Take a giant trash bag full of shredded documents and reassemble them in their original state. The bag contains millions of two-inch segments. Ready? Go!
That’s how Stephen Ficklin, a computational biologist and assistant professor in the Department of Horticulture at Washington State University, describes a project that he, postdoctoral researcher Huiting Zhang, and their class of undergraduate students and graduate studies undertake.
“We are assembling the complete genome of the WA 38 apple which is marketed under the popular variety name Cosmic Crisp™,” Ficklin said.
Sequencing a genome results in hundreds of thousands, if not millions, of DNA fragments, each 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 of these readings must be put together in their order. This is done through pattern matching, aided by sophisticated software packages and high computing power. Ficklin has access to WSU’s high-performance computing cluster, and he and his students use 160 processors to analyze 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 Laboratory 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, could be useful in predicting the risk of postharvest defects that affect the economic value of an apple crop. Even a small improvement in packaging (fruit that reaches the market after being handled and stored) can mean a significant improvement in profitability.
But the development of markers requires very high quality target data and therefore the importance of producing a very precise 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 such a wound that when removed from cold storage, they quickly develop unsightly blemishes. Depending on the severity of the defect, apples may be diverted from the fresh fruit market to less profitable ones, such as fruit juice.
But there are many other potential cold injuries and other defects that could be detected through genetic marker testing that would save packaging companies time, effort and money for store fruit that will be thrown into the slaughter pile. In any event. Soft scald, bitter pit, lentil spot, internal breakdown and browning are just a few of the defects that Honaas, Ficklin and their colleagues hope can help growers predict sooner rather than later during storage.
This work doesn’t just help growers and packers make money. For horticultural researchers, the apple can be a model for understanding how things can go wrong in storage and at other points in the supply chain. Once scientists have grasped the genetic underpinnings of these injuries and defects in one culture, they can search for similar or identical genetic markers in other cultures. And the end result for consumers is a tastier, more consistent food experience.
A pretty cool project on its own, students in the class will also end up with their names on a science publication. Ficklin says he plans to submit for publication in the spring, and every student in the class, along with other collaborators, will be listed as co-authors.
Brendan Hoffmann, undergraduate, was interested in viticulture, but became interested in molecular biology along the way. “I was interested in this course because I wanted to learn the computational process, that is, how to take a large amount of genomic data and make sense of it. It’s also exciting to work with the Cosmic Crisp genome – it’s not every day that a new apple variety comes out!”
PhD student Kara Ryan, who grew up in New York, says she was interested in this project because “the data we’re working with in this class is cutting-edge and of high quality. It is a unique opportunity to have access to such a large amount of data before it is published. Ryan adds that being able to “help create a public resource that opens up new avenues of research related to apples” was exciting, especially as the project will help understand the evolutionary history of apples, how genomes vary over within and between species. , and be used, by Honaas and others, to identify traits of interest.
Undergraduate Kenny Pierro says growing up in cities might be one reason his interest in agriculture and plant science blossomed when he moved to Pullman to attend WSU . “I changed my major from accounting to agricultural biotechnology due to a fascination with plants and their chemical effect on the body. My interests have evolved and become more complicated, focusing on plant genetics. This course showed me what it takes to produce a quality genome assembly.
And, of course, having your name on a scientific paper is, for both Pierro and his comrades, “exciting and alluring.”