First UK sheep farmer to adopt genomic technology explains how he uses it

Genomics may be an alien word for many sheep producers, but it is a term that is going to become more important if the UK is to speed up genetic progress and remain competitive in the lamb market.

However, producers should not let their unfamiliarity with genomics prevent them from embracing the new technology, says sheep farmer Rob Hodgkins.

He started using genomic recorded rams in his 3,400-head New Zealand Romney flock run in partnership with dad Chris, mum Caroline and brother Andy, who were the 2009 Farmers Weekly Awards Sheep Farmers of the Year.

“It’s definitely not technology for tomorrow – it’s happening right here, right now,” he says.

Genomics enables an animal’s genetic potential to be predicted from a young age by comparing its DNA with an “SNP chip”, which is produced using a bank of genetic information representative of the national population. This allows rams to be used at a younger age, rather than waiting for progeny testing.

Reference population

In the UK there isn’t a bank of genetic information representative of the national sheep population, due in part to there being more than 90 breeds in the UK and a gap in data recording.

However, work is being done by Innovis to produce genomic breeding values for maternal and terminal sire breeds.

In New Zealand, genomic values are being used in the sector because it has a large central progeny testing (CPT) reference flock of 5,000 animals that have been accurately recorded, genotyped and DNA analysed. It is the only country to have a commercially available test.

However, to use genomics, any animal tested must have a genetic link back to the reference population, in this case the CPT flock.

The background on genomics

It’s for this reason the Hodgkins family, who sell breeding stock to commercial producers from their Wairere NZ Romney flock in West Sussex, have been able to start using genomic technology.

Their 3,400 head flock is of New Zealand origin and is related to the original 5,000 in the central progeny reference testing flock.

“We first became interested in genomics when my dad and I heard geneticist Dr Alex Ball talk about genomics at the Sheep Breeders Round Table in 2011,” explains Mr Hodgkins.

“Dr Ball said the northern hemisphere was years behind because there was not the massive recorded data in the UK to check genomic values against the physical performance of the animal. Only Australia and New Zealand had enough recorded animals to fully validate the data.

“But that got me and my dad thinking, as we had 100% New Zealand genetics and were recording using the SIL [NZ equivalent of Signet] system as well as Signet. After some correspondence with New Zealand we found we could take advantage of some of their research.”

Wairere flock set-up

The Hodgkins are using genomics in their nucleus flock containing 1,700 ewes.

In 2012 all stud rams in this flock had a DNA 50K SNP chip sample taken, meaning all progeny born to these rams in 2013 have been evaluated with genomic estimated breeding values as well as normal EBVs. These are the first sheep in the UK to be recorded using genomics values.

Mr Hodgkins, who has just completed a Nuffield Scholarship on genomics, says the key to making full use of this information is knowing how to find the right “switch to activate the individual superior genes”.

He explains that in the 5,000 head central progeny testing flock in New Zealand, 22 different areas of gene combinations have been identified covering individual superior performance traits.

“For example, if they identified 50 sheep with the highest EBV for growth rate in this population, the DNA for each of these sheep could then be compared to see which areas of the genome were common across each of those 50 top growth rate sheep.

“Once the gene combination responsible for that particular trait had been identified, other sheep could be tested to see if they carried this gene combination for growth.”

Benefits of genomics

Mr Hodgkins believes genomics used in conjunction with physical performance data gives them increased confidence to use young sires within the flock.

“If you were selecting ram lambs to use based on EBVs you would have lower accuracy levels. But if you use ram lambs whose fathers have been genotyped then you know half of the DNA they are carrying.

“By combining DNA information with actual recorded information, accuracy levels can jump between 5% and 15%. The range in accuracy depends on how heritable some of the traits are,” he says.

For example, Mr Hodgkins had a lamb born in 2012 that had an exceptional EBV score on both SIL and Signet. So he was selected to be DNA tested by taking an ear tissue sample.

“This animal, 08147, came back as being in the top 5% for fat yield and top 10% for meat traits, which was just exceptional. The phrase ‘trust and verify’ sums up what genomics is all about. You trust some of the traits, but genomics just allows you to verify, giving you the confidence to use ram lambs and speed up the genetic gain.”

Cost

When the stud rams were tested at the end of 2012, the 50k SNP test cost about £240 an animal. However, offspring from those stud rams can be tested with a cheaper test because half of their DNA is already known, bringing down the cost.

“The higher the SNP chip number, such as 50,000, the more specific the test, as the DNA is being analysed in 50,000 segment sections. However, there are cheaper genomic tests such as the 5K SNP chip that can be used when one of the parent’s DNA is already known and this only costs £40 an animal,” explains Mr Hodgkins.

From next year the family will start selling high-value rams with a full DNA breakdown to show customers what genesets the animals are carrying.

Tupping time

Mr Hodgkins is able to use genomics by running 22 single-sire mating groups in order to know DNA parentage. Genomic-tested ram lambs are run with just 30 ewes, while mature rams are put with up to 105 ewes. They use the best rams on a wide proportion of ewes.

“If we were to mate all of our best rams with all of our best ewes we would end up with a smaller genetic pool. So we make sure our rams tup a group of ewes of mixed ability.”

The groups remain in a single-sire group for one cycle and then they remove the rams, amalgamate three groups and add in a Hampshire.

If the Hampshire picks up a ewe, which is easily determined by the colour of the lamb’s face, then that ewe will drop out of the elite group and won’t be part of the performance-recorded flock.

This year 1,700 ewes were performance recorded, with 1,700 non-performance recorded in the commercial flock.

Data recording

In order to continue verifying the data, accurate recording is vital. In the 1,700 elite recorded ewe flock the Hodgkins measure eight-week weight, and 21-week weight. Maternal score given at birth, along with lambs ultrasound-scanned for back fat and eye muscle, are also recorded.

“We lamb outside so recording data has to be made easy, says Mr Hodgkins. “We use a handheld computer [Psion] to record and the ewes have a large management tag in the ear so we don’t have to catch them and read their ear tag number because it is easily visible. It takes 30 seconds to record a ewe with twins,” he says.

“Although we are looking at both maternal and terminal traits, at the end of the day we are looking at producing a maternal ewe.

“Mothering traits are key to everything, if you don’t have a ewe with high survivability, good fertility and good milking ability, then you are not going to have a fast-growing lamb.”

Mr Hodgkins says New Zealand sheep producers estimate 30-40% of the profitability of a flock is driven by genetics.

“Genomics is certainly something that will help drive our business as it will give the commercial buyer more confidence.

“Commercial buyers are looking for animals that can work off forage. We get lots of repeat custom and already 90% of our females have been sold for 2014.

“Genomics is not changing the genes, it is just helping speed up natural selection. It isn’t something that couldn’t be done in 10 years using pen and paper, it’s just helping us progress quicker,” he adds.

Innovis geneticist Dr Janet Roden answers questions on genomics.

What is genomics?

The term genomics refers to a whole host of technologies that use information about DNA and DNA sequences.

In sheep breeding we are talking about the use of genomic selection in which we use sequence information from the DNA of individual animals to generate genomic breeding values that help us identify sheep that will be most useful in a breeding programme.

To calculate genomic breeding we first have to establish the association between thousands of small differences in the DNA of individual animals and the differences in their performance.

We can use these relationships to improve predictions of breeding values of future animals based on information about their DNA.

This has the advantage of being available to us very early in the animal’s life, before we have to decide whether to sell the animal or keep it for breeding, and it gives us information on maternal traits even in ram lambs.

What are the benefits of using genomics over EBVs?

It is unlikely genomic breeding values (GBV) will be used to replace EBVs. Instead the genomic information is likely to be used alongside performance records to improve the accuracy of EBVs for traits that have low accuracy.

How far away are we from it in the sheep sector?

At Innovis we are busy with an intensive programme of performance recording and DNA testing in order to build up the essential information we will need to generate genomic breeding values for up to 50 different traits.

We hope to have genomic breeding values for some of these traits, such as meat quality, available to use in our breeding decisions within the next five years.

How can it be used in the sheep sector?

Genomic breeding values will be particularly useful for traits that are currently hard to record in the live animal (such as disease resistance and meat quality), only expressed in one sex (such as prolificacy and mothering ability) or measured late in an animal’s life (such as longevity).

This will involve first building up thousands of detailed records of the traits we want to select for in our breeding populations by using “old-fashioned” performance recording. Alongside this we will need to genotype animals using an SNP chip, which is a way of identifying thousands of very small differences in the DNA of sheep right across their whole genome.

This will allow us to develop the prediction equations that we can use to calculate genomic breeding values.

We will then use these prediction equations to help improve the accuracy of breeding values in our breeding programme.

How accurate is it?

Sarah Alderton, Livestock editor

The use of genomic information will only have marginal effect on the EBVs for easily recorded traits such as growth rate and ultrasonic scanning information, but could significantly increase the accuracy of other traits such as mothering ability, lamb survival and longevity, making these traits easier to improve in our breeding programmes.

You wouldn’t buy a tractor just on looks. You would make sure you did your research – finding out anything else about it such as horse power, engine capacity, fuel type, loading capacity and added extras in the cab. It should be no different when it comes to buying a breeding animal.

Too often you hear comments based solely on physical appearance such as “that’s got a pretty head”. But since the head is the first bit to be chopped off and is not commonly consumed in the UK, what does this matter?

While undoubtedly, physical defects such as lameness, testicle size and jaw defects are important, buying an animal on looks alone is never going to put the UK sheep sector at a competitive advantage.

Estimated breeding values are available in the UK, yet less than 20% of rams sold have EBVs. Compare that with our biggest competitor, New Zealand, where 90% of rams sold have EBVs, and more and more rams are being sold with genomic values too.

So while the UK may pride itself on having beautiful-looking showy animals, is that going to equate to more efficient production and better-quality meat?

The answer to that is no.

Using EBVs and genomic evaluations is a step change the industry is going to have to make if it’s to compete with the big boys.

We are not going to be able to feed a growing population just by selecting pretty looking animals with nice backends, which, let’s face it, have probably only reached the condition they are in by being fed with expensive bought-in concentrates.

We need to be producing animals that lamb easily, need minimal management and that get lambs growing fast, as well as producing a product consumers want. To support a successful future UK sheep industry, something drastic needs to change. We need to look at our breeds, at how they are managed and start using technology to help us achieve a competitive advantage.