When the agribusiness and chemical giant Dupont decided to get into aquaculture, Scott Nichols, the executive in charge, went to see experts at the World Wildlife Fund and the Environmental Defence Fund.

He needed their advice and wanted their support. DuPont planned to feed genetically-engineered yeast to farmed salmon, instead of relying on oils from wild fish captured from the ocean. That would help preserve marine ecosystems, but Nichols was well aware that using genetically-engineered feed could become an issue.

"Sisyphus has a job," he told the experts. "I don't want it."

Since then, DuPont has joined with AquaChile, one of the world's big aquaculture firms, to create Verlasso, a brand of salmon that is marketed as "harmoniously farmed" in the "crystal-clear water of Patagonia". DuPont grows the omega-3 rich yeast. AquaChile grows the fish. Environmentalists like WWF's Jason Clay praise this thoughtful approach to aquaculture, saying "to take pressure away from taking fish out of the ocean is a good thing.".

But there's a problem. Whole Foods Market – the US's most important retailer of organic, natural or sustainable foods – won't carry Verlasso salmon.

Why not? Partly because Verlasso is raising Atlantic salmon in the Pacific Ocean, and Whole Foods prefers suppliers who farm species in their native waters, and partly because Verlasso occasionally uses antibiotics, which are prohibited by Whole Foods. In addition, Whole Foods is seeking to carry fewer foods using GMOs – even though, in this case, the GMO yeast is a substitute for fish oils.

"Our customers prefer non-GMO when possible, so when we can source something without GMOs, we will certainly do that," said Beth Krauss, a Whole Foods spokeswoman, after consulting seafood buyer David Pilat. "If we can get farm-raised salmon without GMO feed being used, we will."

This matters, and not just to Verlasso. Whole Foods recently said that by 2018 it will require all products in its stores to be labelled if they contain GMOs, and will avoid foods with GMOs when possible. Labelling is part of the company's commitment to transparency, but labelling could also stigmatise GMOs, despite the broad scientific consensus in the US that the genetically-engineered crops currently on the market are safe to eat.

More broadly, Whole Foods' aversion to GMOs could stifle efforts to use genetic engineering technology to produce crops that deliver benefits whether to the environment (crops that use less water, or require less land), health (foods with more nutrients), or the economy (higher-yielding crops that cost consumers less). About 17.3 million farmers, most of them in emerging markets of India and China (and most of whom growing cotton), chose to plant biotech crops in 2012, according to the ISAAA (International Service for the Acquisition of Agri-biotech Applications).

While Whole Foods, with annual sales of $11.7bn (£7.5bn) in 2012, is far from the biggest US supermarket chain – Kroger, Safeway, Supervalu, Publix and, of course, Walmart, are all much bigger – the Austin-based retailer and its 350 outlets have an outsized influence, particularly over brands that market themselves as organic, natural or sustainable.

Entrepreneurs Jeffrey Hollender of Seventh Generation, Myra and Drew Goodman of Earthbound Farms and Seth Goldman of Honest Tea have all told me that backing from Whole Foods has helped to drive their growth.

Conversely, companies like Verlasso with a sustainability story to tell will have tougher time getting the word out, as well as getting their product out, if they can't get on shelves at Whole Foods. "We'd love to be in their stores," said Scott Nichols, who is now the director of Verlasso. "They are leaders."

The irony, of course, is Verlasso itself is out to become a sustainability leader. Substituting plant-based feed for fish oils reduces pressure on the oceans. About half of the world's fish oil production goes into farming salmon, according to a comprehensive 2008 FAO study. When compared with conventional fish farms, Verlasso says it gives its salmon more water in which to swim, uses fewer antibiotics and takes extra precautions to prevent fish escapes . "We feel a tremendous urgency to get this right," says Nichols.

Verlasso is seeking certification from the Aquaculture Stewardship Council, a new standard-setting group. While there are a host of problems with farmed Atlantic salmon — the Monterey Bay Aquarium's Seafood Watch ratings recommend that customers avoid them entirely — organisations such as WWF say that, when done responsibly, salmon aquaculture's impact on wild fish populations, marine habitats and water scarcity can be reduced.

Whole Foods has developed its own rigorous standards for aquaculture. Greenpeace, which ranked the seafood policies of 20 big retailers, praises Whole Foods for having "the most rigorous sustainable seafood policy in the industry". Greenpeace opposes the spread of GMOs, citing potential dangers to the environment and human health.

Whole Foods, notably, makes no such claims. Its communication around GMOs refers to customer preferences, which the company says come after customer surveys and dialogue. "We are not making any claims with regard to good or bad," Whole Foods' Beth Krauss said. Purely as a business proposition, its stance towards GMOs will play well with its core audience, particularly parents who are concerned about what their children eat.

Still, it's worth asking: instead of catering to anxieties about GMOs, why not educate people – as Whole Foods has done, effectively, around such issues as animal welfare? GMOs have benefits. They have risks, too – as do all technologies. The job of a responsible company is to weigh those trade-offs. Whole Foods' antipathy towards GMOs could have unfortunate and unintended consequences.

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