Even as the market for organic food has grown to an estimated $39 billion, most consumers would probably be surprised to learn that much of that food is not wholly organic. That’s because it’s not grown from organic seed. According to a new report from the Organic Seed Alliance, as much as 80 percent of organic crops from larger farms (over 480 acres) are not grown from organic seed—which is a violation of the USDA’s National Organic Program. The OSA found that smaller organic farms (on less than 10 acres) are doing better, using organic seed for 75 percent of their production.

The annual report State of Organic Seed highlights something sustainable-farming advocates have been pointing out for years: The $54 billion seed industry is dominated by large, private ag companies that put little investment into supplying the kinds of seeds organic farmers both need and are legally required to use.

Organic food grown from nonorganic seed isn’t some kind of fraud, though it exploits a loophole in the federal standards. Organic farmers are supposed to use organic seeds when they’re available, but they aren’t always available. As the organic market has grown and as the seed industry has consolidated—if a number of acquisitions in the works go through, just three companies will control more than half the global market—suppliers are not producing enough seeds to meet the demand of larger growers, hence the gap found by the report among larger farms.

But, as the alliance points out, this isn’t just about a regulatory requirement. Farmers using organic practices to raise crops from organic seeds “can help address bigger challenges in agriculture,” such as conserving genetic diversity, decreasing the use of agrichemicals and synthetic fertilizers, boosting the nutrition content of crops, and righting “social and economic injustices faced by farmers, plant breeders, and the communities they feed.”

That may seem like a tall order, but seeds truly are the basis of agriculture, and farming that breaks with the status quo can only be done with the right kind of seed—one that can thrive in a more demanding environment of local microclimates and variable growing conditions, one that isn’t tamed and homogenized by pesticides and synthetic fertilizers.

“The big companies narrowed their offerings to focus on seeds that have the largest market, such as varieties that either do well in a lot of locations or ones that are used in centers of large-scale agricultural production like the Sacramento Valley,” Micaela Colley, executive director of OSA, told TakePart in 2014. But those varieties don’t always work well for farmers in wetter, cooler climates—or any climate, really, other than the hot and dry Central Valley of California. So while it may seem like a niche concern to, say, search out a melon variety that can mature by September, at the latest, in the Pacific Northwest, when you consider similar issues across all cultivated fruits and vegetables for all parts of the country (and, really, the world), the scale of the issue becomes clear.

That small farmers are finding more melon, pepper, and sweet corn seeds that are organically produced (and, in some instances, adapted to the local climate) is one positive sign found in the new report. Another has to do less with what’s being planted for consumption now and more with what organic food varieties we’ll be eating in the future. Since the 1980s, land-grant universities that for decades did much of the legwork on developing new breeds of food crops have increasingly become laboratories working on the kinds of products that large ag companies want—things like genetically engineered staple crops. Private funding for land-grant schools now outpaces money from the USDA, and at schools such as Iowa State University, ag students attend job fairs and meet with advisers in the Monsanto Student Services Wing of Curtiss Hall.

Changes in the funding for and focus of historically public plant-breeding programs at universities has led to a shortfall in investment to develop new varieties for organic farming systems and other related research. In its last report, OSA found that there was just $9 million invested in such projects between 1996 and 2010. Just in 2010, the ag industry put $600 million into land-grant agricultural research efforts.

There are significant improvements on the financial side of the organic seed question, according to the OSA report: “Public and private investments in organic plant breeding and other organic seed research have increased by $22 million in the last five years alone.” However, the report continues, “organic seed investments still pale in comparison to funding directed toward other sectors.”

It’s funding for organic plant breeding and research that, rather than just providing farmers with melon varieties that love the cool climate of the Pacific Northwest, could lead to the kinds of crops that can withstand the increasingly erratic weather of the future—crops that may one day be as central to diets as the corn and soy of today.

This article was originally published on TakePart.com. Reprinted with permission.