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U.S. Quinoa Crops Threatened by Little-Known Fly Pest

Closeup image of a fly on a solid medium gray background. The fly's body is dark brownish-black in color, while its head and hind wing stubs (halteres) are yellow, as well as the joints linking leg segments. Its wings, extended vertically above the fly, are transparent with light brown veins.

Quinoa’s emergence as an attractive, climate-resilient crop in the U.S. has been met with a fresh challenge from a stem-boring fly species, Amauromyza karli, previously known in Canada. While research is scant on this new pest, a new profile in the Journal of Integrated Pest Management outlines what we know—and what we need to find out—about reducing its impact on quinoa. As shown here, adult Amauromyza karli flies have dark brown bodies, bright yellow heads, and bright yellow hind wings, which are reduced in all flies (marked with an arrow). The joints linking their leg segments are yellow as well. (Photo courtesy of Ada Szczepaniec, Ph.D.)

By Ada Szczepaniec, Ph.D.

Ada Szczepaniec, Ph.D.

Ada Szczepaniec, Ph.D.

Got any quinoa in your pantry? Some years ago, this excellent grain became an instant celebrity of healthy diet trends and exploded in popularity. Quinoa produces one of the most highly nutritious grains, with high quality proteins and all essential amino acids, fiber, vitamins, and minerals. It is also gluten-free, making it suitable for anyone with gluten intolerance or allergies.

Not only is quinoa an excellent source of food, but it also falls into the category of climate-resilient crops. What does this mean? Quinoa is adapted to extreme growing conditions such as high elevation, poor soil conditions, and high temperature fluctuations. It can also produce adequate yields with a mere 10-15 inches of water per growing season. For comparison, wheat requires 18-21 inches of water, and corn requires 25-30 inches. We are all aware of high incidence of drought limiting our agriculture, and high tolerance for limited water supply is important for sustainability of our food production systems. Quinoa is just the crop we should be growing!

A field of quinoa, in which plants are green and spindly at the bottom but topped with tufted cones of rusty orange. A few plants are visible in detail in the foreground, while the field extends out toward the horizon in the background.

In the U.S., most quinoa is imported from South America, where it has been cultivated for more than 5,000 years, but some 3,000 acres of quinoa have been grown in the San Luis Valley of Colorado since the 1980s (shown here). Quinoa is also grown in Washington, Idaho, and Oregon. (Photo courtesy of Ada Szczepaniec, Ph.D.)

In the U.S., most of our quinoa is imported from South America, where it has been cultivated for more than 5,000 years, but we do produce this crop in the U.S. as well. Some 3,000 acres of quinoa have been grown in the San Luis Valley of Colorado since the 1980s. The valley is located over 7,500 feet above sea level in the western part of Colorado, and, with only 7-10 inches of precipitation a year, it is a water-limited region of the state. Quinoa is also grown in Washington, Idaho, and Oregon, and intense research has been devoted to breeding varieties best suited to our environments in the U.S.

Unfortunately, a new stem-boring insect, Amauromyza karli, a fly in the family Agromyzidae, has disrupted these efforts and affected all quinoa acres grown in Colorado. The impact of this pest was especially pronounced in Colorado in 2022, where 100 percent of the acres of quinoa were affected by this pest, and farmers suffered significant crop and economic losses. In February, my Colorado State University colleague Gabriel Alnajjar and I published a profile of Amauromyza karli in the open-access Journal of Integrated Pest Management.

The fly is not new to our continent; it has been reported in Canada previously, but we know very little about its habits and life cycle. It is a small fly, measuring only one-eighth of an inch (3 millimeters), with a dark brown body and a bright yellow head that is easily distinguishable without any need for magnification. The flies’ reduced hind wings (called halteres) are also bright yellow, as are the joints linking their leg segments. The adults likely do not injure quinoa, but it is the immature stage—the larvae commonly called maggots—that are the main culprit of losses to quinoa.

The larvae of A. karli are white and measure approximately three-sixteenths of an inch (4.5 mm) when fully grown and lack legs or a defined head. The maggots feed inside the stem of quinoa, destroying the pith and killing young plants or significantly reducing yield when colonizing older plants. Like many other agromyzids, the larvae probably exit the stems to spend their pupal stage in the soil before emerging as adults and starting their life cycle anew. Unfortunately, we do not yet know how many generations of the fly occur per year in the U.S., or what some of their non-quinoa hosts are. The likely candidate is a close relative of the crop, common lambsquarters (Chenopodium album), which is an abundant weed in the U.S.

Interestingly, A. karli is not a pest of quinoa in South America. It was also not listed among insects founds in quinoa in a study that surveyed arthropods associated with this crop shortly after it was established in the U.S. in the early 1990s. Without much knowledge of its biology and no information regarding effective pest management tactics elsewhere, it is very challenging to develop recommendations for producers that can be immediately applied in their fields.

We can use some hints about the likely traits of its natural history from other agromyzid flies, but stem-boring insects that are well protected within plant stems and manage to evade pesticides and predators are notoriously difficult to suppress. Thus, we face a twofold challenge: First, we need to learn about the biology of this pest in the U.S. to predict when and why its outbreaks occur; second, we need to develop pest management tactics that will effectively suppress it given its stem-boring habits.

To address this challenge, I designed a project that was recently funded by the U.S. Department of Agriculture National Institute of Food and Agriculture to determine life history traits of A. karli that will be relevant to its management. We will establish peak activity of the flies in the field to inform management tactics such as planting-date modifications and timing of biological and chemical control. We will also work to identify non-crop hosts of A. karli in the field to inform weed management strategies focused on eliminating alternative hosts in vicinity of quinoa.

An effective tactic against many insect pests involves host plant resistance, and we will screen whether currently available and experimental varieties of quinoa have any resistance or tolerance to the fly. Along with my collaborator Jane Stewart, Ph.D., a plant pathologist at Colorado State University, we will also explore whether entomopathogenic fungi (i.e., fungi that can kill insects) can be established as endophytes in stems of quinoa (i.e., live inside the plants) and reduce survival of immature A. karli.

Finally, while it is a long shot given extensive research already showing that pesticides do not generally affect stem-boring pests, we will also test whether systemic insecticides can lower survival or longevity of the larvae. This tactic would allow producers to mitigate the impact of this pest while we work to hone tactics that are more sustainable but also take longer to develop, such as plant resistance and biological control.

The new pest of quinoa is highly likely to cause losses and limit our production of this crop in the U.S. until we develop and effective management strategy. However, it is very important that we do find ways to limit its impact and facilitate expansion of quinoa production. Quinoa is the type of crop we should grow more of to support our food production and ensure food security in the context of increasingly challenging growing conditions, extreme weather patterns, and the importance of decreasing our reliance on imports.

Journal of Integrated Pest ManagementRead More

New Stem Boring Pest of Quinoa in the United States

Journal of Integrated Pest Management


Adrianna (Ada) Szczepaniec, Ph.D., is an associate professor of horticultural entomology in the Department of Agricultural Biology at Colorado State University in Fort Collins, Colorado. Email:

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