Project Number: 5350-22000-017-03
Project Type: Trust

Start Date: Apr 01, 2007
End Date: Mar 31, 2009

Objective:
Develop DNA microarrays containing a comprehensive collection of DNA sequences from fungi found in orchard soil and apple roots in central Washington and evaluate the capacity of the DNA microarray to measure community structure and function for predictive purposes.

Approach:
As a more easily accessible and cost-effective technology relative to slide-based DNA arrays, we will utilize nylon membranes as the printing medium with a colormetric labeling and detection system. To avoid the time and costs needed to design and validate oligonucleotide probes, we will employ the entire internal transcribed spacer (ITS) region (ITS1/5.8S/ITS2) of the fungal ribosomal DNA as both the target and the probe. The fungal ITS regions are well known to be particularly useful for species-level distinctions in fungi . While the 5.8s region is generally conserved, the ITS1 and ITS2 regions are quite variable and collectively should allow maximal potential for distinguishing fungal taxa. The first goal of the proposed study is to compile a comprehensive libray of DNA sequences representing the population of different fungal species resident to orchard soils. From preliminary work it is evident that a high diversity of fungal species (>100) exists in any given orchard, and that detection of such a complex population will require equally diverse sampling strategies. First, we will pair traditional culture-based techniques with molecular-based approaches, accounting for the fact that many of the more prominent fungi are incapable of being cultured. Second, we will stratify the sampling to include a number of environments that we expect to harbor unique fungi with the major distinction being between the soil and root communities. Third, sampling will be spread out spatially to account for differences we would expect both within and across multiple orchards. Documents Trust Agreement with WTFRC. Log 32710. Formerly 5350-22000-012-10T 12/2007.