USDA Forest Service

Pacific Southwest Research Station

Pacific Southwest
Research Station

800 Buchanan Street
Albany, CA 94710-0011
(510) 883-8830
United States Department of Agriculture Forest Service. USDA logo which links to the department's national site. Forest Service logo which links to the agency's national site.

Poplar Molecular Genetics and Genomics

Poplars occupy unique environmental niches, colonize sites after disturbance, and provide habitat and food for a variety of wildlife. Poplars are also used as windbreaks, for stream bank stabilization, in remediation efforts, as a "biofuel" energy crop, and as a source of pulp and chips by forest industry. Poplars are also very amenable to advanced genetic analysis and are currently the only forest tree with a completely sequenced genome.

The Groover lab is establishing new molecular genetic tools that identify and characterize individual poplar genes regulating wood formation and crown architecture. For gene identification, a "gene trapping" system has been established for poplars, which identifies individual genes based on expression of the GUS reporter gene. The sequence of the identified genes is determined by comparison of DNA from the insertion site to the poplar genome sequence. The gene trap lines are available for screening by other researchers, and an Access database describing experiments to date is also available. Contact A. Groover for more information. This work is funded by competitive grants from the USDA NRI program.

The Groover lab is also studying the role of homeobox genes in the regulation of secondary growth and wood formation. The maintenance of a dividing, undifferentiated "stem cell" population within the vascular cambium supplies the daughter cells that are recruited into secondary vascular tissues in trees stems, including secondary xylem (wood). Individual KNOX-class homeobox genes are being characterized that regulate stem cell functions in the cambium, and regulate genes that determine key cell wall properties including lignin content. We have recently been funded by the Department of Energy to determine the role of Class III HD Zip transcription factors in regulating the relative ammounts of xylem and phloem during secondary growth, towards better understanding the role of trees in carbon sequestration and towards developing better biofuels applications. The results from these studies should also give important insight into the evolution of secondary growth in woody plants.

Conifer Molecular Genetics and Genomics - Partnership with UC Davis

Coniferous trees play fundamental roles in forest ecosystems and provide the bulk of raw materials for forest industry in the United States. The Neale lab is part of the UC Davis Department of Plant Sciences, and works in collaboration with the Institute of Forest Genetics to develop genomic science technologies to discover and understand the function of genes controlling important traits in conifers. The program is funded by IFG appropriations and considerable external funding from USDA/NRI Plant Genome, DOE Agenda 2020, the National Science Foundation Plant Genomics, and Weyerhaeuser Company.

Genes occur in various forms in nature called alleles, with each allele having a unique DNA sequence and a unique influence on plant growth and development. The different assemblage of alleles is thus ultimately responsible for the genetic differences among individual trees. We are using two primary strategies to identify and characterize individual alleles of genes that influence traits in conifers ranging from wood formation to resistance to pathogens. The first strategy involves making molecular maps of tree genomes, and then seeking correlations between inherited chromosomal regions and traits of interest. We have used this method, know as Quantitative Trait Loci Mapping, to scan the genomes of both loblolly pine and Douglas fir for regions regulating both wood properties and adaptive traits. In a second strategy, we have sequenced a large number of alleles from expressed genes in conifer species (expressed sequence tags, or ESTs) and developed Single Nucleotide Polymorphism (SNP) assays for individual alleles of interest. We are now determining both SNP genotypes and measuring traits of interest for large numbers of trees. The final step in the process is to look for alleles of individual genes that correlate (and thus regulate) traits of interest. The information from this and other forest tree genetics projects is available through Dendrome, a forest tree genome database.