Genetic research boosts response to diseases afflicting Hawaii’s coffee crop

As the only state that produces coffee, including the legendary Kona variety, Hawaii growers and agriculture officials were alarmed when coffee leaf rust began to spread rapidly across the islands.

The devastating plant fungus, which reduces yields and harms coffee trees by attacking the plant’s leaves, was first recorded on the islands of Maui and Hawaii in 2020. It has since been found on Oahu, Lanai, Kauai, and Molokai. A concerted effort was quickly mobilized in response to the escalating threat.

“We were in the process of preparing for CLR [coffee leaf rust]but it wasn’t the top priority,” said Christopher Manfredi, Managing Director of the Hawaii Coffee Association (HCA). “It is now. “

The partnership – led by the Synergistic Hawaii Agriculture Council (SHAC), with financing of the Food and Agricultural Research Foundation‘s (FFAR) Rapid Outcomes from Agricultural Research (ROAR) program – is pursuing a multi-pronged response to coffee leaf rust (CLR), which causes $3 billion in damage worldwide each year.

The stakes are high. Hawaii’s raw coffee industry is valued at US$113.01 million annually and employs approximately 1,500 farms on 10,000 acres statewide. Most are family run and smaller than two acres. Many more people depend on the industry for their livelihood, which also generates income from the increasing tourism and related businesses.

“Numbers aren’t a good way to talk about the deep, 200-year legacy of coffee in Hawaii,” said Suzanne Shriner, director of SHAC. “The potential income losses for growers are serious, but they also endanger an entire community built around coffee. The Kona region of Hawaii is a mecca for visitors taking farm tours, local shops selling coffee, and all the side jobs and attractions that result from the lure of the coffee bean.”

Growers are already feeling the effects, as the disease causes defoliation that can reduce yields by up to 70 percent and significantly increase production costs. In response, many farmers have increased their raw coffee prices by $1.50 to $3 per pound. The “downstream economic impact” is estimated to be approximately $231.67 million for the 2021-22 season.

“Our growers are desperate for a solution to CLR,” Shriner said. “The FFAR grant enabled researchers and the extension to quickly provide answers to the most fundamental questions about this disease. As our learning curve grows, it builds on the foundation of joint funding from FFAR and our community partners, who matched the funds.” These include the HCA, the Maui Coffee Association, and the Hawaii Coffee Growers Association.

FFAR genetics research is led by Dr. Catherine Aime, a Purdue University professor who is the only academic mycologist in the country to specialize extensively in fungi that cause rust disease.

“Our goal is to generate a high-quality genome for the fungus (Hemileia vastatrix) that causes coffee leaf rust disease (CLR),” explained Aime. This information is used in a variety of ways, including identifying genotyping markers within the genome, to help researchers track rust movement and population dynamics, and to characterize the molecular basis for overcoming host resistance.

“If we can determine (via genotyping) how the rust populations behave and produce diversity, that will inform management programs,” Aime said. “For example, if we find that environmental factors are most important in selecting hypervirulent strains, then it would be appropriate to alter the host’s growth conditions to be less favorable for CLR.” However, if we find that new breeds are constantly emerging, breeding for permanent resistance would be a better strategy.

Aime’s team has already identified the strain of coffee rust affecting Hawaii’s harvest, Shriner said. “Unfortunately, it’s an aggressive variety with big ones [leaf] lesions and a 20-day incubation period.”

Coffee leaves covered with coffee leaf rust, a fungal pathogen that causes defoliation and reduced yields. Photo: Purdue University/Cathie Aime

The research has implications for understanding the disease beyond controlling its outbreak in Hawaii.

“The ultimate goal is to provide the knowledge, based on genomic and population analysis, of how the rust manages to erode host resistance so rapidly,” Aime said. “Once this is understood, we can better plan outbreak containment strategies, whether that involves changes in management or breeding strategies. Rust fungi cause some of our most serious diseases in agricultural crops and forest products. Therefore, any insights into how they overcome host resistance can help inform strategies to control them in other systems.”

While most other coffee-growing regions have planted rust-resistant cultivars, none of Hawaii’s commercially grown cultivars are rust-resistant, according to an HCA white paper. Additionally, none of the fungicides most effective in controlling the disease have been approved for use on coffee in the islands.

“It’s like your house is on fire and you’re working to get a permit to buy a hose,” Manfredi said, noting that growers have been working with state and national researchers and agencies to ensure the safe use of approved systemic fungicides to be made possible quickly for coffee elsewhere and for other food crops in Hawaii.

The HCA is asking for subsidies to help farmers purchase fungicides that are effective against CLR. This stance is supported by a USDA-APHIS economic analysis, which states: “The most practical means of controlling CLR is fungicide spraying, which would cost Hawaiian coffee growers as much as $10 million annually. These additional costs would affect different types of farms differently. Small, non-mechanized coffee farms would likely not be able to afford the additional cost of controlling CLR and would cease coffee production. Larger farms (>15 acres) using mechanization and modern farming methods may be in a better position to continue production as they have high enough yields to generate sufficient income to support the additional costs.”

The analysis also recommends transitioning to CLR-resistant cultivars as a potential long-term solution to reduce the need for fungicide applications. “We estimate that it would cost at least $68.5 million to transplant the fields, or $95.6 million to replant all of Hawaii’s coffee acreage. However, switching to resistant varieties would occur over time.”

Public relations and education are also important parts of the response. As part of the FFAR grant, the University of Hawaii’s College of Tropical Agriculture and Human Resources (UH-CTAHR) is producing materials and training Hawaiian growers in the best-known management practices for CLR. The extension’s faculty and staff help growers recognize and identify CLR on their farms in the critical early stages and provide tips for managing the disease through field remediation, monitoring, proper crop nutrition and fertilizer, pruning and approved fungicides.

“We’re strengthening the fundamentals: soil health, tree health and farm management,” Manfredi said.

Outreach activities included webinars, workshops, field days, farm doctor visits, informational videos, training booths at industry conferences and exhibitions and a website where most of the teaching materials are posted.

Shriner said the research and expansion activities offer benefits beyond slowing or stopping the spread of coffee leaf rust across the islands.

“Control may never be possible. But management could be,” she said. “The FFAR grant enabled researchers and the extension to quickly provide answers to the most fundamental questions about this disease and gather adequate data to develop a comprehensive strategic plan. As our learning curve grows, it builds on the foundation of joint funding from FFAR and our community partners, who matched the funds. The response from growers and the community has been appreciative.”

Image: Ripe coffee cherries ready for harvest. Photo: Wikipedia Commons/Jonathan Wilkins


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