Goal is to obtain genome sequences for pesky powdery mildews
By Karyn Houston
Plant & Microbial Biology
Two UC Berkeley scientists will lead a team of international researchers to obtain genome sequences for 11 powdery mildew fungi, a key step forward in managing a pesky pathogen that causes billions of dollars in agricultural losses each year, if untreated.
PMB Associate Professor Mary Wildermuth and PMB Professor Shauna Somerville will do the genome sequencing work with resources from the U.S. Department of Energy Joint Genome Institute.
Powdery mildew affects a number of crops, and wreaks significant havoc on the grape industry. The mildew also negatively affects bioenergy crops, including eucalyptus and camelina.
Wildermuth and Somerville are hoping their work will ultimately reduce the amount of pesticides being used to control powdery mildew now. At the present time, pesticides are the only way farmers can control the mildew in many crops.
"Using varieties that have been bred for powdery mildew disease resistance is the control strategy most widely used in barley and some other crops," Somerville said. "Information we will gain from the genome sequences about the "tool kit" used by powdery mildews to cause disease will also aid in the development of disease resistant crop varieties, which is turn will reduce pesticide use."
Obtaining the genome sequence - a laboratory process that determines the complete DNA sequence of an organism's genome at a single time -- will enable researchers to better understand ways to combat powdery mildew.
A major benefit will be to develop new strategies for limiting powdery mildews, thereby reducing extensive chemical treatments, Wildermuth said, since use of fungicides is the most popular way to get rid of the mildew in most crop species.
Powdery mildew genomes of ~150 MB in size have challenged researchers trying to get complete genomes due to the unusual percent of their genome, as high as 90%, that is comprised of repeat elements. Currently, complete genomes exist only for Blumeria graminis that colonize cereals, like barley and wheat.
Wildermuth, Somerville, and collaborators will utilize the expertise and resources of the DOE-JGI and its Fungal Genomes Program to study the comparative genomics of powdery mildews and associated plants through a recently selected Community Science Program proposal. This includes sequencing of powdery mildew genomes that infect eucalyptus, camelina, grape, tomato, lettuce, cucumber, hops, strawberry, and pepper.
Further efforts will investigate fungal and plant gene expression in tandem at three infection phases:
• Germination of the powdery mildew spore
• Formation of the fungal feeding structure in the host plant
• Fungal surface growth and reproduction to form new spores.
Powdery mildews are “obligate biotrophs”, meaning that they can only grow and be cultivated on living plant tissue. These stealth pathogens manipulate the plant to provide resources while minimizing their detection and activation of plant defenses.
By comparing powdery mildew genomes adapted to different plants, the group can identify minimal gene sets required for obligate biotrophy. These minimal gene sets include those required to breakdown cell walls and redirect carbon metabolism – two items of great interest to the Department of Energy. Researchers can also figure out what determines the specific plants that a powdery mildew can colonize. For example, powdery mildews that infect pepper do not infect grapes.
The 11 powdery mildew fungi that will be studied in this project are phylogenetically diverse and adapted to very different host plants.
All of the data obtained from this research will be publicly available and searchable at the DOE JGI MycoCosm website: http://jgi.doe.gov/fungi.
Powdery mildew project collaborators include: Yai Bai (Wageningen UR, Nederlands), Uwe Braun (Martin-Luther-Universitat, Halle, Germany), Rachel Brem (Buck Institute for Research on Aging, Novato, CA), Lance Cadle-Davison (USDA-ARS, Geneva, NY), Ian Dry (CSIRO, Urrbrae, Australia), David Gent (USDA-ARS, Corvallis, OR), Ralph Huckelhoven (Technische Universitat Munchen, Germany), Levente Kiss (Plant Protection Institute, Budapest, Hungary), James McCreight (USDA-ARS, Salinas, CA), Alejandro Perez Garcia (University of Malaga, Spain), and Susumu Takamatsu (Mie University, Tsu, Japan).