Douglas-fir Transcriptome Observatory
The basis of climatic adaptation in Douglas-fir (Pseudotsuga menziesii) - possibly the most ecologically and economically important forest species in coastal western North America - is poorly understood, and this limits our ability to predict population changes to climate and offer science-based prescriptions for management. The Transcriptome Observatory merges a large-scale translocation study with expressed gene (transcriptome) sequencing to define seasonal leaf transcriptomes and identify expressed genes showing significant differences between geographic region. Our goal is to identify genes that contribute to climatic sensing and adaptation in this conifer.
Mitochondrial DNA sequences are the most commonly-used molecule for characterizing animal biodiversity. Our group has adapted Multiplexed Sequencing-by-Synthesis (see Cronn et al., 2008 () to enable high-throughput genetic analysis of complete animal mitochondrial genomes. This work is being conducted with Michael Schwartz at the USFS Wildlife Genetics Laboratory (), with primary focus on Fisher (Martes pennanti) and other regionally rare carnivores.
Development of DNA tools to aid genetic conservation and restoration in Port-Orford-cedar
Port-Orford-cedar (Chamaecyparis lawsoniana) is a conifer native to coastal Oregon and northern California which is of horticultural importance. This project is in the process of developing molecular markers for this taxon to determine whether genetic variation in resistant Port-Orford-cedar breeding populations is similar in kind and amount to trees in unmanaged natural populations. This marker system will then also be used to identify geographic regions harboring Port-Orford-cedar that possess novel genetic variation and consider expanding resistance testing of those populations or expanded seed collections for ex situ genetic conservation as well as characterize the baseline genetic data for Port-Orford-cedar to be used for future management consideration relating to climate change and genetic conservation efforts.
Antelope Bitterbrush Landscape Genetics
Antelope bitterbrush (Purshia tridentata) is an important forage and cover shrub in the inter-mountain region of western North America.
Development of Microsatellites using Sequencing-By-Synthesis Technology
Development of microsatellites (simple-sequence repeats) has historically been a time consuming and expensive task. We developed an approach to isolate and sequence microsatellites by combining traditional hybridization/enrichment with multiplexed massively parallel sequencing-by-synthesis technology. The approach is rapid and inexpensive, and the resulting library of microreads contains tens of thousands of microsatellite-containing sequences.