Genomics, a UK overview.

Genomics is a hot topic in Canada, so following a recent trip to the country, Joanne Pugh takes a look at the science and its relevance to UK farmers.

IN Canada there is much talk about genomics and considerable excitement about using a bull's DNA to predict how good a sire he will be.

There is similar enthusiasm in the USA but the small amount of information coming to the UK appears confusing.

This may be because the first semen company to launch the concept in the UK - the New Zealand company LIC - has since run into difficulties, offering refunds to Kiwi farmers who have already invested in the technology.

LIC has also promoted genomics as a replacement for progeny testing, reducing its own progeny testing programme from 300 bulls per year to 100. With genomics equivalent to testing a handful of daughters, that led to backlash against the technology.

But such scepticism is less prevalent in North America, where semen companies are already using genomics, describing them as an additional tool rather than a progeny testing replacement.
Genomic information will be included in the North American proof runs next year (January in the USA and April in Canada), something that will certainly affect UK farmers. Therefore some clarity is needed.

What is genomics?

Genomics is the study of DNA. Previously 'gene markers' have been promoted to identify specific traits but, because complex traits are not controlled by a single gene and the cost of the technology has fallen dramatically, genomics relies on a panel of 58,000 gene markers instead.
Using this panel relies on developing a 'key', which is done by genomically testing bulls that have already been progeny tested. Because scientists already know what traits those bulls have they can draw parallels between recorded traits and genomics, then apply the information to predict what traits non-progeny tested bulls may pass on.

For example, if 100 progeny tested bulls have high milk protein and a certain combination of DNA markers, any non-proven bull with the same combination of DNA markers can be assumed to also have high milk protein.

The 'key' is vital and the more animals used to develop it the better. For example, LIC used around 2,500 proven bulls and several semen companies in Canada and USA combined resources to process around 5,000 bulls. Holsteins are ahead of the game because of a larger population and greater databank.

LIC withdrew its 'DNA proven' Holstein Friesian semen (sold before bulls had daughters on the ground) because its predictions (the 'key') did not match the initial progeny testing data.
The company says the Jersey and KiwiCross breeds do match up but it is 'prudent' to stop selling the Holstein Friesian semen while it 'works to understand' what has happened.
How reliable is genomics and how will it be used?

At no point has any semen company claimed genomic selection is as reliable as progeny testing, and only two companies (LIC and the Dutch CVR) have reduced their progeny testing programmes.

Most semen companies are promoting three uses for genomics:

1. Better selection of bulls for progeny testing.
All the big semen companies are now using genomics, selected young bulls on their pedigree, parent average (PA) and genomic evaluation.
Brian Van Doormaal of the Canadian Dairy Network says the reliability of PA is 24 per cent and this increases to 42 per cent when combined with genomics.
Although this reliability will increase as DNA technology improves and more data is included in the 'key', Jacques Chesnais, senior geneticist for L'Alliance Boviteq, the research arm of Semex, says it will never rival the 80-95 per cent reliability of progeny testing.

2. More reliability for farmers using young sires.
Because of the greater reliability of PA combined with genomics, farmers who use unproven bulls will get better results (although still not as good as using proven sires).

3. Potential use of 'bull teams'.
Some semen companies are marketing genomically tested bulls in teams, saying this is a way to spread the risk of using young, unproven bulls.
New Zealand is used to bull teams and LIC is a big promoter of them. Semex will also provide them 'in markets where demand is sufficient' but teams are unlikely to gain much popularity with countries used to mating individual cows to specific bulls.

How will progeny testing be affected?

Most companies will continue to progeny test because of the demand from farmers for high reliability proofs.

Also, the 'key' will only improve if data continues to be collected, and more data will be needed as and when new traits start to be selected for.

Mr Van Doormaal says: “The only limitation will be the collection of high quality data. We need to record more and more accurately then ever before, not the other way round.”
How does this affect UK dairy farmers?

Genetic information used in the UK by non-commercial companies (eg DairyCo and Holstein UK) goes through Interbull, which 'converts' national genetic evaluations into international figures.
However, Interbull currently cannot convert genomic information, and will not be able to for at least another 12 months.

Brian Garrison of Select Sires, says this is 'not ideal' but UK farmers can still gain some information from ranking tables published in other countries.

Marco Winter from DairyCo urges caution when doing this, as figures published overseas cannot be automatically transferred to the UK. For example, 65 per cent reliability in Canada or the USA will be less in the UK.

He says genomics is a 'good technology' and 'an additional tool' as long as farmers do not mistake it as being as reliable as a proven bull. Those using unproven young sires would gain from genomics but using a genomically tested bull in place of a proven bull would be 'very high risk'.
He recommends using more than one genomically tested/unproven bull and to ignore claims using 'bull teams' increases reliability to equal that of proven bulls.