A network of U.S. scientists is intensifying efforts to develop more climate-resilient apple trees as increasingly volatile weather patterns threaten orchards across major fruit-growing regions, raising concerns about long-term risks to an industry that generates roughly $23 billion in annual economic activity.

Researchers at Cornell University, the United States Department of Agriculture and several partner institutions are focusing on rootstocks, the underground foundation of commercial apple trees that influences growth, productivity and resistance to environmental stress.

The work has gained urgency since a series of severe temperature swings damaged orchards in the northeastern United States in 2015, an event that some researchers later linked to a phenomenon known as “rapid apple decline.”

Terence Robinson, a horticulture professor at Cornell University, recalled how unusually warm temperatures in February 2015 were followed by a sharp cold snap that swept through New York and into fruit-growing regions of Pennsylvania.“We got a warm-up in February, and then a big cold air mass moved into New York and pushed all the way down into the fruit-growing area of Pennsylvania,” Robinson said.

“In the spring, we started seeing tree damage.”Scientists concluded that the rapid temperature drop, estimated at as much as 65 degrees Fahrenheit within days, disrupted trees that had already begun emerging from winter dormancy. Researchers found particularly severe damage in rootstocks rather than trunks or branches.

The findings drew attention to vulnerabilities in some of the apple industry’s most widely used rootstocks, including the M9 variety developed more than a century ago at England’s East Malling Research Station.Commercial apple trees are typically produced through grafting, a process that combines two different plants.

The upper fruit-bearing portion, known as the scion, comes from commercial varieties such as Gala or Red Delicious. That section is attached to a separate rootstock selected for characteristics including tree size, productivity and disease resistance.

Because rootstocks determine how trees absorb water, respond to stress and tolerate environmental conditions, scientists increasingly view them as central to protecting orchards from climate-related disruptions.Robinson and USDA scientist Gennaro Fazio jointly oversee the Geneva Apple Rootstock Breeding Program, based in Geneva, New York.

The initiative, operated by Cornell University and the USDA, is the only commercial apple rootstock breeding effort in North America focused on developing new foundations for orchards.Since 1968, researchers in the program have crossed and evaluated thousands of apple rootstocks.

Early efforts concentrated largely on disease resistance, particularly protection against fire blight, a destructive bacterial disease affecting apple and pear trees.More recently, researchers have expanded their priorities to include drought tolerance, resistance to high-salinity soils and improved survival during unstable winter conditions.

“We still continue wanting to have a rootstock that is dwarfing, because dwarf orchards are much more profitable, and that produces early,” Robinson said. “We have broadened our list of goals for this program to include drought resistance, tolerance of high-salt-content soils and the ability to withstand more moderate winters.”The process is lengthy.

Developing a commercial rootstock can take decades because scientists must cross parent trees, evaluate offspring for desirable characteristics and test performance across multiple climates and growing conditions.Cornell released its first commercial rootstock in 1997, nearly three decades after the program began.

Some varieties introduced in 2023 originated from genetic crosses first made during the 1970s.“It requires long-term commitment to learn to love apple rootstocks,” Robinson said.Researchers say the challenge has become more complicated because climate variability is increasing faster than orchard replacement cycles.

Apple orchards are typically expected to remain productive for 15 to 30 years, meaning growers must make planting decisions without knowing exactly how weather patterns may evolve over the lifespan of their trees.

Lee Kalcsits, a professor of tree fruit physiology at Washington State University, leads the Strengthening Pear and Apple Resistance to Climate project, known as Sparc, a national research collaboration studying how extreme weather affects fruit trees.

Kalcsits said breeding efforts should prioritize adaptability rather than designing trees for one specific future climate scenario.“We need to be mindful that the rootstocks we select are adaptable,” he said. “It’s not that they’re adapted to a future climate, but that they’re adaptable.”Research published by Kalcsits and colleagues in 2024 found that both fall and spring temperatures are warming in major U.S. apple-growing regions.

Warmer conditions can interfere with the chilling requirements apple trees need before flowering and can also cause trees to leave dormancy earlier, increasing exposure to damaging cold events.Scientists say abrupt winter fluctuations have become a growing concern as climate-driven disruptions to atmospheric circulation allow Arctic air masses to move farther south into the United States.

Robinson said damaging cold snaps have struck major apple-producing areas, including southern Pennsylvania and western Michigan, four times since 2015.Rootstocks can influence how trees respond to those conditions by affecting dormancy timing, cold tolerance and water use.

Some newer rootstocks developed through the Geneva program have shown reduced damage during false springs followed by hard freezes compared with older standards such as M9.Researchers are also turning to wild apple populations from central Asia, where domesticated apples originated, to expand genetic diversity and identify additional stress-resistance traits.

Experimental rootstocks are tested nationwide through a research collaboration known as NC-140, which evaluates orchard performance across multiple states. One test site operates at North Carolina State University’s Mountain Horticultural Crops Research Station near Asheville.

Mike Parker, a tree fruit extension specialist at North Carolina State University, said scientists monitor survival rates, trunk growth, fruit size and yields over many years before recommending new rootstocks to commercial growers.“When we put the replicated trials in multiple states, there’s things that we find out real quick, like that this rootstock is a dog and ain’t going to fly,” Parker said.

“We would much rather kill trees at our research station than have growers lose trees on their farm.”Parker has overseen the university’s rootstock evaluations since 1996 and, like Robinson, is approaching retirement.

Robinson said he is concerned that long-term agricultural breeding programs may struggle to attract younger researchers, many of whom prefer working on commercially visible fruit varieties rather than root systems that can take decades to develop.

He also expressed concern that funding agencies could eventually scale back support for long-duration breeding programs if policymakers conclude that existing rootstocks are sufficient for current industry needs.“I fear that they’ll say: ‘We have enough rootstocks, let’s just close down this effort,’” Robinson said.

“And for things that we’re facing right now, we probably have a good series of rootstocks available. But it’s these emerging problems, that you don’t really think of or didn’t plan for, that you might not be able to respond to if they shut down the program.”