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USDA-Funded Research Leads to Loblolly Pine Genome
USAgNet - 01/14/2013

Researchers at the University of California-Davis, with funding from the U.S. Department of Agriculture (USDA), released the initial draft genome sequence of the loblolly pine, an important conifer species that is used as a feedstock for biofuels and can aid in climate change mitigation. The announcement was made at the 2013 Plant and Animal Genome Conference in San Diego, Calif.

"Loblolly pine plays an important role in American forestry, and I am excited to announce that we now have a much-needed tool in unlocking the secrets of these trees," said Sonny Ramaswamy, director of USDA's National Institute of Agriculture (NIFA), which funded the research. "I look forward to our continued work with the University of California-Davis and their application of this new knowledge."

NIFA awarded the $14.6 million grant to UC Davis in 2011. Dr. David Neale leads the 5-year project with collaboration from five other organizations. The team used the latest next-generation sequencing technology to generate 16 billion short sequence fragments, representing 60-fold coverage of the massive loblolly pine genome. Pine genomes are extremely large at 10 times the size of the human genome, making this assembly the largest ever successfully completed. The team generated roughly 1.2 trillion bases of DNA.

"USDA competitive grant programs, such as the Agriculture and Food Research Initiative and its predecessor the National Research Initiative, have made significant and important contributions in building the capacity and infrastructure of forest genomics research toward increasing the productivity and health of American forests," Neale said. "Now, with the funding of pine genome sequences, forest tree breeders are poised to use modern breeding technologies that are already routine in agricultural crop and livestock breeding. These technologies will also be critical in maintaining adapted and healthy forests facing climate change."

This draft assembly, which is being made publicly available through the team's website, will provide a valuable resource for gene discovery while the project team prepares its analysis of the genome for publication. The data gained from the genome sequence could accelerate breeding efforts and enhance the tree's use as a feedstock for biofuels and biopower.

"This is critical for the forest genetics community as the ability to accelerate breeding trees will produce healthier forests in light of climate change and increased disease and insect pressure," said Dr. Jim Reaves, Forest Service deputy chief for research and development. The Forest Service's Southern Research Station conserved and supplied the plant tissue for the project and provided quality control on the DNA samples that were sequenced.

Increased planting of fast growing varieties of loblolly pine and other agroforestry crops will also contribute to carbon sequestration and help to mitigate the effects of climate change.

Loblolly pine is the most economically important tree species in the United States. Southern pines provide 58 percent of the timber in the country and 15 percent globally. The native range of loblolly pine spans 14 states from southern New Jersey south to central Florida and west to Texas where it makes up more than half of the existing forest. It is likely the knowledge gained from this sequence will apply across much of the Pinaceae family, containing most of the commercially important conifers of the world.

UC Davis is joined by the following organizations on the 5-year Loblolly Pine Genome Project: Children's Hospital of Oakland Research Institute, Washington State University, Texas A&M University, Indiana University, Johns Hopkins University and the University of Maryland. The draft assembly was built using the MaSuRCA assembler developed at the University of Maryland and Johns Hopkins University, which was specifically modified to handle the very large amount of data generated by the project. The sequenced pine germplasm came from the North Carolina State University Cooperative Breeding Program and was produced by a mating made by the Virginia Department of Forestry.

The team is also currently working on sequencing a second important conifer species, sugar pine from California.

The award was made through NIFA's Agriculture and Food Research Initiative (AFRI). AFRI is NIFA's flagship competitive grant program and was established by the 2008 Farm Bill. AFRI supports work in six priority areas: 1) plant health and production and plant products; 2) animal health and production and animal products; 3) food safety, nutrition and health; 4) renewable energy, natural resources and environment; 5) agriculture systems and technology; and 6) agriculture economics and rural communities.

Through federal funding and leadership for research, education and extension programs, NIFA focuses on investing in science and solving critical issues impacting people's daily lives and the nation's future. More information is available at: www.nifa.usda.gov.

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