The Plant Genetics and Silviculture Team studies the genetic structure and basis of adaptation in plants distributed across forested lands in the Pacific Northwest region of the U.S. (Alaska, Oregon and Washington). Our molecular lab uses genotyping and genomics approaches to map the distribution of geographic genetic variation as part of our continuing effort to identify genetic and gene expression responses to weather and climate, both of which play an important role in local adaptation.
- July-2012: Transcriptome analysis for the development of SNP markers in sagebrush, an important restoration shrub. http://www.biomedcentral.com/1471-2164/12/370
- June-2011: Detailed examples of how to sequence and identify thousands of microsatellites on the Illumina Genome Analyzer. http://onlinelibrary.wiley.com/doi/10.1111/j.1755-0998.2011.03033.x/abstract
- May-2011: What can you get with only 0.5X genome coverage of a milkweed genome? A LOT! See http://www.biomedcentral.com/1471-2164/12/211
- May-2011: The plant lab steps into the unknown - Fisher mitogenomes! http://www.biomedcentral.com/1472-6785/11/10/
- Mar-2011: Taxon-specific microsatellite enrichment, sequencing and detection on a short read sequencer? Yes! Information can be found at http://openwetware.org/wiki/Conifermicrosat
- Aug-2010: "An introduction to next-generation sequencing". This all-day workshop was held at the 2010 Botany Meeting. Information can be found in the Short_read_toolbox" archive at http://openwetware.org/wiki/Short_read_toolbox
- Feb-2010: More genomes! Whittall et al., "Finding a (pine) needle in a haystack: chloroplast genome sequence divergence in rare and widespread pines." Mol Ecol 2010 Feb; 19(s1): 100-114.
- Feb-2010: The Western Transcriptome "RNASeq-apalooza I" RNA prep party was a success. Groups from USFS Pacific Southwest Station, Pacific Northwest Station, and UC-Berkeley prepared RNA-Seq libraries for Sugar Pine, Tan Oak and Douglas-fir. The effort yielded 4.5 Gbp of data!
- Dec-2009: 37 genomes! Parks et al., "Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes." BMC Biol 2009; 7 84. See commentary, "Christmas Tree asks 'Who's my Daddy?", http://www.youtube.com/watch?v=TG70_WMYfdY
USDA Forest Service
Pacific Northwest Research Station
3200 SW Jefferson Way
Corvallis, OR 97331