New genomic measure could slow march of inbreeding

A new measure to give dairy producers more reliable information on inbreeding has been launched by AHDB.

The genomic inbreeding coefficient uses the animal’s actual genetic make-up (or genotype) to identify its genetic diversity.

This is said to be a considerable improvement over the method of calculating inbreeding used previously.

See also: How a spring-calving herd started using genomics

Marco Winters, head of animal genetics for AHDB, explains: “Calculating an animal’s level of inbreeding has, until now, been a fairly crude process, based on the probability of particular genes being inherited from each parent.

“However, while it’s known that half an animal’s genes come from each parent, identifying which half is passed on is a random and unpredictable process.”

He likens the new method to the calculation of genomic predicted transmitting abilities (PTAs), which have been used by dairy producers for more than 12 years.

Level of inbreeding

“By knowing the actual sequence of genes, we have a more accurate idea of an animal’s level of inbreeding and of what makes a good pairing in a breeding programme,” he says.

“By making a better match at the gene level, we can slow down the march of inbreeding.”

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

“A further benefit of the genomic approach is that animals whose parentage has been misidentified, or those with incomplete pedigrees, will gain as reliable an inbreeding coefficient as any other animal,” he says.

The switch to the genomic inbreeding coefficient follows extensive research by AHDB and others around the world.

Molecular geneticist and animal genetics manager at AHDB Dan Pitt, who has undertaken the latest research, describes the method used to calculate the new coefficient.

“It broadly involves 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.

“Runs of homozygosity indicate inbreeding, and the more runs there are, the more inbred the animal,” Dr Pitt explains.

Balanced approach to breeding

His preliminary work has also quantified the losses from inbreeding, which amount to 0.35% in production for every 1% inbreeding – equivalent to 28kg milk for a typical 8,000kg yield.

“This means we have to be careful to limit close matings, but producers can easily outweigh the effects of inbreeding by good genetic selection,” he says.

“However, it’s important genetic selection is carried out holistically and no single trait is allowed to fall behind,” he warns.

“Instead, a balanced approach to breeding must give traits such as disease resistance and fertility high priority.”

Mr Winters adds that many people recall the losses in traits such as fertility and lifespan over 30 years ago.

“At that time, there was no great effort to record fertility or survival traits, so the assumption was made that inbreeding was responsible.

“But now we can 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 to fine-tune the coefficient may focus on recent inbreeding, which is proving to be more damaging than inbreeding in the back pedigree.

The new coefficient has been published by AHDB since December 2022, and is now included in its services, including Herd Genetic Report and Inbreeding Checker.

See more on herd genetic reports on the AHDB website  and the AHDB’s Inbreeding Checker.