American Agriculturist Logo

Genetics used to fight fire blight

A project in New York is developing fire blight-resistant apples.

Kara Lynn Dunn

April 28, 2023

3 Min Read
Cornell apple genetics researcher Awais Khan looking at apples hanging in tree
FIGHTING FIRE BLIGHT: Cornell apple genetics researcher Awais Khan is providing apple geneticists, breeders and fire blight management experts more data on fire blight pathogens, aggressiveness of the fire blight strains and apple varieties that are most susceptible. Photos courtesy of Awais Khan

Fire blight, a highly destructive disease caused by the bacteria Erwinia amylovora, can leave orchards with tens of millions of dollars in damage in a single year.

Awais Khan, a Cornell University associate professor, is providing apple geneticists, breeders and fire blight management experts more data on fire blight pathogens, aggressiveness of the fire blight strains and apple varieties that are most susceptible. This data will support the breeding of varieties with durable resistance and improve fire blight management.

“The severity of a fire blight outbreak is determined by the interaction of resistance genes in the apples, the growth stage of host trees, the genetics of the fire blight pathogen strain and environmental conditions,” Khan explains.

Generally, apple cultivars will respond differently to different bacterial strains. With funding from the New York Farm Viability Institute, Khan collected and analyzed samples of Erwinia amylovora strains from 40 orchards across Long Island, the Hudson Valley, the Champlain Valley and the Finger Lakes regions. This effort has significantly increased the number of strains from New York state in Khan’s collection of about 1,500 strains worldwide.

Khan used genome sequencing to characterize the genetic diversity of fire blight strains and to evaluate infection levels of more than 100 strains of the fire blight bacteria on a set of high-value apple scion and rootstock cultivars. The scion (aboveground) and rootstock (belowground) of apple trees are genetically different.

“Dr. Khan’s research is filling in knowledge gaps about fire blight and building a foundation for apple breeding programs aimed at increasing resistance,” fourth-generation apple grower Ted Furber says.

Furber operates a 550-acre diversified orchard in Wayne County near the Lake Ontario shoreline. The orchard celebrated its 100th anniversary in 2022.

“Fire blight can be devastating,” he says. “In 2021, we lost trees in the orchard and in the nursery. That outbreak is the worst I have experienced. It cost us tens of thousands of dollars in replacement cost. A fire blight outbreak can put an orchard out of business.”

Breeding for resistance

Fire blight can infect different parts of apple trees including blossoms, branches and rootstocks.

It can spread quickly — particularly in warm, humid weather — and can overwinter in old cankers. It can happen without warning despite forecasting and preventative spraying.

“Changes in fire blight bacterial strains and the composition of apple varieties planted over time, and weather in a region may explain sudden and unpredicted fire blight outbreaks across New York state and globally," Khan notes.

Growers facing fire blight infection respond by cutting and removing infected cankers, pruning infected branches and, in severe cases, removing entire trees or blocks.

Many high-value apple and cider apple varieties are susceptible.

“Apple cultivars that have some level of resistance to particular strains of fire blight may have susceptibility to new strains,” Khan says. “Knowledge on the susceptibility of the publicly favored conventional scion and cider varieties to the fire blight bacterial strains most commonly found in New York state will assist resistance breeding efforts of these economically high-value apples.”

This research will eventually help growers make decisions about cultivar selection; how to manage fire blight, such as when to spray; and how precisely to prune. Findings may also be applied to improve the accuracy of apple fire blight forecasting models.

For more information on Khan’s work, visit

For a database of apple diseases and susceptibility to fire blight by variety, visit

Dunn writes from her farm in Mannsville, N.Y.

Read more about:

Subscribe to receive top agriculture news
Be informed daily with these free e-newsletters

You May Also Like