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Populus Trichocarpa Genome-Wide Association Study (GWAS) Population SNP Dataset Released

  • Tuskan, Gerald | Oak Ridge National Laboratory
  • Muchero, Wellington | Oak Ridge National Laboratory
  • Chen, Jin-Gui | Oak Ridge National Laboratory
  • Jacobson, Daniel | Oak Ridge National Laboratory
  • Tschaplinski, Timothy | Oak Ridge National Laboratory
  • Rokhsar, Daniel S | Joint Genome Institute
  • Schackwitz, Wendy S | Joint Genome Institute
  • Schmutz, Jeremy | Joint Genome Institute
  • DiFazio, Stephen P | West Virginia University Department of Biology
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Overview

Description

This dataset includes genetic variations found in 882 poplar trees, and provides useful information to scientists studying plants as well as researchers more generally in the fields of biofuels, materials science, and secondary plant compounds. For nearly 10 years, researchers with DOE's BioEnergy Science Center (BESC), a multi-institutional organization headquartered at ORNL, have studied the genome of Populus - a fast-growing perennial tree recognized for its economic potential in biofuels production. This Genome-Wide Association Study (GWAS) dataset includes more than 28 million single nucleotide polymorphisms, or SNPs that have been derived from 17 trillion bases of sequence data generated from 882 undomesticated Populus genotypes. Each SNP represents a variation in a single DNA nucleotide, or building block, that can act as a biological marker and/or causal allele within a protein sequence, helping scientists locate genes associated with certain characteristics, conditions or diseases. The results of this analysis have been used, among other things, to 1) seek genetic control of cell-wall recalcitrance - a natural characteristic of plant cell walls that prevent the release of sugars under microbial conversion and restricts biofuels production and 2) identify the molecular mechanisms controlling deposition of lignin in plant structures. Lignin is a polyphenolic polymer that strengthens plant cell walls and acts as a barrier to microbial access to cellulose during saccharfication - the process of breaking cellulose down into simple sugars for fermentation. Although the dataset's most immediate applications are in fundamental plant sciences, ORNL researchers plan to use the GWAS data to inform applied work in areas such as cleaner, sustainable transportation biofuels, carbon fiber for lightweight vehicles and alternatives to conventional plastics and building insulation materials.

Funding resources

DOE contract number

DE-AC05-00OR22725

Originating research organization

Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Other contributing organizations

Joint Genome Institute

Sponsoring organization

Office of Science (SC), Biological and Environmental Research (BER) (SC-23);Center for Bioenergy Innovation (CBI)

Details

DOI

10.13139/OLCF/1411410

Release date

December 6, 2017

Dataset

Dataset type

GD Genome/Genetics Data

Acknowledgements

Users should acknowledge the OLCF in all publications and presentations that speak to work performed on OLCF resources:

This research used resources of the Oak Ridge Leadership Computing Facility at the Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725.

Keywords

  • snp genotypes poplar p.trichocarpa gwas