The biggest chicken producers in the U.S. will have to overhaul their breeding programs within just a few years to meet tough new animal welfare guidelines promoted by Amazon and other major food sellers.

The Global Animal Partnership (GAP), an animal welfare certifier whose five-step method is championed by Amazon’s Whole Foods, is set to lower the number of breeds that meets its standards. According to people familiar with the process, it’s virtually impossible for any conventional chicken breeds — which make up more than 90% of U.S. production — to make the cut.

The chickens that most of the world eats grow at lightning speed and prodigiously convert feed into protein. That’s made meat cheaper and more accessible to more people.

But high productivity has had trade-offs. A two-year study commissioned by the GAP had preliminary results seen by Bloomberg that concluded the world’s most ubiquitous chickens had poor outcomes due to genetics. The birds sat for most of their lives, and had more foot injuries and more problems like white strips of fat and tough, woody textures throughout their muscles. Their bodies grew faster at times than their organs, resulting in small lungs.

“We’re driving toward super efficient, lots of muscle mass. But the birds themselves have problems,” Anne Malleau, executive director of GAP, said in an interview about the project, before Bloomberg obtained the study. “Because of the selection, we’ve changed the muscle fibers. It’s a consequence of the selection that we’re seeing these muscle problems.”

GAP will release its new standards and updated breed list in the coming weeks. The chicken breeds certified by GAP will drop from 27 to a much lower number, which will rise as more breeds are tested.

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While the new rules don’t go into effect until 2026, the move could drive changes in the industry with over 200 companies including Popeyes Louisiana Kitchen and Chipotle Mexican Grill promising to transition to breeds that meet GAP’s standards.

Consumers have become increasingly interested in animal welfare, and more willing to pay for food with ethical claims. But because the costs of producing slow-growing birds are substantially higher than industrial chickens, breed changes on a large scale could lead to more expensive meat across the board. Whether consumers will accept that remains to be seen.

“Everyone is going to have to make a decision that’s best for their family, but there are also wider implications,” Malleau has said of the higher costs. “There’s an ethical decision that we need to make, where we’re paying a little bit more for chicken and it means that these birds have a better life.”

Any changes would take time. The vast majority of chicken genetics is for industrial birds, and controlled by two companies, Tyson Foods-owned Cobb-Vantress and Alabama-based Aviagen. Tyson is the biggest American meat producer. Breeding is a slow process that takes years, by selecting desired traits over multiple generations of birds.

Cobb-Vantress said it evaluates more than 50 traits in its selection program, and more than half of them are related to improved health and welfare. Trevor Gies, a senior marketing manager at Cobb, also said the study commissioned by GAP was flawed.

“Conventional breeds were overfed protein, under ventilated and our recommendations for hatching were not followed,” Gies said. That “resulted in issues that do not reflect what today’s commercial chicken farming operations are really experiencing.”

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A representative for Aviagen declined to comment on the study.

GAP has powerful backers. Whole Foods, which uses the program for its 365 brand, said it will comply with the new breed list when it’s released.

“We are aware of — and supportive of — GAP’s commitment to slower-growing broiler breeds,” a Whole Foods spokesman said in a statement. “Once that list is finalized, we will start working toward those breeds with GAP’s recommendation.”

Some chicken producers are already making moves to adjust to the higher standards.

Perdue Farms, the fourth-biggest U.S. chicken producer, has been preparing for an updated breed list for five years. In 2016, it began experimenting with heritage and hybrid breeds, which aren’t as susceptible to muscle problems like woody breast. The company has tested 15 different breeds so far.

Bruce Stewart-Brown, the senior vice president of technical services and innovation at the company, said the mounting concern around breeds will become as big as the movement to antibiotic-free chicken that started 20 years ago.

“As they identify those new breeds, and if we’re going to raise GAP birds, then we have to evolve to the breeds of their new standard,” he said in an interview.

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Breed issues have been front and center lately because a line of roosters owned by Cobb-Vantress was found to have fertility issues that rippled throughout the industry, causing losses for Tyson and also affecting U.S. output at a time when chicken demand is increasing rapidly.

Some scaled-up alternative breeds have already emerged. Cooks Venture, an Arkansas-based producer and genetics company, developed a breed over 12 years with heritage lines. Chief Executive Officer Matt Wadiak said the company’s largest asset is genetics, which they intend to sell to other companies to help meet slow-growing bird commitments.

“The often suggested idea that the only choice we have to feed people at scale must come at the expense of animal welfare, and lack of genetic diversity, is simply wrong,” he said.