by any milk-recorded herd, not just NMR.

1. Ask yourself how you will use the information produced from genotyping heifers and get a breeding plan in place.

2. Contact NMR and tell them which animals you want to be tested. Milk records will be used to find each animal and identify the sire and dam, irrespective of who you record with.

3. A “tissue sample unit” for each animal will then be sent to the farm. This includes an individual vial with a specific barcode linked to each animal and a paper printout of animal details in a bag.

4. A set of specialist pliers are provided to enable an ear tissue sample to be taken from each animal by the farmer. This acts like an ear piercing. (Other companies may ask for hair samples.)

5. The tissue sample is put in the labelled vial and a prepaid jiffybag and sent back to the office.

6. Samples are then sent to a lab in Ireland (lab choice will vary depending on company used). It produces a genotype for each animal.

7. Once a month, genotypes are sent to AHDB Dairy for analysis.

8. Genomic breeding values for each female are produced and published online for the farmer to look at. The whole process takes about four to six weeks.

9. Farmers can then rank animals based on specific traits of interest and breeding decisions can then be made in discussion with an adviser.