Poplar Population Genomics

Overview

Populus species are economically, ecologically, and environmentally important; they are harvested for paper pulp and particle board production, and hold potential for playing important roles in CO₂ biosequestration and biofuel production. Moreover, Populus is the model organism for hardwood tree genomics and physiology. Population genetic tools needed to conduct association mapping and understand evolutionary history are not, however, available for any Populus species. We are developing these tools for Populus balsamifera, using them to conduct an association mapping study designed to identify the genetic basis for phenotypic variation in bud set (an important determinant of cold adaptation and growth rate), and applying comparative population genomic analyses to test whether the same nucleotides and genes are responsible for phenotypic variation and adaptive evolution of bud set in North American P. balsamifera and European P. tremula.

Development of these genomic tools and the association mapping will be accomplished through collaboration with Canadian researchers at the AAFC-PFRA Shelterbelt Centre (http://www.agr.gc.ca/pfra/shelterbelt_e.htm) who are establishing long-term common gardens of P. balsamifera. These common gardens will be maintained as a long term resource and are available to the wider scientific community; therefore, the data we generate will greatly facilitate future association analyses on additional traits (wood density, drought tolerance, etc.). The comparative population genomic analyses of adaptation to northern latitudes will be accomplished through collaboration with Dr. P. Ingvarsson, University of Umea, Sweden (http://www.emg.umu.se/en/researchers/par-ingvarsson.html), who is conducting complementary studies in the European aspen (P. tremula).

Broader impacts and intellectual merit: All genomic tools, including SNP data, SNP assay conditions, genomic diversity estimates, and phenotypic observations will be made publicly available on this site as they are generated. These data will greatly facilitate, in time and money, future association analyses of functionally-important genes in poplar. Moreover, our association analyses have the potential to identify gene or nucleotide polymorphisms that influence latitudinal patterns in timing of bud set. This work also will characterize the population structure of genetic diversity in balsam poplar, information that will aid in efficient sampling of germplasm for tree improvement and developing locally adapted genotypes for forestry and agroforestry. Finally, this research will make possible comparative population genomic analysis that will provide insight into fundamental evolutionary processes -- the repeatability of adaptation at the nucleotide level.
Numerous training opportunities in plant genomics and bioinformatics for undergraduate students, graduate students, and post-doctoral researchers are available. Please contact us if you are interested. We also are developing an undergraduate training program focused on development and execution of scientific projects, and written and verbal communication of results.
We also will be developing laboratory exercises in DNA sequence analysis, population genomics, and association mapping for undergraduate courses. After these exercises are developed and tested in courses taught by the PIs, they will be made available through this site and the Plant Genome Research Outreach Portal.
Finally, this proposed research promises to illuminate the population genomics of a keystone species of Arctic boreal communities and the tree with the northernmost distribution in North America, and thus complements the themes of the International Polar Year (2007-2008).