Combining latest genomic technology with farmer’s eye

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Combining the latest genomic technology with the Farmer’s Eye can bring the most benefits in terms of efficiency and the bottom line. Genomics can also help protect cattle against TB and reduce methane emissions.

Dr Sotirios Karvountzis of Mendip Vets is excited by the constantly evolving opportunities geonomics present. But he warns that while the science is precise, its application needs to be far more nuanced. It’s important to select the desired genes for a given environment and outcome.

And he says there is a good way to sum up the use of new technology and the more traditional approach when discussing EBVs (estimated breeding values) and gEBV (genomic estimated breeding values). It’s the old saying, ‘The apple never falls far from the tree….’.

He explains: “All mammals, all creatures – anything that has got DNA in it – when they are  born, not all the offspring are equal to each other. Not all hit the deck running, others go slower, others go backwards.

“Humans are the exception, with the ability to put mind over matter, but in the rest of the animal kingdom they are not equal to each other. So, to take one example, the ability to grow relatively quickly to reach a certain age at a certain weight….

“That is a well defined characteristic, it’s what we call heritable, therefore it’s predictable. There are certain lines of cattle, sheep, pigs, that are able to put on more weight quicker than others.

“These animals are hitting the deck running. Others don’t. This process is repeatable. The difference is down both to genes and to the environment (the phenotype)”

The technology is available to select the most appropriate lines with the characteristics likely to achieve the desired outcome. Genomic testing can look at up to 200,000 genes, adding to the understanding of breeding stock for various attributes.

It is appropriate for sheep and goat producers as well as for suckler and dairy farmers, but the sheer volume of data available to the dairy industry makes it particularly useful. A range of advantages can be achieved by pooling information from AHDB herd genetic reports, the Signet database and genomic tissue sampling.

He explains: “The first approach would be selecting sires for a dairy farmer who wants to improve lameness, they want to improve yields or, lately very popular, to reduce the TB genomes.

“They call it TB advantage. TB resistance is a heritable characteristic and some animals are more resistant than others, so it’s to do with genetics.

“We will sit down with farmers and set priorities. We will look at what sires improve yield, improve fertility and also, added to it, improve resistance to tuberculosis.

“Then we refer to lists of possible sires. Some people buy all their sire semen from one company. Others have the ability to pick and choose. AHDB offer an independent, unbiased data base. We put in bull names and they come up with the likelihood to improve yields, fertility, mastitis or tuberculosis resistance.”

The short listed bulls are screened for price, followed by an assessment of the conformation of the animals on the farm. Dr Karvountzis advises that this is where the traditional approach, an eye for a good looking cow, is important.

He explains: “A cow with good conformation is likely to be more productive, as there is a proven link between performance and appearance.

“A cow with a wider rump is likely to yield more. It’s 60% to 80% certain, meaning that about 1 in 5 cows will not behave as predicted.

“If we then test for the genes that govern higher milk yields and we find that they are present in the cow with the wide rump, then through statistical analysis the prediction goes up to 99% ie only 1 in 1,000 cows will not behave as predicted.”

The process involves taking genetic tissue samples from heifers and their genomic potential tested when served by the short listed sires a year or so later. The combination of stockmanship with the latest technology increases the reliability of the prediction.

The science is still very new and it’s important to avoid sires whose genes improve one aspect but might compromise another. Bulls whose offspring have a high butterfat content often don’t produce a huge amount of milk.

Dr Karvountzis says: “We’re independent, not affiliated to any breeding company. I will look at the bulls they’ve been using and make a shortlist of what they have used, having visited the AHDB website.

 “We will get an idea of how many of those have been improving, what they are good at and what they are bad at and then we’ll sit down and see how many of those have been used and where. This is the important part, where you sit down and talk to the farmer.

“Very often the bulls that I wondered why he was using, there is usually a good reason behind it. The priorities are for a different characteristic, for example a bull that doesn’t pass on good cell counts might be good for TB resistance.”

The cost of tissue sampling is an issue and although it is reducing, it is still around £26 to £28 per animal plus VAT. This means that he advises a farmer to consult records of the previous breeding performance and to rule out for instance the bottom 25% of the herd.

It was better to focus on the better animals, creating a genomic breeding group with proven predictability. The sample group can then be monitored and breeding strategy centred around them.

Dr Karvountzis estimates that about 35% of dairy farmers now use genomics to improve the herd. They are usually the more forward thinking, but not necessarily the biggest farmers.

The desired outcome and the farming environment then governs the best genes to select from and, in the dairy industry, the appropriate bulls selected. A farmer in a TB hotspot might want to prioritise selection for TB advantage over fertility, lameness or mastitis.

He says the use of genomic testing isn’t as widespread in sheep flocks, simply because it’s so much more difficult to get consistent, reliable breeding data. The scattered spread of flocks  means there are far fewer pieces of information from which to draw conclusions and reliability is reduced.

And he adds: “The starting point is flipping a coin 50/50, so if I cross white with white will I get white. So I say Yes, on the basis that it’s 50% reliable, which means every other one will be white and every other one will be something else.

“You want it to be 99% which means 1 in every thousand will behave differently from what you predicted. This is what happens with sheep all the time, because the numbers are not there the volume, the strength of the observation is not there and therefore the strength of the prediction is not there.”

A possible way forward is for a group of sheep farmers to pool resources and pre-select from a shared group of ram lambs the ones that are likely to do well for certain characteristics. This would bring huge advantages in terms of saving money and time.