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Largest Poplar Tree SNP Dataset Presented at PAG Conference

NEW YORK (GenomeWeb) – Researchers at the Department of Energy's Oak Ridge National Laboratory (ORNL) have published what they called the largest SNP dataset of genetic variations in poplar trees.

The GWAS data — collected through nearly 10 years of research by scientists at the ORNL-led BioEnergy Science Center (BESC) — was presented yesterday at the Plant and Animal Genome Conference in San Diego. It consists of more than 28 million SNPs derived from approximately 900 resequenced poplar genotypes.

The data "gives us unprecedented statistical power to link DNA changes to phenotypes," Gerald Tuskan, a corporate fellow and leader of the Plant Systems Biology group in ORNL's Biosciences Division, said in a statement.

The research has many implications, especially for applications such as biofuel production, ORNL said. The data is already being used to study cell-wall recalcitrance, a characteristic of plant cell walls that prevents the release of sugars under microbial conversion and inhibits the production of biofuel.

For their part, BESC researchers are using the dataset to identify the molecular mechanisms controlling deposition of lignin in plant structures, a polymer that strengthens plant cell walls and prevents cellulose breakdown into simple sugars for fermentation. Lignin can be used to create plant-based chemicals, polymers, and materials such as sustainable transportation fuels, carbon fiber, alternatives to conventional plastics, and building insulation materials.

"We can identify the genes and genetic variants that move carbon through the lignin pathway, and then take that knowledge and, through genomic selection, develop plant materials that are tailored to work with microbes to yield the targeted product," Tuskan said.

He also noted that the poplar SNP data could be used to the benefit of human medical research. ORNL researchers have used the GWAS to identify which genes in the trees control callus formation and wound healing. These genes are analogous to human genes that are involved in tumor formation, Tuskan added, and knowledge of the surrounding gene expression networks in trees could also inform cancer research.

The dataset is currently available here.