Organic Carrot Breeding Delivers Novel Varieties, Cutting-edge Research

All photos courtesy of Organic Seed Alliance.

The U.S. organic industry continues to grow, with sales of organic food reaching $45 billion in 2017 and the number of organic farms estimated at over 14,200, an 11 percent increase in one year. Organic carrots increasingly make up a larger share of overall carrot production—14 percent of the estimated 100,000 acres of carrots grown in the U.S. are certified organic (compared to three percent of total vegetables grown organically).

Growing carrots organically isn’t easy, however, given the extensiveness of major diseases and pests, and the cost of managing weeds. More than 80 percent of U.S. carrot acreage is infested with one or more of the most common pests or diseases: root-knot nematodes, Alternaria leaf blight, and other foliar and storage diseases, such as cavity spot. The future of organic carrots therefore relies on the development of effective, non-chemical methods for addressing these challenges, including managing weeds in this slow-to-establish crop.

Breeding a Key Factor
“Organic farming takes a whole-systems approach to addressing plant nutrition and challenging weeds, diseases, and pests,” says Micaela Colley, program director for Organic Seed Alliance. “In important ways, organic growers rely on the genetic characteristics of the seed they plant even more than other growers, since most pesticides and fertilizers are not allowed under organic regulations.”

“That’s where plant breeding comes in,” Colley adds.

Seed provides growers the genetic tools to confront day-to-day challenges in the field, and breeding plants in the environment of their intended use—in this case, under organic conditions—can yield many benefits. Enter the Carrot Improvement for Organic Agriculture (CIOA) project, a multi-regional plant breeding collaboration between the United States Department of Agriculture’s (USDA)/Agriculture Research Service (ARS), University of Wisconsin-Madison, Purdue University, University of California-Riverside, Organic Seed Alliance, and Washington State University. It is the first publicly funded organic carrot breeding project in the U.S., and the USDA’s Organic Research and Extension Initiative (OREI) grant program recently awarded the project a second round of four-year funding—and for good reason. The project’s successes thus far are noteworthy.

Dr. Philipp Simon is the coordinator of CIOA and has been breeding carrots for 40 years. He holds a joint position with USDA/ARS and the University of Wisconsin-Madison’s Horticulture Department. Simon has learned a lot in the last decade about the needs of organic carrot growers and how CIOA can turn their production challenges into breeding opportunities. To that end, CIOA’s main goal is to develop orange and novel colored carrots with improved disease and nematode resistance, improved weed competitiveness, and better nutrition and flavor. That’s quite the genetic package, but progress toward releasing new varieties has been efficient—and relatively quick—thanks to the project’s variety trial network that expands across the U.S.

Variety Trials
In 2018, CIOA variety trial sites were located in California, Hawaii, Indiana, Maine, Washington, Wisconsin, Vermont, and Virginia. Each site tested a different mix of 34 promising advanced breeding populations (these are varieties that are nearly uniform enough to release commercially). Simon is especially excited to see more evidence that the most important traits are “fixed.” This means that from general appearance to disease resistance to flavor, CIOA partners are finding that the varieties in development are performing relatively similar across trial locations.

“From a breeding standpoint, the process of putting together the right combination of traits and then having them reliably expressed across regions is so important,” Simon explains. “CIOA’s extensive trialing network is providing us more confidence that certain traits will express in varying environments, allowing us to accurately report just how well the overall varieties perform in different regions across the U.S.”

Simon says that two traits in particular are worth noting: top size and nematode resistance. Research shows that carrots with bigger tops help suppress weeds, a costly production challenge for all carrot growers, not just organic. CIOA breeders have had success in incorporating this trait into breeding lines to support better weed competition.

CIOA is also having success in breeding orange and novel colored carrots that demonstrate resistance to the two major species of root knot nematodes, tiny roundworms not visible to the naked eye. Nematodes live in soil and feed on plants, leading to malformed, stubby, and hairy roots, and tougher skin and lower yield. Furthermore, growers who aren’t organic are losing access to chemical fumigant and spray controls, making breeding for resistance that much more important to the entire industry.

Emerging Science
CIOA’s research is contributing to emerging science regarding beneficial microbe associations with crops as well. Plants (including carrots) associate with a diverse assemblage of microbes living on the surface and within plant tissues, which is now commonly called the plant microbiome. Some of these microbes have the potential to help plants acquire nutrients and withstand biotic and abiotic stress, so identifying factors that affect their recruitment and survival is important to optimizing plant growth. CIOA partner Dr. Lori Hoagland and her research team at Purdue University have determined that a carrot’s genotype plays a small, though significant, role in shaping these beneficial endophyte communities, indicating it may be possible to select varieties that are more apt to recruit them from soil. Other studies are underway to determine if researchers can identify differences in carrot genotypes in how they interact with soil microbes to facilitate organic matter decomposition, which could be important for managing organic nutrients.

The CIOA project team takes a participatory approach to plant breeding, where farmers, formal plant breeders, and members of the seed and food industry collaborate on setting project priorities and evaluating the results. Evaluations have also closely involved consumers of organic carrots to ensure that breeding projects not only meet the needs of growers with traits like disease-resistance, but also meet the expectations of the market. Not surprisingly, flavor and nutritional content are of top priority to consumers of organic carrots. CIOA hosted seven variety tastings in 2017 and 2018 to gather feedback on their projects from consumers, focusing on flavor, texture, color, and appearance. This feedback is evaluated and then informs breeding decisions moving forward.

Novel Colored Carrots
Novel colored carrots—yellow, red, and purple—are increasingly popular among consumers and chefs, yet they’re in need of serious breeding attention. Much of the colored carrot germplasm collection hasn’t been improved for, or even tested in, organic systems. One exciting finding is that within this collection is the expression of important traits, including large tops, bolt resistance, and vigorous seedling growth. CIOA breeders are improving this material to also include disease and pest resistance characteristics as well as good flavor and nutritional value. For example, breeders are testing CIOA carrots for their level of carotenoids and anthocyanins (both are naturally occurring pigments that offer health benefits), among other nutritional elements.

The CIOA project takes a classical approach to carrot breeding, starting with intercrosses to combine traits from two breeding stocks in one offspring population. So, for example, intercrossing breeding stock with good flavor and an unrelated nematode resistant carrot, to develop a new breeding line with both good flavor and nematode resistance. As CIOA breeders develop DNA markers to track genes controlling these traits in carrots, the 5 to 10 year process of combining traits will be be reduced. That is good news because carrot growers and consumers are interested in improvements for many traits.

Micaela Colley is program director for Organic Seed Alliance, a partner in CIOA. In this photo Colley is reviewing carrot variety trials in El Centro, California.

Simon says one challenge the project has encountered is finding suitable carrots for the Southeast region, where the subtropical climate proves difficult for production. But trials in Virginia, and in the tropical climate of Hawaii, have provided promising leads on which material is worth pursuing as part of CIOA’s breeding work. They hope to identify even more material in 2019 to help meet this need.

CIOA partners Dr. Philipp Simon and Micaela Colley evaluate carrot variety trials in El Centro, California.

New Releases
For now, CIOA is poised to release several varieties adapted across geographical regions in the U.S. Project partners plan to release at least half a dozen varieties within the next two years, including a purple-orange carrot and some red varieties. Reds are of special interest to organic growers, who report having limited options that have good flavor.

CIOA has already released some breeding lines with exceptional nematode resistance to other breeders, including a carrot breeding collaborative in British Columbia, as well as to the organic seed industry. These lines support the breeding work of others, resulting in even more improved varieties entering the marketplace. CIOA’s intent is for the products of their work to remain in the public domain: free of intellectual property rights that restrict the ability of farmers and breeders to freely operate. CIOA believes it’s important that everyone have continued access to use and further develop these new varieties and breeding lines that were supported through public funding.

The Carrot Improvement for Organic Agriculture (CIOA) project will soon release new colored carrot varieties that were bred under organic farming conditions. Pictured here are carrots in a variety trial conducted in El Centro, California.

CIOA partners also hope new varieties coming out of their project will be produced organically and successfully commercialized to help organic operations meet the requirement to use certified organic seed when available. Although gaps remain in the organic seed supply, availability in organic seed has expanded tremendously over the last 15 years. Organic plant breeding has played an important role in this growth to ensure that more diverse organic seed options are available—and it will continue to play a meaningful role.

2018 Farm Bill
Congress recently passed the 2018 Farm Bill, which more than doubles the amount of research funding available to the USDA’s OREI program, CIOA’s funding source. By 2023, $50 million will be available each year to support research that benefits existing organic growers as well as transitioning growers who face a steep learning curve when adopting organic practices. Because organic research often focuses on soil health and alternative pest and disease management, the results benefit all farmers—not just organic.

“One of the long-term impacts of CIOA—and of publicly funded organic research in general—is that graduate students working on this project are developing expertise in organic systems,” says Colley. “They represent the next generation of plant breeders and agricultural researchers. And the demand for and interest in organic farming is only growing.”

This article first appeared in Carrot Country.


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