Planting the trees, getting them to produce healthy fruit and then successfully harvesting from the orchard takes a lot of work for those in the apple industry – so optimizing management to limit post-harvest apple rots while in storage makes sense.

That was the focus of a discussion led by Kari Peter, Ph.D., of Penn State Extension at the most recent Great Lakes Expo. (The research she shared was contributed to by Johanny Castro, Ph.D. student in plant pathology at Penn State.)

Their research used data from eight packinghouses in Pennsylvania and two in Maryland. A total of 975 apples showed evidence of rot over two seasons (after being in storage for at least six months).

The post-harvest rots found in these Mid-Atlantic packinghouses were about 41% brown rot; 33% black rot; 14% blue mold; 6% non-pathogen associated rots; 4% bitter rot; and 1% extensive brown rot.

Peter reported the fungi causing these issues were Alternaria rot (29.6%); Phlyctema vagabunda, aka bull’s eye rot (27.6%); blue mold (14.6%); gray mold (7.1%); Diaporthe rot (3.9%); and bitter rot (3.5%). Various other fungi contributed another 7.4% of the post-harvest apple decay, and non-pathogenic causes made up the remaining 6.9%.

In this study, Alternaria showed higher incidences than average. It infects fruit both in the field and post-harvest. It is ubiquitous, meaning it can infect multiple crops and colonize multiple environments. It also produces mycotoxins (alternariol and tenuazonic acid).

Alternaria has a low sensitivity to fungicides from multiple FRAC groups, Peter said. And worryingly, research from 2024 also found it can be a wood pathogen, causing apple cankers.

The biggest group of post-harvest rots were the brown rots, which include bull’s eye rot, gray mold and Diaporthe rot. Brown rots were prevalent in all eight of the packinghouses looked at. And the incidence of them in four of the packinghouses was above average levels (40%).

“Brown rots infect fruit mostly pre-harvest – so field spray programs and cultural practices are critical,” Peter said.

Bull’s eye rot and Diaporthe rot are also known for causing cankers. Peter urged growers to get rid of dead wood in the orchard to help eliminate spore sources.

Mainly a post-harvest problem, blue mold fungi need an opening, like a wound, to cause disease. They produce mycotoxins such as patulin, which is carefully regulated in processed apple products.

Peter noted packinghouse facilities, dump tank water and cold rooms are the main sources of blue mold in apples, so sanitation is very important. It is a very aggressive pathogen, and it will take advantage of other rots.

Post-Harvest Fungicides

It’s not all doom and gloom after the apples are plucked from the trees. Peter believes post-harvest control is possible against blue mold and Alternaria.

She and Castro tested two fungicides, fludioxonil (Scholar®) and pyrimethanil (Penbotec™), for post-harvest control of rots. Peter reported fludioxonil was the only fungicide with good efficacy against Alternaria.

Fludioxonil and pyrimethanil are still effective against blue mold – “but blue mold sensitivity to them is decreasing, and you need to be aware of that,” Peter said.

An advanced case of blue mold in an apple. Photo courtesy of Gerald Holmes, Strawberry Center, Cal Poly San Luis Obispo, Bugwood.org

For a little doom: Neither of the two fungicides were effective in fighting bull’s eye rot. In testing, they found fludioxonil had zero response against it, even at four times the label rate.

The take home lesson from that test? “Rotate your fungicides,” Peter stated.

Other key points to remember in post-harvest management to try to avoid rots:

  • Sanitation, sanitation, sanitation, both in the field and in storage
  • Don’t stretch spray intervals – time your fungicide sprays properly during the season and especially before harvest
  • Practice fungicide resistance management by rotating FRAC groups (which is especially important for post-harvest fungicides)
  • Remember that orchard health is key for preventing susceptibility to wood pathogens