Dr. Awais Khan illustrates some of the genetic diversity in the Cornell apple germplasm collection. (Provided photo — Cornelll CALS School of Integrated Plant Science)

Apples are the most-consumed fruit in the United States. The annual estimated total value of the American apple industry is $23 billion, with just five cultivars — Fuji, Gala, Granny Smith, Honeycrisp and Red Delicious — making up two-thirds of production. Of these, Honeycrisp is easily the most valuable, having nearly twice the value per pound, if not more, than any of the others.

A few of weeks ago, I was sharing a couple of Honeycrisp apples with a friend and his granddaughter. As the youngster devoured a slice of apple … and then ate another … and another … and another … enjoying the juicy sweetness of each crunchy bite, she asked, “Where do apples come from?”

I wanted to say, “Cornell University.” And I wouldn’t have been lying. After all, Cornell’s apple breeding program is the oldest of its kind in the United States and one of the largest in the world. But Cornell’s apple breeding program is just one of the three biggest university-based apple breeding programs in America. The other two are at the University of Minnesota and Washington State University.

Essentially, they are where new apples come from. Breeders at all three colleges are endlessly experimenting. They relentlessly cross different varieties of apples hoping to produce superior-quality fruit; apples that will enhance production for orchardists and/or compete in global markets by meeting or exceeding the demands of apple-buying consumers.

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Where do Honeycrisp apples come from?

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Although more than 70 varieties of apples have been developed and brought to market by Cornell University apple breeders (e.g. Cortland, Empire, Jonagold, Macoun), Honeycrisp apples were developed at the University of Minnesota (UMN). It’s interesting to note that the UMN apple research program came about because, as New York Tribune Editor Horace Greeley wrote about Minnesota in 1860, “one cannot grow apples there.”

It’s interesting to note too, that Honeycrisp apples were developed in 1974, but weren’t released to the public until 1991. Although it was (and still is) widely believed that the Honeycrisp apple is a cross between Honeygold and Macoun, in 2004, a group of scientists used DNA to prove that the parentages of the Honeycrisp were Keepsake and an unreleased variety known as MN 1627; both of which were also developed at UMN.

Breeding an all-around

high-quality apple

As the name implies, Honeycrisp apples are both intriguingly sweet and explosively crunchy. Their consistent crispness, however, is not a characteristic of freshness. It’s the result of breeding.

Honeycrisp apples are loaded with sugar. Brix is the term used for measuring sweetness in an apple. And the Honeycrisp has a 12.6 Brix level, meaning that sugar makes up 12.6% of the juice in a Honeycrisp apple.

But they also retain a somewhat delicate acidity, which manages to balance and, to some extent, offset their sweetness. On top of which, they’re good keepers. When properly stored, they maintain their crisp texture and tantalizing sweetness for several months. They also maintain their sweetness throughout the cooking process.

What’s more, the Honeycrisp cultivar has shown notable cold-hardiness and resistance to apple scab, the most economically significant fungal disease of apples worldwide. Unfortunately though, the Honeycrisp cultivar is prone to bitter pit; a physiological disorder characterized by the development of dark, sunken lesions on the fruit, particularly towards the calyx-end. Bitter pit occurs in all apple varieties, but disproportionately affects Honeycrisps.

Identifying the genetic basis of bitter pit is crucial for mitigation of the disorder and the eventual development of bitter pit-free apple cultivars.

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Cornell researchers have sequenced the Honeycrisp apple genome

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“If we don’t know the genome and the genes in Honeycrisp, then we cannot specifically target and select for favorable traits and select out unfavorable traits through breeding,” says Awais Khan, an associate professor in the School of Integrative Plant Science at Cornell AgriTech, formerly the New York state Agricultural Experiment Station in Geneva. Professor Khan is the first and co-corresponding author of the paper, “A Phased, Chromosome-scale Genome of Honeycrisp Apple,” published in September, in the peer-reviewed journal, Gigabyte.

A genome, as defined by the National Institutes of Health (NIH) National Human Genome Research Institute, is “the entire set of DNA instructions found in a cell.” Each genome contains all of the information needed to build that organism and allow it to grow and develop.

The Golden Delicious apple genome was the first to be sequenced. That was in 2010. Since then, several advances in genetic-sequencing technology have taken place, making it possible for researchers to sequence, assemble, and now publish the Honeycrisp apple genome in a comparatively short time. And by using those advanced methods, researchers were able to cover 97% of all the protein-coding genes in the Honeycrisp genome. By comparison, the 2010 Golden Delicious genome assembly only covered 68% of the genes.

In a recent post, Dr. Khan stated,

“We have made genome assembly of Honeycrisp apples and all associated sequence and metadata publicly available to download and use!” Funding for the research came from the New York state Department of Agriculture and Markets through the state Apple Research and Development Program, the Washington Tree Fruit Research Commission, and the U.S. Department of Agriculture’s Agricultural Research Service.