New Tool for Untangling the Loblolly Pine Genome

by Sarah Farmer, SRS Science Delivery Group
Nurul Faridi with the new laser capture microdissection microscope. Photo by Texas A&M AgriLife Communications.

Nurul Faridi with the new laser capture microdissection microscope. Photo by Texas A&M AgriLife Communications.

Plucking a chromosome out of a single cell is an intricate business. But that’s exactly what U.S. Forest Service Southern Research Station (SRS) scientists and partners at Texas A&M University will be able to do with a new laser capture microdissection microscope.

The microscope has a laser beam 10 times thinner than a human hair, making it possible to isolate single cells or chromosomes from tissues.

“One of the most exciting applications for us is to be able to isolate individual chromosomes from tree and other plant cells,” says Nurul Faridi, research geneticist at the SRS Southern Institute of Forest Genetics. One of the species Faridi and colleague Claudio Casola of Texas A&M University are focusing on is loblolly pine (Pinus taeda).

Loblolly pine’s entire genome has already been sequenced, but sequencing is only one step towards understanding the species. Its genome is about eight times longer than the human genome, and scientists do not yet know how the genetic information is organized across the tree’s 12 pairs of chromosomes.

Faridi and his colleagues have previously microdissected one loblolly pine chromosome, but the new microscope will allow them to isolate and amplify others.“Ultimately, we hope to generate high quality assemblies of all the loblolly pine chromosomes,” says Faridi. Understanding where on the chromosomes each of the 80,000 genes are located will help scientists understand how loblolly pine, as well as other conifers, adapt to different environmental conditions.

SRS and Texas A&M University, partners in research for almost a century now, purchased the microscope together. The microscope has applications in medicine, agriculture, and other disciplines, and will benefit both institutions for years to come.

For more information, email Nurul Faridi at

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Posted in Genetics, Southern Pines

SRS Funds Graduate Student’s Pollinator Study

by Sarah Farmer, SRS Science Delivery Group
Deerberry, a type of wild blueberry, is an important early spring forage plant for bees. Photo by Robert Mohlenbrock, courtesy of USDA NRCS Wetland Science Institute.

Deerberry, a type of wild blueberry, is an important early spring forage plant for bees. Photo by Robert Mohlenbrock, courtesy of USDA NRCS Wetland Science Institute.

Through its Partnership Enhancement Initiative, the U.S. Forest Service Southern Research Station (SRS) provides funding to students – especially minority students – and professors interested in studying natural resource issues.

One of the recent grant recipients was Hampton University, a historically black university in Virginia. “The grant funded Michael Mitchell – a Master of Science graduate student – as he completed his coursework and conducted research,” says Barbara Abraham, associate professor at Hampton University and principal investigator of the study.

The project involved identifying other forage plants used by native bee pollinators of wild blueberries, and identifying bee species in the high elevation forests and natural areas near the Mountain Lake Biological Station in Virginia.

Over the two-year study period, Abraham and Mitchell captured almost a thousand bees, either directly from flowering plants or in bowl traps. Mitchell identified bees to family and often genus, and Sam Droege, a scientist with the U.S. Geological Survey (USGS) Patuxent Wildlife Research Center, examined specimens under a microscope to verify the identifications.

Results from the research project will also contribute to a nationwide bee survey that Droege designed. The survey relies on a network of monitoring stations on public lands, including the SRS Coweeta Hydrological Laboratory, and the Crossett, Bent Creek, Hitchiti, Santee, and Stephen F. Austin Experimental Forests.

A number of rare native bees were collected including two species never seen in Virginia before. In general, there was very high species diversity during late spring through early summer. “We also documented nonnative bees in the study area,” says Abraham. “Most of the collected bees were native, and the most common nonnative species were honeybees and mason bees.”

The researchers found that when flowering, wild blueberry bushes were visited by 12 pollinator species, which was more diversity than any of the other plants in the study supported. “However, many of the bee species that visited blueberries also visited other flowering plants,” says Abraham. Other important native plants for bee species included early-blooming rhododendron, wild geranium, bee balm and daisy fleabane, followed by later bloomers such as mountain laurel, milkweed, and nonnative plants such as clover and chicory.

“The experience Mitchell gained in research methods, data collection and analysis, and collaboration will be valuable as he pursues a career in natural resources,” says Abraham. Ultimately, Mitchell hopes to work with a federal agency such as the Forest Service.

For more information, email Barbara Abraham at

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Posted in Experimental Forests, Fish & Wildlife

Dreaming of Giants: The Future of American Chestnut Restoration

by Sarah Farmer, SRS Science Delivery Group
Stacy Clark examines a young chestnut tree. Photo by U.S. Forest Service.

Stacy Clark examines a young chestnut tree. Photo by U.S. Forest Service.

For almost a hundred years, foresters have dreamed of the American chestnut’s return. “As the 21st century unfolds, the chestnut restoration goal may be closer to reality,” says U.S. Forest Service Southern Reseearch Station (SRS) scientist Stacy Clark.

“Chestnut restoration will require an integrated approach that uses traditional breeding, advanced seedling technology, and forest management,” says Clark, research forester with the SRS Upland Hardwood Ecology and Management unit, and lead author of a new review article recently published in the Journal of Forestry that evaluates restoration efforts thus far and offers recommendations for the future.

Two nonnative fungi that cause chestnut blight and ink disease essentially erased the American chestnut tree from the landscape by the early 20th century, and although new shoots continue to emerge from ancient roots, they eventually succumb to blight. Tree breeders have attempted to produce blight-resistant trees for decades, but research was largely unsuccessful until a backcross breeding approach using Chinese chestnut and modern biotechnology techniques became available.

Through a combination of traditional breeding and biotechnology, scientists at the American Chestnut Foundation are developing chestnut seedlings that are expected to have the blight resistance of their Chinese parents, but the appearance and ecological traits of their American parents. Researchers at the Connecticut Agricultural Experiment Station and the American Chestnut Cooperators’ Foundation are also developing disease-resistant trees with breeding and biological control of the blight.

In 2009, researchers began testing blight resistance by planting seedlings from the American Chestnut Foundation in national forests. The Forest Service Northern Research Station established several test plantings, and Clark, along with her SRS colleagues, initiated the largest study, which had eleven test plantings and spanned three states. “Our study is ongoing, but results from the first four years show that ink disease was the biggest threat to the chestnut seedlings,” says Clark. In some sites, less than 40 percent of the seedlings lived, although in other sites more than 80 percent survived.

Planting high quality seedlings could be the best way to overcome ecological challenges to restoration. “Healthier seedlings would be more likely to be competitive, recover from animal damage, and tolerate drought and other weather events,” says Clark.

“Restoring the American chestnut to our forests is theoretically possible,” says Clark. “However, without continued research and partnership, success will be limited.” Clark and her colleagues suggest that the Forest Service develop short-term (five year) restoration goals such as establishing and maintaining long-term multidisciplinary experiments. Although several long-term studies are in progress, they are only designed to test blight-resistance. “As with any disease, chestnut blight interacts with genotype and environment,” says Clark.

Test plantings on national forests currently rely on general funds that can be used for regenerating species such as oak or pine. “Chestnut test plantings are more expensive to implement and usually less successful compared with other vegetation work,” says Clark. Clark and her colleagues also emphasize the importance of partnerships and the need for communication between national forests, scientists, and other stakeholders.

American chestnut vanished before forestry research as we know it existed, so the full impact of its disappearance is unknown. However, chestnut was a keystone species with tremendous wildlife value, and because of its edible nuts and high-quality timber it was also important to local economies. “There are multiple barriers to restoration,” says Clark. “But the iconic nature of American chestnut, its ecological value, and the long history of investment in breeding for blight resistance demand continuation of restoration efforts.”

Read the full text of the article.

For more information, email Stacy Clark at

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Posted in Restoration, Upland Hardwoods