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USDA-Funded Researchers Map the Loblolly Pine Genome

During the month of April we will take a closer look at USDA’s Groundbreaking Research for a Revitalized Rural America, highlighting ways USDA researchers are improving the lives of Americans in ways you might never imagine, including research into trees that could fuel new energy solutions.

A team of researchers led by the University of California–Davis has mapped the complete genome of the loblolly pine. And if you don’t think that understanding the genetic makeup of loblolly pine is a big deal, perhaps you cannot see the forest for the trees.

Loblolly pine, the most commercially important tree in the United States, is the source of most paper products in this country and 58 percent of timber. On the surface, that might be reason enough for the USDA’s National Institute of Food and Agriculture (NIFA) to invest $14.6 million in 2011 toward science that could increase the productivity and health of American forests.

Loblolly pine also looms large on the horizon as a feedstock for the next generation of American biofuel.  President Obama’s goal of reducing the United States’ dependency on foreign oil by 30 percent by the year 2030 will be met, in large part, by producing home-grown biofuel. According to Genome Biology, approximately 75 percent of that biofuel will have to come from non-grain, non-food sources called lignocellulosic biomass – and loblolly pine could be a major contributor to filling that need.

Mapping the loblolly genome, then, became an important part of the plan in terms of improving the health and sustainability of this important plant. But, mapping a genome is no easy task, and the loblolly pine proved to be the greatest challenge to date for this type of research. The loblolly genome is the largest ever sequenced and is about seven times larger than the human genome.

To sequence a genome, scientists must first examine the DNA of their subject and then “map” the location of each nucleotide (the “A, C, T, and G” bases) of the entire DNA chain. Scientists use this information to find the best traits, such as disease resistance, and develop better future generations.

The challenge of overcoming the sheer volume of loblolly data is a triumph of its own for the research team.  According to David Neal, team leader and professor of plant sciences at UC–Davis, the team could “read” the nucleotide letters, but only in short batches. The problem was putting together the 16 billion fragments in a way that would allow them to read the complete story of the loblolly pine.

Researchers met this task by employing a new technique developed at the University of Maryland.  Team members overlapped smaller sections of data to form larger chunks and then threw away the redundant information. The process eventually meant the computer had 100 times less sequence data to deal with. The success of this process may help speed up future genome-mapping projects.

The loblolly project team consisted of UC–Davis, Johns Hopkins University, the University of Maryland, Indiana University–Bloomington, Texas A&M University, Children’s Hospital Oakland Research Institute, and Washington State University.

Their complete articles of this research were published in the March 2014 issues of GENETICS and Genome Biology.

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