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

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 polymermore » 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. « less
Authors:
; ; ; ; ; ; ; ;
Publication Date:
DOE Contract Number:
DE-AC05-00OR22725
Product Type:
Dataset
Research Org(s):
Oak Ridge Leadership Computing Facility; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org:
Office of Science (SC), Biological and Environmental Research (BER) (SC-23); Center for Bioenergy Innovation (CBI)
Subject:
snp genotypes poplar p.trichocarpa gwas
OSTI Identifier:
1411410

Tuskan, Gerald, Muchero, Wellington, Chen, Jin-Gui, Jacobson, Daniel, Tschaplinski, Timothy, Rokhsar, Daniel S, Schackwitz, Wendy S, Schmutz, Jeremy, and DiFazio, Stephen P. Populus Trichocarpa Genome-Wide Association Study (GWAS) Population SNP Dataset Released. United States: N. p., Web. doi:10.13139/OLCF/1411410.
Tuskan, Gerald, Muchero, Wellington, Chen, Jin-Gui, Jacobson, Daniel, Tschaplinski, Timothy, Rokhsar, Daniel S, Schackwitz, Wendy S, Schmutz, Jeremy, & DiFazio, Stephen P. Populus Trichocarpa Genome-Wide Association Study (GWAS) Population SNP Dataset Released. United States. doi:10.13139/OLCF/1411410.
Tuskan, Gerald, Muchero, Wellington, Chen, Jin-Gui, Jacobson, Daniel, Tschaplinski, Timothy, Rokhsar, Daniel S, Schackwitz, Wendy S, Schmutz, Jeremy, and DiFazio, Stephen P. 2016. "Populus Trichocarpa Genome-Wide Association Study (GWAS) Population SNP Dataset Released". United States. doi:10.13139/OLCF/1411410. https://www.osti.gov/servlets/purl/1411410.
@misc{osti_1411410,
title = {Populus Trichocarpa Genome-Wide Association Study (GWAS) Population SNP Dataset Released},
author = {Tuskan, Gerald and Muchero, Wellington and Chen, Jin-Gui and Jacobson, Daniel and Tschaplinski, Timothy and Rokhsar, Daniel S and Schackwitz, Wendy S and Schmutz, Jeremy and DiFazio, Stephen P},
abstractNote = {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.},
doi = {10.13139/OLCF/1411410},
year = {2016},
month = {1} }
  1. The Oak Ridge Leadership Computing Facility (OLCF) was established at Oak Ridge National Laboratory in 2004 with the mission of accelerating scientific discovery and engineering progress by providing outstanding computing and data management resources to high-priority research and development projects. OLCF unveiled Titan in 2013, which is capable of 27 petaflops. Titan is one of the first hybrid architecture systems—a combination of graphics processing units (GPUs), and the more conventional central processing units (CPUs) that have served as number crunchers in computers for decades. The OLCF gives the world’s most advanced computational researchers an opportunity to tackle problems that wouldmore » be unthinkable on other systems. The DOI Portal can be found at https://doi.ccs.ornl.gov/. « less
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