Largest Affymetrix Genechip Plant Microarray Experiment

Affymetrix Genechip

The Virginia Bioinformatics Institute has completed the largest ever Affymetrix GeneChip microarray study for a plant experimental system in an academic research setting.

The 2600-chip experiment explores the counter-play of plant and pathogen genes during infection of soybean with the root-rot pathogen Phytophthora sojae, with a focus on mechanisms of long-lasting disease resistance. P. sojae causes severe damage in soybean crops and results in $100-200 million annually in losses for commercial farmers in the United States alone.

Much information has been obtained by careful study of single resistance genes in plants. However, this "low hanging fruit" approach has not resulted in significant long-lasting resistance of crops. Plants in which a single gene has been modified are quickly overcome by new strains of pathogens. The GeneChip experiment is part of a project aimed at understanding and improving a more long-lasting form of disease resistance called quantitative or multigenic resistance.

Adam Jerauld, Affymetrix Team Leader in the Core Laboratory Facility (CLF) remarked: "Our facility was able to successfully complete the data generation stage for this 2600-chip experiment within a six-month period. This was possible due to a highly effective collaboration between the research scientists and the ability of our team to scale-up our array processing capabilities. We also received first-rate technical support from Affymetrix."

Clive Evans, CLF Manager at VBI, commented: "The Affymetrix GeneChip microarrays used in the study comprise probes for 38 000 soybean genes and 15 800 P.sojae genes. We increased the productivity of our Affymetrix processing four-fold to accommodate the scale of this project."

"VBI is a National Customer Array Center with world class scientists working in the plant and biomedical sciences. It is an ideal place to conduct the largest Affymetrix agriculture microarray experiment to date by a not-for- profit facility," said Fredrick Pollock, Director of Strategic Business at Affymetrix. "We worked with the soybean research community to develop the content for the Soybean Genome Array. Affymetrix currently produces 17 arrays as part of its GeneChip Consortia Program and we are excited about working with the leading agricultural researchers on further projects designed to improve crop yields and the nutritional value of the food we eat."

The Affymetrix microarray experiment combines two approaches, transcriptional profiling and quantitative trait locus (QTL) mapping. These approaches are well suited for dissecting complex biological processes that involve the interactions of many genes. The information obtained from this study will be valuable for understanding how legumes may be protected from a wide variety of pathogens, and how many hosts may be protected against oomycete pathogens. Project team leader and VBI Professor Brett Tyler said: "With the massive data set from the CLF now in hand, the data-analysis phase of the project will begin and is expected to take 18 months."

VBI's CLF is a multi-user resource providing various high-throughput technologies and other state-of-the-art technology-related services. The CLF currently provides analysis platforms for DNA sequencing and genotyping, gene expression analysis, and proteomics.

The project is supported by cooperative agreement DBI-0211863 from the National Science Foundation Plant Genome Research Program. The project is a multidisciplinary collaboration involving Saghai Maroof (Department of Crop and Soil Environmental Sciences, Virginia Tech), Ina Hoeschele (VBI), Anne Dorrance (Ohio State University) and Steve St. Martin (Ohio State University).

The Virginia Bioinformatics Institute (VBI) at Virginia Tech has a research platform centered on understanding the "disease triangle" of host- pathogen-environment interactions in plants, humans and other animals. By successfully channeling innovation into transdisciplinary approaches that combine information technology and biology, researchers at VBI are addressing some of today's key challenges in the biomedical, environmental and plant sciences.