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Kremer A.,French National Institute for Agricultural Research | Kremer A.,University of Bordeaux 1 | Abbott A.G.,Clemson University | Carlson J.E.,Pennsylvania State University | And 7 more authors.
Tree Genetics and Genomes | Year: 2012

An overview of recent achievements and development of genomic resources in the Fagaceae is provided, with major emphasis on the genera Castanea and Quercus. The Fagaceae is a large plant family comprising more than 900 species belonging to 8-10 genera. Using a wide range of molecular markers, population genetics and gene diversity surveys were the focus of many studies during the past 20 years. This work set the stage for investigations in genomics beginning in the early 1990s and facilitated the application of genetic and quantitative trait loci mapping approaches. Transferability of markers across species and comparative mapping have indicated tight macrosynteny between Quercus and Castanea. Omic technologies were more recently developed and the corresponding resources are accessible via electronic and physical repositories (expressed sequence tag sequences, single-nucleotide polymorphisms, candidate genes, cDNA clones, bacterial artificial chromosome (BAC) libraries) that have been installed in North America and Europe. BAC libraries and physical maps were also constructed in Castanea and Quercus and provide the necessary resources for full nuclear genome sequencing projects that are currently under way in Castanea mollissima (Chinese chestnut) and Quercus robur (pedunculate oak). © 2012 The Author(s).

News Article | March 22, 2016
Site: phys.org

When Europeans came to the New World in the 16th century, they brought measles and smallpox with them. Without the immunity Europeans had cultivated over the years, the native people in America quickly fell ill. Millions died as a result. Today, trees in the New World are also dying from diseases that were introduced through global trade. However, trees are much more vulnerable than humans. "The immune system of trees does not work in the same way as those of humans. Trees must rely, for the most part, on genetic resistance," said Jeanne Romero-Severson, director of the University of Notre Dame's Tree Genetics Core Facility (TGCF) and professor of biological sciences. "The trees that best resist the attacks of pests and pathogens live to produce descendants that can do the same. Over millions of years, the trees, pests and pathogens usually reach a balance, where the pests and pathogens only kill the weak or damaged trees." The sudden introduction of foreign pests and pathogens allows no time for genetic resistance to develop. For example, when chestnut blight was introduced more than 100 years ago, the American chestnut tree did not have the genetic variants to fight off the disease. This tree species is very persistent in its fight for survival, but eventually an infected tree will die. "The Chinese chestnut tree and chestnut blight evolved together, so a balance was struck. Chinese chestnuts therefore developed genetic resistance," said Romero-Severson. "Fortunately, the American chestnut and Chinese chestnut can make healthy, fertile hybrid trees." The American Chestnut Foundation was founded in 1983 to save the American chestnut by crossbreeding the species with Chinese chestnut trees. The foundation is spearheading the cause as its scientists breed chestnut blight-resistant hybrids. The core facility has become an important part of the effort through the development of a DNA "fingerprinting" database for all the chestnut species that people have crossbred with the American and the cultivated European chestnut trees. "Simplistically speaking, many crossbred chestnuts are resistant to blight, but that does not mean you would plant one just anywhere," said Romero-Severson. "Our lab is creating a DNA fingerprinting database to identify the ancestry of any chestnut tree. The tree's ancestry can tell us where that tree might grow best." The DNA fingerprint of a tree can reveal its inherited ability to live within certain environments and survive many threats including frost, insect pests and more. Additionally, the American Chestnut Foundation uses DNA fingerprinting for cultivar identification and pedigree analysis for cultivated chestnut tree growers. Cultivar identification services support local growers in Indiana, Michigan and Ohio, allowing cultivated trees to produce nuts that people can enjoy in the Midwest. More information: To learn more about the Tree Genetics Core Facility, click here: sites.google.com/a/nd.edu/treedna/

The 27-year-old traditional breeding program, which has attempted to infuse blight resistance from the Chinese chestnut tree into American chestnuts, is receiving a boost from tree molecular geneticists at Penn State and five other universities working collaboratively in a bid to improve the process. While traditional breeding has been taking place, so have parallel lines of research into genetic modification and also bio-control of the fungus that causes the blight. "Teams of researchers are now at a crossroads where all three methodologies may be combined to provide a more robust product," said Sara Fitzsimmons, a research technologist who is also director of restoration for The American Chestnut Foundation, the group leading the chestnut-restoration effort. "By merging successes in genetic modification, hypovirulence and traditional breeding, restoration of a disease-resistant American chestnut tree is closer." The chestnut blight—which wiped out the American chestnut species across its 180-million-acre range in the first half of the 20th century—is caused by a fungus inadvertently introduced from Asia. Some view the loss of the chestnuts, which produced untold tons of food for wildlife and food and lumber for humans, as one of the worst U.S. ecological disasters. "We didn't account in our time estimates for how long it would take after we got nuts with blight resistance to plant out orchards and select progeny with the strongest resistance and eliminate material susceptible to the blight," said Fitzsimmons. "When we plant these trees with nuts generated by our latest generation of backcrossed trees, only 1 percent have the resistance that we are looking for. So you can imagine, if we're planting 27,000 trees, only about 270 have the combination of blight resistance and American chestnut characteristics we need." The chestnut orchard in The Arboretum at Penn State and the Chestnut Foundation's Meadowview Research Farms in Virginia contains the latest generation of traditionally bred plant material with the most chestnut blight resistance and American character. At the Penn State orchard last spring, Fitzsimmons and her colleagues conducted controlled pollination of selected trees. The tactic underlines challenges faced by researchers trying to bring back the American chestnut. "Because we still haven't finished planting out the orchard and we still haven't finished selecting and culling highly blight-susceptible trees we planted a few years ago, the blight-susceptible trees are pollinating trees that are selected and resistant," she explained. "So, when we collect nuts in this orchard, they have a wide variety of resistance and very few have full resistance, because there is so much pollen at this location." Fitzsimmons and other researchers bagged flowers on selected trees to keep unwanted pollen away and introduced pollen from trees known to have a high level of blight resistance. Blight resistance is measured after the fungus that causes the disease is applied to wounds made in the young chestnuts' trunks or branches. "When we were collecting open-pollination nuts, we were hoping that they wouldn't have this much susceptibility in the progeny, but because there is so much susceptibility in the pollen cloud, we were not able to get rid of it," Fitzsimmons explained. "So this year, we took the best of the best, and we performed controlled pollination. Controlled pollination, however, yields about 50 percent or fewer nuts than open pollination does. "These control-pollinated nuts will be a true test of levels of resistance possible in this population." The American Chestnut Foundation started its cross-breeding program in 1989, and Penn State got involved in 1997. The first orchard was planted by Professor Emeritus of Forest Genetics Henry Gerhold on State Game Land 176, not far from the University Park campus, as part of Christmas tree improvement research he was conducting. Kim Steiner, professor of forest biology and now arboretum director—and also the senior science adviser to The American Chestnut Foundation—then conducted silvicultural trials with chestnuts at the University's Stone Valley Recreation Area, starting in 1997. The chestnut orchard in The Arboretum at Penn State was started in 2002. In 2004, Professor of Molecular Genetics John Carlson started to examine the underlying molecular components of blight resistance. In a project funded by the National Science Foundation from 2006 to 2009, his laboratory identified several potential blight-resistance genes by painstakingly comparing genes expressed in cankers of susceptible American and resistant Chinese chestnut plants. With funding from The Forest Health Initiative, Carlson since 2009 has led a project to sequence and characterize the entire genome of one of the blight-resistant donor Chinese chestnut trees in the chestnut foundation's breeding program, with an eye toward identifying all of the resistance genes. Carlson, director of Penn State's Schatz Center for Tree Molecular Genetics, is now collaborating with tree geneticists and researchers at the University of Kentucky, Clemson University, Virginia Tech, the University of Tennessee at Knoxville, the State University of New York at Syracuse and the foundation to unravel the mystery of blight resistance. The group also is testing a genome-sequence-based system to accelerate the selection of blight-resistant plants that now are genetically American, using nuts harvested this fall from the trees that underwent controlled pollination in the Penn State orchard. Developing blight resistance in American chestnut is complex and challenging, concedes Carlson, who also has applied molecular-genetics techniques to modify poplar trees for bioprocessing and biofuels. "Our aspirations are to move the resistance genes from Chinese chestnuts into American chestnuts and find out which combinations of genes would give the best resistance," he said. "That has proven to be extremely complicated because more than a few genes are involved, and we haven't yet pinned down which ones are the most important. Genetic engineering groups have been testing about a dozen blight-resistance genes that have been identified. We have to test them in combination because we know that blight resistance is not a single-gene trait, so we have to test multiple combinations of genes, which is very difficult to do and takes time." If biotechnology researchers do develop a genetically modified, blight-free American chestnut, current federal regulations would limit distribution of the plants, Fitzsimmons noted. An estimated five years will be required to have the product deregulated by governmental agencies before it is available for widespread distribution and planting. "We expect to have research plantings of GMO backcross trees within the next two years," she said. "While GMO cannot be allowed to open pollinate under current regulations, GMO American chestnuts appear to offer an excellent chance of creating a blight-resistant American chestnut." The Chestnut Foundation also is planning to soon deploy a biocontrol, developed by pathologists from West Virginia University and the University of Maryland, to weaken the fungus that causes chestnut blight. The biocontrol involves infecting the fungus that causes chestnut blight with a virus that makes the fungus sick and reduces its virulence. "We are now focusing on the three Bs in concert to restore the American chestnut—breeding, biocontrols and biotechnology," Fitzsimmons said. "This gives us a bigger suite of tools to fight off this fungus and blight." But even if all of these initiatives to restore the American chestnut come off without a hitch, it may take a century or more to see chestnuts again across their former range, from Maine to Florida, she concedes. Based on research she is conducting in Maine and Vermont on naturally regenerating sites, it looks like it takes at least 20 years for a plot of chestnuts just to become established beneath a forest canopy. "Tree breeding, especially hardwoods, takes extraordinary patience because results often aren't seen over a lifetime—we knew that," she said. "To see a naturally regenerating American chestnut population regaining its reproductive niche in the ecological landscape will take a long time—50 years at least after we plant nuts from truly blight-resistant trees." No matter how long it takes, the chestnut reintroduction effort is monumental, Steiner stressed, because it is likely the most complex and long-term attempt to rescue a plant species ever pursued. Breeding trees to develop blight resistance is difficult enough, but in this particular case the rescue requires transferring genes from one species to another while still maintaining the genetic diversity of the original species. "A 'horticultural' solution—where a successful product is commonly a single, clonally propagated genotype—is not sufficient because we are attempting to restore a species to the wild where it must survive, reproduce and eventually evolve on its own," Steiner said. "A remarkable feature of this project is that it is being performed by a small non-profit with the help of thousands of volunteers. Fortunately, the work of the foundation has catalyzed millions of dollars in research by collaborators such as John Carlson, and this has greatly assisted progress." Explore further: Using DNA 'fingerprinting' to understand ancestry and immunity of trees

Clark S.L.,U.S. Department of Agriculture | Schlarbaum S.E.,University of Tennessee at Knoxville | Saxton A.M.,University of Tennessee at Knoxville | Hebard F.V.,The American Chestnut Foundation
New Forests | Year: 2016

European and American chestnut species (Castanea) have been decimated by exotic species, most notably chestnut blight (Cryphonectria parasitica), since the early nineteenth century. Backcross breeding programs that transfer blight disease resistance from Chinese chestnut (C. mollissima) into American chestnut (C. dentata) offer promise for chestnut restoration, particularly for the American chestnut which was a keystone species in eastern North America. Nursery prescriptions and conformity to desired American chestnut traits following planting must be tested, however, before blight resistance can even be evaluated. We tested early field performance of American and Chinese chestnut and hybrid seedlings from the third backcross generation (e.g., BC3F3) in two-aged regeneration harvests on highly productive sites in the southern Appalachians, USA. We also tested a common nursery prescription of grading seedlings by size prior to planting. BC3F3 seedlings had similar 4-year survival to American chestnut seedlings, but generally had smaller stem heights and ground-line diameters (GLD). Although blight had not yet substantially challenged some sites, the BC3F3 seedlings had blight incidence similar to the Chinese chestnut which was lower than the American chestnut. Visual seedling grading affected planting shock and stem height and GLD by the end of year 4. Large size-class seedlings had more stem dieback and 5 % lower survival compared to small size-class seedlings, but larger trees exhibited the same height in year 3 as small trees in year 4. Advanced breeding material (BC3F3) was successfully established during the stand initiation phase of forest development on highly productive sites, but deviations in desired growth rate of the American chestnut was evident. Visual grading of seedlings affected establishment of breeding material, and should be considered in the restoration process. © 2015, Springer Science+Business Media Dordrecht (outside the USA).

Kubisiak T.L.,Southern Research Institute | Nelson C.D.,Southern Research Institute | Staton M.E.,Clemson University | Zhebentyayeva T.,Clemson University | And 9 more authors.
Tree Genetics and Genomes | Year: 2013

The Chinese chestnut (Castanea mollissima) carries resistance to Cryphonectria parasitica, the fungal pathogen inciting chestnut blight. The pathogen, introduced from Asia, devastated the American chestnut (Castanea dentata) throughout its native range early in the twentieth century. A highly informative genetic map of Chinese chestnut was constructed to extend genomic studies in the Fagaceae and to aid the introgression of Chinese chestnut blight resistance genes into American chestnut. Two mapping populations were established with three Chinese chestnut parents, 'Mahogany', 'Nanking', and 'Vanuxem', totaling 337 progeny. The transcriptome-based genetic map was created with 329 simple sequence repeat and 1,064 single nucleotide polymorphism markers all derived from expressed sequence tag sequences. Genetic maps for each parent were developed and combined to establish 12 consensus linkage groups spanning 742 cM, providing the the most comprehensive genetic map for a Fagaceae species to date. Over 75 % of the mapped markers from the Chinese chestnut consensus genetic map were placed on the physical map using overgo hybridization, providing a fully integrated genetic and physical map resource for Castanea spp. About half (57 %) of the Chinese chestnut genetic map could be assigned to regions of segmental homology with 58 % of the peach (Prunus persica) genome assembly. A three quantitative trait loci (QTL) model for blight resistance was verified using the new genetic markers and an existing interspecies (C. mollissima × C. dentata) F2 mapping population. Two of the blight resistance QTLs in chestnut shared synteny with two QTLs for powdery mildew resistance in peach, indicating the potential conservation of disease resistance genes at these loci. © 2012 The Author(s).

Saielli T.M.,University of Vermont | Schaberg P.G.,U.S. Department of Agriculture | Hawley G.J.,University of Vermont | Halman J.M.,University of Vermont | Gurney K.M.,The American Chestnut Foundation
Canadian Journal of Forest Research | Year: 2012

American chestnut (Castanea dentata (Marsh.) Borkh.) was functionally removed as a forest tree by chestnut blight (caused by the fungal pathogen Cryphonectria parasitica (Murr.) Barr). Hybrid-backcross breeding between blight-resistant Chinese chestnut (Castanea mollissima Blume) and American chestnut is used to support species restoration. However, preliminary evidence suggests that backcross material may not have the cold hardiness needed for restoration in the northern portions of the species' range. The cold tolerance of nuts is of concern because reproductive tissues are particularly sensitive to freezing damage. We assessed nut cold tolerance for 16 American chestnut, four Chinese chestnut, and four red oak (Quercus rubra L.) (a native competitor) sources to better assess genetic variation in nut hardiness. We found that Chinese chestnut nuts were less cold tolerant than American chestnut and red oak nuts and that American chestnut sources from the south were less cold tolerant than sources from the north, with significant differences among sources within all regions. We also assessed how sources varied among temperature zones (sources separated by average winter temperature lows at source locations). Sources from the cold temperature zone were more cold tolerant and less variable in hardiness than sources from warm and moderate zones.

Saielli T.M.,The American Chestnut Foundation | Schaberg P.G.,University of Vermont | Hawley G.J.,University of Vermont | Halman J.M.,University of Vermont | Gurney K.M.,The American Chestnut Foundation
Forest Science | Year: 2014

The backcross breeding of American chestnut (Castanea dentata [Marsh.] Borkh.) with Chinese chestnut (Castanea mollissima Blume) may provide an effective method to increase resistance against chestnut blight and help restore American chestnut throughout its historic range. However, the comparative adaptation (e.g., cold hardiness and growth) of American and Chinese chestnut source material in the north has been largely overlooked. We assessed first-year growth and shoot winter injury of 13 genetic sources of American chestnut and 2 sources each of Chinese chestnut and red oak (Quercus rubra L., a native competitor) under three silvicultural treatments (open, partial, and closed canopy overstories) in Vermont, USA. Seedlings grown under open canopies that provided greater access to light exhibited greater growth than seedlings grown under partial and closed canopies. However, open canopies also resulted in lower winter temperatures that increased winter injury. Chinese chestnut seedlings had significantly greater growth but experienced greater winter injury than American chestnuts, whereas red oaks generally grew the least and experienced intermediate levels of winter injury. There were also differences in growth and winter injury among American chestnut sources: seedlings from warm and moderate temperature zones (based on meteorological data recorded near source origins) grew more in height and diameter but experienced greater winter injury than seedlings from colder climates. © 2014 Society of American Foresters.

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