Project Objectives

  1. To develop a high-throughput gene discovery pipeline to identify naturally occurring variation in genes critically important in cellulose and lignin biosynthesis in poplar using the DNA sequencing, SNP genotyping and bioinformatic infrastructures previously built for pine species.
  2. To perform single nucleotide polymorphism (SNP) discovery using high throughput DNA sequencing (Agencourt Biosciences) and SNP genotyping (Illumina and/or Affymetrix) to associate genetic variation in genes involved in cellulose and lignin biosynthesis with phenotypic variation in cellulose quantity, quality and extractability in a large clonal black cottonwood (Populus trichocarpa) genetic test plantation belonging to GreenWood Resources.


The DOE’s “Breaking the Biological Barriers to Cellulosic Ethanol” report identifies poplar as one of the key feedstock species for cellulosic ethanol production in many regions of the country, including California. In contrast to herbaceous biofuels species such as corn, switchgrass and miscanthus, poplar has several important advantages. The primary advantages are market opportunities and storage. Poplar can be grown for multiple products including high-valued solid wood products and for pulp and paper.

This provides growers multiple market opportunities and additional incentive to produce the crop. Second, poplar is a woody perennial and can be stored “on the stump” unlike switchgrass that must be dried and stored. Poplar can be grown on a wide variety of site conditions and in some situations requires few inputs.

There has been modest genetic improvement of poplar in the US. A large number of artificial hybrids have been developed and many have superior growth and yield qualities. Poplars have been used extensively in the US and Europe for basic research on wood formation, specifically on the lignin and cellulose biosynthetic pathways. Some poplars can be genetically transformed and GMO poplars have been developed by modifying the expression of genes in the lignin and cellulose biosynthetic pathways. Much less has been done, however, to characterize naturally occurring variation in genes of these pathways. We have done extensive work in loblolly pine (Pinus taeda) to characterize naturally occurring genetic variation in the lignin and cellulose biosynthetic pathways and have used the association genetics approach to show how DNA sequence variation in these genes underlies phenotypic level variation for wood properties traits such as wood density, microfibril angle and lignin/cellulose content. These same approaches can now be applied to poplar. There are two very important resources available in black cottonwood that will facilitate association genetic studies.

First, are the extensive genetic resources, breeding and genetic test plantations of GreenWood Resources and second is the recently published complete genome sequence of black cottonwood. These resources, combined with the resequencing, SNP genotyping and bioinformatics pipeline we have built for pine, ensure rapid discovery of naturally occurring genetic variation in genes of the lignin and cellulose biosynthetic pathways.

Anticipated Impact

Poplar will undoubtably be a key species in future cellulosic ethanol production. Furthermore, poplars harbor abundant genetic variation that can be repackaged through traditional plant breeding approaches, thus avoiding regulatory, biosafety and social concerns over genetically engineered trees.

Traditional breeding methods based on phenotypic selection are, however, slow and can lack precision for improving certain traits. Genomic-based breeding approaches offer significant potential for the genetic improvement of poplars for cellulosic ethanol production. The expected outcome of the project proposed here is the development of a high throughput gene discovery pipeline that will provide the genomic information to be feed directly into applied poplar breeding programs.