Take a giant garbage bag full of shredded documents and put them back together. The bag contains millions of two-inch units. ready? go over!
Stephen Ficklin, a computational biologist and assistant professor in Washington State University’s Department of Horticulture, describes the project he, postdoctoral researcher Huting Zhang, and their undergraduate and graduate students are conducting.
“We are collecting the complete genome of the WA 38 apple that is marketed as the popular variety Cosmic Crisp™,” Ficklin said.
Sequencing a genome yields hundreds of thousands or even millions of pieces of DNA; Each one “reads,” Ficklin explained. To make sense of the genome, to understand the inner workings of an organism, all the reads must be assembled in the correct order. This is done through pattern matching with the help of sophisticated software packages and lots of computer 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 collected apple genome will be used to inform work being done by Lauren Honas, a research scientist at the USDA ARS Tree Fruit Research Lab and a Ficklin collaborator. Honas and his collaborators develop techniques to identify specific genetic markers. The markers, Honaas explained in a guest lecture for Ficklin’s class, can be useful in predicting the risk of postharvest defects that affect the economic value of the apple crop. Even a small improvement in packaging – the fruit that goes to market after it is picked and stored – can mean a huge improvement in profitability.
However, developing markers requires very high-quality target data and therefore a very accurate assembly of the Cosmic Crisp™ genome is essential.
A test developed by Dave Rudel (also at the ARS Tree Fruit Research Lab) and used by marketers in Washington State to detect surface heat burn. When some apples are stored in cold storage, they are damaged by blemishes that are not readily apparent when pulled from cold storage. Depending on the severity of the defect, apples may be diverted from the fresh fruit market to other less profitable ones such as fruit juice.
But there are many other cold injuries and other defects that can be detected by genetic marker tests, which can save packing houses time, effort and money, and store fruit that ends up in the garbage heap. Anyway. Soft burn, bitter pit, lentil pitting, internal spoilage and browning are some of the defects Honas, Ficklin and colleagues hope to help predict earlier, not later in storage.
This work not only helps growers and processors earn money. For horticulturists, apples can be a model for understanding how things go wrong in storage and at other points in the supply chain. When scientists understand the genetic inheritance of these injuries and defects in one crop, they can look for the same or similar genetic markers in other crops. And the end result for consumers is a tastier and more consistent eating experience.
A good enough project on its own, students in the class end up with their names on their scientific publications. Ficklin said he plans to submit it for publication in the spring, and each student in the class, as well as other collaborators, will be listed as co-authors.
Undergraduate Brendan Hoffman was interested in viticulture, but along the way he became interested in molecular biology. “I was interested in this course because I wanted to learn the computational process – how to take large amounts of genomic data and make sense of it. Working with the Cosmic Crisp™ genome is also fun – a new apple variety doesn’t come out every day!”
Kara Ryan, a doctoral student who grew up in New York City, said she was interested in this project because “the data we get to work with in this department is high quality and qualitative. It is a unique opportunity to have access to this amount of information before publication. Ryan added: “It was exciting to be able to be a part of creating a public resource that opens up new avenues of apple-related research, particularly as the project allows us to understand the evolutionary history of the apple, how genomes vary within and between animals, and to identify traits of interest, used by Honas and others.”
When undergraduate Kenny Pierro moved to Pullman to attend WSU, he said growing up in the cities may have contributed to his blossoming interest in agriculture and plant science. “Due to my fascination with plants and their chemical effects on the body, I changed my major from accounting to agricultural biotechnology. My interests evolved and became more complex, focusing on plant genetics. This class showed me what it takes to make a quality genome assembly.
And of course getting his name on a scientific paper is “exciting and exciting” for Piero and the other students.