Stephen Ficklin, a computational biologist and assistant professor in the Washington State University Department of Horticulture, has spoken out about a project that 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. 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.
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.