Known for their distinctive long horns, the Ankole cattle of western Uganda have evolved over millennia to withstand their harsh environment, with its lengthy dry spells and abundance of local maladies such as trypanosomiasis, a disease spread by the tsetse fly. But after flourishing for almost 10,000 years, the Ankole have begun to rapidly disappear.

Farmland is dwindling in Uganda due to the expanding human population, and Ankole require vast areas to graze. Local herders have responded to the pressure by replacing them, cross-breeding Ankole cattle with industrial species such as the European Holstein. But while these hybrids gain favourable genetic traits from the Holstein, producing more milk and meat, and requiring less land to keep, there is a hidden cost.

The genetic adaptations which enabled the Ankole to survive in such a harsh climate are diluted in the new hybrids, which lack the immune capabilities to resist local diseases. Instead of reaping profits, the herders now spend much of their money on antibiotics and pesticides to keep the animals healthy. In Burkina Faso, farmers who made similar decisions in recent years have lost almost all of their livestock to disease.

But this problem isn’t restricted to impoverished African nations. Across the UK and much of the rest of the world, the cattle farming industry is facing increasing challenges due to environmental pressures as well as the consequences of genetic selection programmes aimed at increasing income.

Research has shown that between 2000 and 2014, nearly 100 native livestock breeds worldwide became extinct, as farmers attempted to boost falling profit margins by either cross-breeding or replacing them altogether with a small handful of industrial breeds.

“If we don’t do anything to change this, it could spell long-term disaster for the farming industry particularly in the context of climate change,” says Catarina Ginja, a researcher in biodiversity and genetic resources at the University of Porto’s Cibio-InBio laboratory. “The industrial breeds may not be capable of resisting new disease epidemics, which could arise as the climate warms over the next century.

“We already had some alarming examples of how vulnerable these breeds can be to a deadly pandemic in the recent past, for example the mad cow disease outbreak in the 1990s, although that was unrelated to climate change. It’s a serious concern.”

The reason why industrial breeds are particularly vulnerable to new bacterial or viral infections is because they have very little genetic diversity compared with local breeds, due to decades of inbreeding. Ginja estimates that for breeds like the Holstein, millions of these cows originate from a mere handful of bulls.

Over the past 15 years, this has been exacerbated by the advent of genomic sequencing. Breeders can now specifically select cattle with combinations of genes that are known to optimise milk and meat production, and because these are the only animals in the herd that are allowed to mate, over time the entire population becomes descended from a few individuals. This year scientists from the Netherlands published a study showing that genetic diversity in Dutch cattle populations has dropped alarmingly over the past three decades due to such breeding programmes.

But because breeders are solely prioritising genes which improve milk and meat yields, any unusual genes which may have offered immune protection against infections become lost. In addition, inherited disorders caused by a single mutation are far more common, as all the animals are effectively related. A common problem for Holstein cattle breeders is Bovine leukocyte adhesion deficiency (Blad) which can spread from one individual bull. Cattle with Blad are prone to recurrent infections and heal very slowly.

“Breeders want to produce more and more, and they now know what genetic traits to favour in the population, in order to increase meat or milk production,” says Stéphane Joost, a researcher at École polytechnique fédérale de Lausanne, who chaired a recent European research project on the future of farm animal genetic resources. “But it’s like capitalism in general. They become too extreme. The key is recognising there are limits which are not to be passed.”

Breeders are aware of these potential problems, but they try to compensate for it in different ways, rather than changing their overall strategy. “They try to negate any health problems that emerge by giving specific vitamins and drugs to the animals,” Joost says. “And if it’s too expensive to cure them from a particular disease, they let them die. They also buy frozen semen from different banks across Europe, which contains the original genetic material of the species, and inject that into females in the herd at regular intervals to try to maintain the genetic diversity at a certain level.”

However, buying semen and drugs is expensive. This means that keeping cattle farming economically viable is a very fine balance. As an example, one study last year showed that while the volume of milk produced by European dairy farms had increased in recent years, profit margins had fallen as production costs - ranging from labour resources to cattle feed – were rising far faster than milk prices. The study showed that in 2013, dairy farms in Slovakia were actually losing €165 per tonne of milk produced.

As a result of this, any unforeseen events can cause major problems.

Joost points out that this year’s abnormally hot European summer has caused considerable problems for cattle farmers across the continent. They have been forced to spend heavily on air conditioning units to regulate the temperature and humidity for their herds.

“Because they’re not very adaptable, they can’t handle consistently high temperatures,” he says. “Unless their environment is artificially cooled, their stress levels rise, they start to weaken, their metabolism slows down, the combinations of different hormones begin to change, and they become less productive. But the artificial cooling also costs a lot.”

As the effects of human-induced climate change take hold over the next century and temperatures rise, some scientists fear that the cattle farming industry could be heading for disaster, unless steps are taken to improve the genetic diversity of these animals.

“Most of the world will face increasing aridification, and droughts,” says Professor Mike Bruford, a molecular ecologist at Cardiff University who co-ordinates the ClimGen project, an initiative looking into ways to increase the resilience of livestock to climate change.

“The current industrial breeding programmes may not be sustainable as temperatures and the amount of forage available change.”

But at the same time, going back to solely using local breeds simply isn’t a sustainable option for many farming businesses. The economic returns are not viable, and the carbon footprint from rearing them is extremely high due to the large amounts of land they need. An advantage of breeds like the Holstein is that they require relatively little space.

“The carbon budget of cattle production is already enormous,” Bruford says. “This is because of the amount of land being occupied for forage rather than absorbing carbon, as well as the infrastructure needed to produce beef and milk. From a carbon perspective, the most environmentally friendly way to farm cattle is intensively with industrial breeds.”

However, scientists believe that the same genomic sequencing tools which have accelerated the inbreeding crisis in industrial cattle, could actually solve some of the problems that farmers are likely to face on a warming planet.

These tools are increasingly able to be used to identify other important traits, for example combinations of genes relating to heat tolerance and the immune system. This could help industrial breeds deal more rapidly with environmental change, as well as produce sufficient milk and meat.

“These traits can be conserved and prioritised in these animals in parallel with the genetic traits relating to milk and meat production,” Joost says.

However, Bruford points out that implementing these strategies will take careful planning and may need to be regulated by national authorities to ensure that the cattle farming industry survives in the long-term.

“Farming is a private enterprise, people are there to make money as well as provide food so this kind of genetic selection in cattle breeding needs to be very carefully co-ordinated going forwards,” Bruford says. “Farmers need guidance from the government. For too long, we’ve let them get on with it and haven’t provided adequate support. If you don’t have a strategy, then you’re left with cattle that are productive but aren’t well adapted to their landscape, and that’s when problems arise.”