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Genomic measure can help limit inbreeding (Feb 23)

Producers have sought to limit inbreeding for many years, and now there is an additional tool to help limit its harmful effects. We spoke to a leading geneticist to find out more.


TEXT ANN HARDY



A measure of inbreeding has been launched by AHDB, which is more accurate and biologically meaningful than using parent average figures. The genomic inbreeding coefficient uses the animal’s actual genetic make-up, or genotype, to identify its own individual genetic diversity. The same information is also used to predict the inbreeding of future matings, providing a better estimate of how inbred planned progeny are likely to be.


This is important because inbred cattle, with little genetic diversity within their genome, are known to experience some loss of vigour.


“The genomic inbreeding coefficient follows on the heels of genomic predicted transmitting abilities – PTAs – which UK producers have been successfully using for more than 10 years,” says AHDB’s geneticist Marco Winters


“Before we had this genomic information, calculating the inbreeding coefficient was a fairly crude and imprecise process, based on the probability of particular genes being inherited from each of an animal’s parents,” he says.


“We know that half its genes come from each parent, but which half is passed on is a random and unpredictable process. When this estimate is multiplied for successive generations, it can potentially result in significant inaccuracies when the inbreeding coefficient is calculated from the animal’s pedigree.”


But the genomic figure is available, it will be published in the UK for every genotyped female. The scale of its expression will be the same as the previously-used pedigree inbreeding coefficient.


“The most obvious and practical benefit of this approach is that cattle whose parentage has been misidentified, or those with incomplete pedigrees, will gain as reliable an inbreeding coefficient as any other,” says Mr Winters. And the scope of the new index extends further, due to extensive research by AHDB scientists and others around the world.


Quantified losses


“The work involved an assessment of the genes on the animal’s DNA, but particularly identifies runs of homozygosity – something which occurs when several of the same copies of genes are inherited from each parent,” says AHDB’s animal genetics manager Dan Pitt, describing how the coefficient was calculated.


“Runs of homozygosity are an indication of inbreeding and the more runs there are the more inbred the animal,” he explains.


Preliminary work has also quantified losses from inbreeding, which amount to 0.35% in production for every 1% inbreeding – equivalent to 28kg of milk for an 8,000-kilogramme yield.


“It’s important to limit close matings, but producers can easily outweigh the effects of these by good genetic selection,” says Dr Pitt.


He adds that a maximum target figure for inbreeding is less relevant today compared to a decade ago, but ongoing research – particularly into the effects of historic and recent inbreeding – will inform future advice. “Our work indicates that historical inbreeding, accumulated more than five generations ago, may not contribute to the same extent as inbreeding resulting from more recent generations. So, a better insight and understanding of this will help further improve the management of future matings.”


That said, he stresses that it’s particularly important that any genetic selection is carried out holistically and that no single trait is allowed to ‘fall behind’.


“A balanced approach to breeding, to give traits such as disease resistance and fertility high priority, must be taken,” he says.


Monmouthshire-based Lyndon Edwards was quick to use the genomic inbreeding coefficient for selecting sires for use on his 250-cow Holstein herd. Using AHDB’s Inbreeding Checker, he found the average figure for the bulls he was planning to use was virtually the same, whether based on parent average or the genomic calculation. “But, within that average, there were outlying bulls at both ends of the scale, one of which we stopped using altogether, while others were more suited to our herd,” he says.


By using the sires that suited his herd better than expected, he has been able to achieve an average 1% reduction in inbreeding coefficient in his heifer calf crop, compared with former calculations.


“And it can be as much as two or even three percentage points better on some of the resulting calves,” he says.


Avoid inbreeding



Sire selection: informed decisions can be made to prevent inbreeding


He’s using bulls that produce smaller, fertile and more robust cows with good udders, a high butterfat percentage, and good disease resistance. “We pick a team of around six sires, any one of which could be used on any of our cows. But, if all else is equal, the Inbreeding Checker will be used to determine which of those bulls will be bred to a specific cow.”


“Many producers remember the losses in respect to traits such as fertility and lifespan more than 30 years ago,” adds Mr Winters. “At that time, there was no great effort to record fertility or survival traits, so the assumption was made that inbreeding was responsible.


“But we’re now able to avoid such effects by breeding for a wider cross-section of traits and actively monitoring animal performance, which would immediately show any detrimental trend.”


Ongoing research at AHDB will further fine-tune the figure and in the mean time producers can benefit from the greater accuracy of the new coefficient, which has been published since December 2022 and is now included in AHDB services, including Herd Genetic Report and Inbreeding Checker.


However, as with any predicted mating, the inheritance of genes is still a random process, and only after offspring are born can their genomic inbreeding be tested.


Find out more about AHDB Inbreeding Checker at: https://ahdb.org.uk/inbreeding-checker.

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