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Horticulture students assemble Cosmic Crisp™ apple genome

Closeup of a Cosmic Crisp apple.
The WA 38 apple, better known as Cosmic Crisp™.

Take a giant trash bag stuffed with shredded documents and reassemble them into their original state. The bag contains millions of two-inch segments. Ready? Go!

That is how Stephen Ficklin, a computational biologist and assistant professor in the Washington State University Department of Horticulture, describes a project he, post-doctoral researcher Huiting Zhang, and their class of undergraduate and graduate students are undertaking.

“We are assembling the complete genome of the WA 38 apple which is marketed as the popular variety Cosmic Crisp™,” Ficklin said.

Sequencing a genome results in hundreds of thousands or even millions of DNA fragments, each one called a “read,” Ficklin explains. To make sense of a genome in a way that can be used to understand the inner workings of an organism, all those reads have to be assembled in their proper order. This is done by pattern matching aided by sophisticated software packages and lots of computing horsepower. Ficklin has access to WSU’s high performance computing cluster and he and his students are using 160 CPUs to crunch the sequence data and assemble the Cosmic Crisp™ genome.

The assembled apple genome will be used to inform work being done by USDA ARS Tree Fruit Research Lab research scientist and Ficklin collaborator, Loren Honaas. Honaas and his collaborators will develop techniques to detect specific genetic markers. The markers, Honaas explained in a guest lecture to Ficklin’s class, might be useful to predict the risk of post-harvest defects that affect the economic value of an apple crop. Even a tiny improvement in pack-out — fruit that goes to market after handling and storage — can mean a serious upgrade in profitability. 

But developing markers requires very high-quality target data and thus the importance of producing a very accurate assembly of the Cosmic Crisp™ genome.

A test developed by Dave Rudell (also at the ARS Tree Fruit Research Lab) and already in use by a commercial packer in Washington State is for the detection of superficial scald. Some apples, when placed in cold storage, develop an injury such that when pulled from cold storage they quickly develop unsightly blemishes. Depending on the severity of the defect, the apples may be diverted from the fresh fruit market into other less profitable ones, like fruit juice.

But there are lots of other potential chilling injuries and other defects that could be detected by means of tests for genetic markers that would save packing houses the time, effort, and money of storing fruit that is just going to be dumped into the cull pile eventually anyway. Soft scald, bitter pit, lenticel blotch, internal breakdown and browning are just some of the defects Honaas, Ficklin and their colleagues hope to be able to help growers predict earlier rather than later during storage.

This work doesn’t just help growers and packers make money. For horticultural researchers, apple can be a model to understand how things can go wrong in storage and at other points in the supply chain. Once scientists grasp the genetic underpinnings of these injuries and defects in one crop, they can look for similar or the same genetic markers in other crops. And the end result for consumers is a tastier and more consistent eating experience.

A cool enough project on its own, the students in the class will also end up with their names on a scientific publication. Ficklin says he plans to submit for publication in the spring, and every student in the class, plus other collaborators, will be listed as co-authors.

Undergraduate Brendan Hoffmann was interested in viticulture, but got interested in molecular biology along the way. “I was interested in this course because I wanted to learn the computational process — how to take a large amount of genomic data and make sense of it. It’s also exciting to be working with the Cosmic Crisp™ genome — it’s not every day a new apple variety comes out!”

Doctoral student Kara Ryan, who grew up in New York City, says she was interested in this project because “the data we get to work with in this class is cutting edge and high quality. It’s a unique opportunity to have access to such a large amount of data prior to it being published.” Ryan adds that being able to “be a part of generating a public resource that opens up new avenues of research related to apples” was exciting, especially since the project will result in understanding the evolutionary history of apples, how genomes vary within and between species, and be used, by Honaas and others, to identify traits of interest.

Undergraduate Kenny Pierro says that the fact that he grew up in cities might be one reason his interest in agriculture and plant science flourished when he moved to Pullman to attend WSU. “I changed my major from accounting to agricultural biotechnology because of a fascination with plants and their chemical effect on the body. My interests evolved and became more complicated, focusing on the genetics of plants. This class showed me what it takes to produce a quality genome assembly.” 

And, of course, having his name on a scientific paper is, for both Pierro and his fellow students, “exciting and enticing.”

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