Development of a high quality reference genome sequence for loblolly pine, Douglas-fir and sugar pine by means that can serve as a model approach for sequencing other large, complex genomes and empower the forest tree biology research community and the broader biological research community in the practical use and application of this resource.
Current Focus: Annotation of the loblolly pine genome (v1.01) and generation of a reference transcriptome for Pinus lambertiana (sugar pine)
NGS technologies are being employed to accelerate the development and use of genetic information to improve firs for use as Christmas trees, an important specialty crop. The initial focus will be on improving postharvest needle retention. A two-step process will be used to identify single nucleotide polymorphic markers (SNPs) with predictive power: 1) candidate genes will be identified via RNA sequencing and 2) SNPs in candidate genes will be screened for association with phenotypes by targeted sequencing of genomic DNA. Additional traits of interest addressed are resistance to Phytophthora root rot and adaptability of two promising exotic species that will be evaluated across fir production regions in a related ongoing collaborative project.
Current Focus: RNA-Seq analysis of Abies fraseri (Fraser fir)
Whitebark pine is warranted for listing under the Endangered Species Act due to widespread impact of blister rust and other causes. Low frequency genetic resistance to blister rust exists within naturally occurring populations. Marker-assisted tree breeding can allow tree breeders to circumvent the use of common gardens and screen parent trees for phenotypes such as pathogen resistance based on tree DNA alone. Screening for rust-resistance markers with a SNP assay can expedite and economize the process of screening trees for restoration or breeding efforts.
Current Focus: RNA-Seq and expression analysis to identify candidate genes of resistant and suseptible Pinus albicaulis (whitebark pine) individuals
Evaluation of Montane Forest Genetic Resources: Implications for Conservation, Management, and Restoration of whitebark pine in the Lake Tahoe Basin
Determine adaptive genetic variation in whitebark pine for ecologically important plant traits (disease resistance, water-use efficiency, drought adaptation, phenology, and growth) across the Lake Tahoe Basin. DNA will be isolated from needle samples from 240 trees in over 8 populations of whitebark pine. RAD-Seq will be used to identify polymorphisms genome-wide and perform association with ecologically important adaptive traits.
Current Focus: Develop RAD-Seq protocol for Pinus albaicaulis (whitebark pine) trees
The Dendrome project provides custom informatics tools and databases to manage the multitude of information resulting from high-throughput genomics projects in forest trees from sample collection to downstream analysis. This resource is further enhanced with systems that are well connected with federated databases, automated data flows, machine learning analysis, standardized annotations and quality control processes. The supporting TreeGenes database contains several curated modules that support the storage of data and provide the foundation for web-based searches and visualization tools. Annotated transcriptomic studies resulting from next-generation sequencing are now available for several forest tree species which includes visualization of the assemblies in GMOD’s GBrowse interface. DiversiTree, a user-friendly desktop-style interface, queries the TreeGenes database and is designed for bulk retrieval of resequencing data. It provides the community with access to data types describing individual tree samples including ESTs, primer sequences, SNPs, genotypes and phenotypes. The variety of outputs available allows users to perform high-resolution dissection of traits and relate molecular diversity to functional variation. Recent development has focused on web services to connect geo-referenced individuals with important ecological and trait databases in the form of a new utility known as CartograTree. The combined resources of the Dendrome project serve as a powerful knowledge environment for genotype-phenotype information resulting from a multitude of large-scale genomics projects.