The UK and the genomics race

Published 1 June 10

Genomic technologies are said to have the capacity to increase the rate of genetic improvement by around 50 percent. But so far, the UK has shown little sign of participating in the genomics race and appears to be lagging behind much of the world. Ann Hardy talked to Marco Winters of DairyCo breeding+ to find out where we stand today, what genomics can do for UK cattle and if, as an industry, we can ever catch up.

 

Why do we need this technology?

We need it because we can improve the rate of genetic gain in British dairy cows through the use of younger, higher genetic merit bulls. Estimates of the increased genetic improvement vary from 50 percent to 100 percent, with the precise figure depending on its uptake and which bulls farmers choose to use. Our estimates at DairyCo are more conservative at this stage, but even at 15 percent improvement over the current rate of gain, we estimate a return to the industry of around £20m in 10 years' time.

The benefits of the genetic gain lie far more in the traits which are difficult to measure early in a bull's life than in the production traits. This includes traits such as longevity, fertility and disease resistance.

 

The UK uses a high proportion of foreign bulls so can't we rely on the foreign genomic proofs now coming through?

I'd use the same arguments against this as I would against the UK abandoning progeny testing or any genetic evaluation full stop. For a start, the UK has different breeding objectives from other countries. And secondly, genetics don't perform in exactly the same way in different countries. We need to find bulls that are suitable for UK conditions, so we need UK genomic evaluations.

Furthermore, the UK has some completely different needs from other countries. For example, few countries will be as interested in TB resistance as we are, but before we can investigate this, we need to develop the capabilities to do the genomic evaluations.

It's also worth noting that some other countries' genomic evaluations are run by commercial companies, which raises the potential of commercial bias. This is not the case in the UK, where DairyCo genetic evaluations are completely independent of any commercial influence.

 

We hear that the UK is coming from behind in the field of cattle genomics. What has caused the delay?

When the technology first became available in early 2008, genotyping and the surrounding R&D was undertaken very much on a country by country basis and was driven by the large multi-national breeding companies wishing to make a more informed choice about bulls entering progeny test. The major benefit appeared to lie with the AI companies, the costs involved were extremely high at the time - potentially running into millions - and it was not something DairyCo felt able to recommend UK dairy farmers should invest in at that stage and cost. At the time, there was also a general unwillingness to share resources, so if we as a country had wanted to be involved, we would have had to do it on our own.

However, behind the scenes, we were undertaking background work with EGENES - the Edinburgh Genetic Evaluation Services which is led by Dr Mike Coffey and based at SAC - who carry out genetic evaluations on DairyCo's behalf and have been leading an international consortium (called Clubware) to develop the relevant software.

 

So what's the position today?

Early last year, the mood completely changed as the countries involved realised that it was too big a task for each of them to manage on their own. The technology stands or falls by the numbers of animals genotyped and the more bulls you can get into your reference population, the better. A few thousand will get you started, but ideally, you'd like 10,000 animals in this population, so clearly collaboration across borders was going to be needed to meet this goal.

As the magnitude of the task became apparent, so a general willingness for the UK to take part in a shared approach increased.

Meanwhile, Cogent and Genus had been investing in genotyping a large number of their own bulls, but would never be able to obtain genomically enhanced UK evaluations while there was no SNP-key for the UK.

But an industry group within the UK now feels the time is right to become involved in developing a SNP-key for the UK, so allowing British farmers to benefit from genomically enhanced UK evaluations.

This collaboration is being driven by DairyCo - who the industry partners have appointed as the custodians of the information - and will be developed together with our partners at EGENES. It also involves Cogent and Genus as well as all those organisations who contribute data to UK genetic evaluations. This currently includes NMR, CIS, UDF and Holstein UK.

The DairyCo board has committed some money, which will be used to get Clubware software fully operational and develop a genotype bank to enable genomic evaluations to be carried out by EGENES. At the same time, DEFRA has also committed some funding towards providing genotypes through an initiative known as the Ruminant Genetic Improvement Network.

The benefit of this is that we are now already in a position to start pooling and swapping genotypes with other countries.

Does it mean we will have a reference population of animals in the UK?

Thanks to the investment of Cogent, Genus and DEFRA, alongside the opportunity to collaborate with other international partners, we have already started to build up this population and within a few months, we hope to have around 3,000 bulls in our genotype bank and we continue to explore opportunities to increase this further over the next few months.

But is the UK in a position to ever catch up?

Absolutely. Remember, at this stage we're only a year behind the very first countries to have genomic evaluations available, and because the technology is now in its second phase, we may well be at a small advantage. As of last month, a new high density SNP-chip has become available which measures over 800,000 SNPs. This compares with 54,000 in the previous chip which means it will be far more informative. It also means that over 1,000 bulls used in the UK will be genotyped with this high density chip whereas some other countries may have to re-genotype some of their bulls which were previously tested with the lower density chip.

At the same time, the costs involved have plummeted, which means that the UK industry can obtain far more information at a relatively low cost.

What information will be available?

We will be able to provide genomically enhanced evaluations immediately for all traits we currently measure and evaluate. Alongside these, there will be the potential for some new traits to be evaluated, such as disease resistance (eg for Johne's and TB, which are known to be heritable), as well as fatty acid profiles in the milk indicating saturated versus unsaturated fats, and potentially even feed conversion efficiency. In time, there might even be scope to develop genomically enhanced indexes for traits such as methane production.

How will the evaluations be expressed?

The USA expresses genomically enhanced Predicted Transmitting Abilities as gPTAs and the UK is likely to do the same. The 'g' signifies a genomic component to the index, alongside the usual parent and ancestry element. Eventually, daughter information will take over in importance from the genomic and ancestry information, although these will remain a small and diminishing component of a proof.

Can the technology be used for a farmer's own livestock?

Definitely. If a farmer wants to select replacements for his own herd, he will be able to genotype, say, two full sisters at birth to find out which is best. Although they will both have the same parent average (Pedigree Index) information, they could have quite different genotypes, and one may have far better prospects for things like milk production, fertility, cell counts or lifespan. We are now able to confidently say that the genomically enhanced evaluation will be far more reliable than a Pedigree Index, so the test could be worthwhile for many breeders and could have a worthwhile payback over the cow's lifetime.

How much is the test likely to cost?

We've spoken about the new high density chip which will still be quite expensive, but alongside it, a low density chip - of only about 3,000 SNPs - has also been developed. Although this sort of SNP-chip will provide less information on its own, as part of the wider system it will probably be adequate for selection purposes. It's not possible to say at this stage what its cost will be, but I'd estimate that the full test will be around £50. 

What about the breeds other than Holstein?

The current technology only works within breeds, and therefore the smaller populations are not yet able to benefit from the work being done by the Holstein breeding industry. However, the new, high density SNP-chip is expected to change that, which hopefully will unlock the potential to use the same SNP-key across different breeds, including crossbreds. The UK, as one of only a few countries in the world to provide an all-breed genetic evaluation system, launched earlier this year, is therefore ideally placed to capture the full potential for all breeds.

So when will we have genomic evaluations for the UK?

We are aiming to have official genomically enhanced evaluations for bulls in the UK in 2011.

Glossary

Genome - The entire complement of the animal's genetic material.

Genomics - the study of an animal's genome functions.

Genotype - The measure of an animal's genetic makeup.

Phenotype - The observable physical traits of an animal (such as stature or milk yield) which is a combination of both its genetic makeup and environmental influences.

Reference population - A population of several thousand animals whose actual performance and genotype are compared to establish relationships between the two. From these relationships, a SNP-key can be devised.

SNP (Single Nucleotide Polymorphism) - A measurement of genetic variation, which can be used to describe an animal's genotype.

SNP-chip - A means of measuring different SNPs.

SNP-key -  A key, which is specific to a cattle population, which 'unlocks' or translates an animal's genotype, as measured by the SNP-chip, into a genetic index such as a genomic Predicted Transmitting Ability (gPTA).

 Article originally produced for Dairy Farmer, June 2010

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