Feb 14, 2019

Genome data means improved crops for vast rose family

Encompassing not only hundreds of rose varieties, but thousands of species of useful, beautiful and edible plants including apples, almonds, cherries, pears, raspberries and strawberries, the rose family of plants, Rosaceae, is vast and valuable, adding more than $15 billion annually to the U.S. economy.

For 15 years, scientists at Washington State University have improved our knowledge of this plant family through a national research effort called the Genome Database for Rosaceae (GDR).

With GDR, scientists can access and explore Rosaceae plants’ genetics, genomics and breeding data through a suite of integrated data mining tools, speeding up research into better crops and stronger, healthier plants.

Sook Jung and Dorrie Main, scientists in the Department of Horticulture, and 13 other WSU horticulture scientists, detailed the evolution and future direction of GDR in the January 2019 issue of Nucleic Acids Research.

“Crop research is increasingly driven by big data,” says Jung, “data that must be organized, analyzed, curated and integrated in a database to allow scientists to use and access it for both basic and applied research.”

With its full slate of Web resources, and database and analysis tools that use high‑performance computers including WSU’s Kamiak computer cluster, GDR provides that, said Main.

The volume of data in GDR has vastly increased over the past few years, and today, the database includes whole genomes and data from dozens of economically important species, made available by new advances in sequencing technology.

This wealth of data brings new opportunities to:

• Understand the wide range of plants in Rosaceae
• Share knowledge
• Improve crop performance, helping growers, the agricultural economy and environment, and human nutrition

“Thanks to resources like GDR, integrated data is driving research that reduces the gap between discovery and application,” Jung said. “That leads to development of new, more sustainable cultivars with higher nutritional and commercial quality, and enhanced resistance to disease and environmental stress.”

WSU co‑authors include Taein Lee, Chun‑Huai Cheng, Katheryn Buble, Ping Zheng, Jing Yu, Jodi Humann, Stephen Ficklin, Lisa DeVetter, James McFerson, Kristin Scott, Morgan Frank, Heidi Hough, and Kate Evans.

National collaborators on the paper, titled “15 years of GDR: New data and functionality in the Genome Database for Rosaceae,” include colleagues at Clemson University, the University of Minnesota, the University of Florida, the University of Connecticut, the University of Tennessee, the University of Kentucky, and the Cedar Lake Research Group.

– Seth Truscott, Washington State University