Source: USDA Forest Service - Southern Research Station submitted to NRP
GENETICS AND GENOMICS OF FOREST TREES AND PESTS
Sponsoring Institution
Forest Service/USDA
Project Status
EXTENDED
Funding Source
USDA INHOUSE
Reporting Frequency
Annual
Accession No.
0413591
Grant No.
(N/A)
Cumulative Award Amt.
(N/A)
Proposal No.
(N/A)
Multistate No.
(N/A)
Project Start Date
Oct 1, 2009
Project End Date
Sep 30, 2022
Grant Year
(N/A)
Program Code
[(N/A)]- (N/A)
Recipient Organization
USDA Forest Service - Southern Research Station
200 WEAVER BLVD., PO BOX 2680
ASHEVILLE,NC 28804
Performing Department
(N/A)
Non Technical Summary
This project will study genes and their effects on traits that interact with other organisms and the environment. This work can lead to breakthroughs in our understanding of ecosystem structure and function and development of new genetic technologies for forest management.
Animal Health Component
30%
Research Effort Categories
Basic
70%
Applied
30%
Developmental
0%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2010611108045%
2010611116020%
2010621106020%
2010621108015%
Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
0621 - Broadleaf forests of the South; 0611 - Conifer forests of the South;

Field Of Science
1060 - Biology (whole systems); 1160 - Pathology; 1080 - Genetics;
Goals / Objectives
The overall objective is to elucidate genetic and structural genomics of forest trees and their pests with applications in evolutionary biology, forest management, and tree improvement. Specific objectives include: 1) Mapping the Genome and elucidating molecular cytogenetics of important forest tree species and their most damaging disease and insect pests; 2) Quantifying genetics of economic and ecologic traits, including mapping genes that regulate and control these traits; and 3) quantifying population genetics of important forest species, including those that are sensitive, threatened or endangered.
Project Methods
Continued areas of research will: develop genetic interaction models for resistance to important tree insects and diseases, to help scientists and land managers better understand and manage against losses to forest pests; develop genetic markers for forest tree species which pinpoint the genomic location of important insect and disease resistance genes, to help tree breeders more efficiently develop trees for long-term resistance; identify the DNA sequence of specific genes conferring insect and disease resistance in forest trees, to help scientists better understand the underlying metabolic pathways involved in pest defense responses; develop genetic markers that can be used to estimate virulence allele frequencies in natural populations of the fusiform rust fungus, to allow forest managers to predict the likely resistance of various families when planted under field conditions; evaluate genetic variation of resin yield in loblolly and longleaf pine populations, to provide tree breeders and forest health professionals a more complete picture of a likely southern pine beetle defense mechanism; model southern pine beetle outbreaks in clonal populations of loblolly pine, to provide information to forest managers about genetic diversity needed to manage risk of stand failure in clonal forestry; evaluate genetic variation for adaptive traits of longleaf pine, to provide scientists and land managers with increased knowledge of the speciesâ¿¿ biology and options for management; model escape of transgenes and their allele frequency behavior over generations, to obtain a better understanding of the impact that genetically modified organisms (GMOs) may have on native tree populations and forest ecosystems; provide federal and state land managers an assessment of current and predicted genetic population structures, levels of inbreeding, and patterns of gene flow for pondberry and other endangered forest species; provide southern tree breeding cooperatives data on how levels of diversity in first generation selections, as well as advanced generation selections, compare to those existing in natural populations, such information will help tree breeders assess and track the affects of small population breeding and help them select new trees that might be incorporated into their existing breeding programs; provide forest genetic and tree improvement colleagues with a DNA fingerprint kit that can be used to determine parentage, provenance, or population parameters of North American pines.

Progress 10/01/19 to 09/30/20

Outputs
OUTPUTS: - The reference genome for Castanea mollissima (Chinese chestnut) was finalized and published. C. mollissima is the source of disease resistance genes for C. dentata (American chestnut). The work was in collaboration with Penn State, the University of Tennessee and several others, including the American Chestnut Foundation (TACF). - An accurate detection/identification method was developed and published for the Fusarium decline pathogen (F. torreyae) of Torreya taxifolia (Florida torreya). T. taxifolia is a critically endangered conifer tree species native to a small area in the Apalachicola River valley in northern Florida and southwest Georgia. This work was a collaboration with the University of Florida and the Atlanta Botanical Garden. - A cyto-molecular characterization of Fraxinus mandshurica (Manshurian ash) and F. quadrangulata (blue ash) was completed and published. These two ash species are potential sources of resistance genes to the emerald ash borer (EAB). EAB is killing native ash trees in the US at an alarming rate. This work was in collaboration with the US Forest Service⿿s Northern Research Station. PARTICIPANTS: Project scientists include: C. Dana Nelson, Research Geneticist/Project Leader; Nurul Faridi, Research Cytogeneticist; Tyler Dreaden, Research Plant Pathologist. The project collaborates with many scientists and institutions across the southern and eastern US. During FY20, the project partially supported one ORISE fellow at Monticello, AR and one research associate at the University of Kentucky. TARGET AUDIENCES: - Chestnut genetics research targets the forest genetics, pathology and restoration communities in the US and elsewhere. We are providing basic information on the genetics and genomics of American and Chinese chestnuts for use in developing disease resistant American chestnuts and understanding how to deploy them across the landscape to effectively restore the species. The restoration community includes NGOs, such as the American chestnut Foundation, forest managers within federal and state land management agencies, private landowners and citizen scientists throughout the Appalachian region. - Torreya taxifolia research targets the forest genetics, pathology and restoration communities in the US and elsewhere. We are providing basic information on the genetics and ecology of T. taxifolia and the pathogen that is causing torreya decline (Fusarium torreyae). The restoration community includes NGOs, such as the Friends of Torreya State Park, the Atlanta Botanical Garden, federal and state natural resource agencies, private landowners and citizen scientists throughout the Apalachicola River basin. - Ash cytogenetics research targets the forest genetics and restoration community in the US and elsewhere. We are providing basic information of the cytogenetics of Fraxinus (ash) species for use in developing emerald ash borer resistant ash trees and populations for species restoration The restoration community includes NGOs,forest managers within federal and state land management agencies, private landowners and citizen scientists throughout North America. PROJECT MODIFICATIONS: No project modifications are required or anticipated at this point.

Impacts
- The reference genome for Castanea mollissima (Chinese chestnut) is an important resource for the chestnut genetics community in the US, Europe and Asia the species restoration effort in the US. The genome provides information on specific genes located in various parts of the genome including genes involved in reaction to pathogens causing chestnut blight and Phytophthora root rot. These diseases are responsible for the near complete elimination of American chestnut from the Appalachian forests of the US. - An accurate pathogen detection method is needed by plant propagators to ensure they are not spreading the pathogen with newly propagated T. torreya seedlings or cuttings. Propagation of multiple genotypes of T. torreya is needed to ensure the conservation of the species in the face of the Fusarium pathogen. - Cytogenetic information for ash species is needed by forest geneticists and trees breeders to facilitate the breeding of ash for developing resistance to the emerald ash borer. Species with similar cytogenetic features are more likely pair well in crossing to produce a full array of seedlings for resistance screening.

Publications

  • Anderson, Peter H.; Johnsen, Kurt H.; Butnor, John R.; Gonzalez-Benecke, Carlos A.; Samuelson, Lisa J. 2018. Predicting longleaf pine coarse root decomposition in the southeastern US. Forest Ecology and Management. 425: 1-8. https://doi.org/10.1016/j.foreco.2018.05.024.
  • Bain, John; Day, Frank; Butnor, John. 2017. Experimental evaluation of several key factors affecting root biomass estimation by 1500 MHz ground penetrating radar. Remote Sensing. 9(12): 1337-. https://doi.org/10.3390/rs9121337.
  • Butnor, John R.; Verrico, Brittany M.; Vankus, Victor; Keller, Stephen R. 2018. Ethanol exposure can inhibit red spruce (Picea rubens) seed germination. Seed Science and Technology, 46, 2, 259-265. 7 p.   https://doi.org/10.15258/sst.2018.46.2.07.
  • Butnor, John R; Verrico, Brittany M; Johnsen, Kurt H; Maier, Christopher A; Vankus, Victor; Keller, Stephen R. 2019. Phenotypic variation in climate-associated traits of red spruce (Picea rubens Sarg.) along elevation gradients in the southern Appalachian Mountains. Castanea 84(2):128⿿143.
  • Capblancq, Thibaut; Butnor, John R.; Deyoung, Sonia; Thibault, Ethan; Munson, Helena; Nelson, David M.; Fitzpatrick, Matthew C.; Keller, Stephen R. 2020. Whole⿐exome sequencing reveals a long⿐term decline in effective population size of red spruce ( Picea rubens ) . Evolutionary Applications. 19(1): 45-. https://doi.org/10.1111/eva.12985.
  • Condon, Bradford J.; Crocker, Ellen V.; Almsaeed, Abdullah; Abbott, Albert G.; Nelson, C. Dana; Staton, Margaret. 2019. TreeSnap: a citizen science tool to help our forests. In: Clark, Stacy L.; Schweitzer, Callie J., eds. Oak symposium: sustaining oak forests in the 21st century through science-based management. e-Gen. Tech. Rep. SRS-237. Asheville, NC: U.S. Department of Agriculture Forest Service, Southern Research Station: 176.
  • Conrad, Anna O; Crocker, Ellen V; Li, Xiaoshu; Thomas, William R; Ochuodho, Thomas O; Holmes, Thomas P; Nelson, C Dana. 2019. Threats to oaks in the eastern United States: Perceptions and expectations of experts. Journal of Forestry. 118(1): 14-27. https://doi.org/10.1093/jofore/fvz056.
  • Conrad, Anna O; Yu, Jiali; Staton, Margaret E; Audergon, Jean-Marc; Roch, Guillaume; Decroocq, Veronique; Knagge, Kevin; Chen, Huadong; Zhebentyayeva, Tetyana; Liu, Zongrang; Dardick, Christopher; Nelson, C Dana; Abbott, Albert G. 2019. Association of the phenylpropanoid pathway with dormancy and adaptive trait variation in apricot (Prunus armeniaca). Tree Physiology. 39(7): 1136-1148. https://doi.org/10.1093/treephys/tpz053.
  • Crocker, Ellen; Condon, Bradford; Almsaeed, Abdullah; Jarret, Benjamin; Nelson, C. Dana; Abbott, Albert G.; Main, Doreen; Staton, Margaret. 2020. TreeSnap: A citizen science app connecting tree enthusiasts and forest scientists. Plants, People, Planet. 2:47-52. https://doi.org/10.1002/ppp3.41.
  • Dreaden, Tyler; Hughes, Marc; Ploetz, Randy; Black, Adam; Smith, Jason. 2019. Genetic Analyses of the Laurel Wilt Pathogen, Raffaelea lauricola, in Asia Provide Clues on the Source of the Clone that is Responsible for the Current USA Epidemic. Forests. 10(1): 37-. https://doi.org/10.3390/f10010037.
  • Echt, Craig; Josserand, Sedley. 2018. DNA fingerprinting sets for four southern pines. e-Research Note SRS-24. Asheville, NC. : U.S. Department of Agriculture Forest Service, Southern Research Station. 11 p.
  • Islam-Faridi, Nurul; Mason, Mary E.; Koch, Jennifer L.; Nelson, C. Dana. 2020. Cytogenetics of Fraxinus mandshurica and F. quadrangulata: ploidy determination and rDNA analysis. Tree Genetics and Genomes 16(1): 26. 7 p. https://doi.org/10.1007/s11295-020-1418-6.
  • Islam-Faridi, Nurul; Sakhanokho, Hamidou F.; Nelson, C. Dana. 2020. New chromosome number and cyto-molecular characterization of the African Baobab (Adansonia digitata L.) - ⿿The Tree of Life⿝. Scientific Reports. 10(1): 155-. https://doi.org/10.1038/s41598-020-68697-6.
  • John R. Butnor, Kurt H. Johnsen, Robert Eaton,Thomas Christensen, and Chris A. Maier. 2018. Alternative collection methods for red spruce (Picea rubens) cones. In: Kirschman, Julia E., comp. Proceedings of the 19th biennial southern silvicultural research conference; 2017 March 14-16; Blacksburg, VA. e-Gen. Tech. Rep. SRS-234. Asheville, NC: U.S. Department of Agriculture, Forest Service, Southern Research Station, pp.410-412
  • Kim, Dohyoung; Medvigy, David; Maier, Chris A.; Johnsen, Kurt; Palmroth, Sari. 2020. Biomass increases attributed to both faster tree growth and altered allometric relationships under long⿐term carbon dioxide enrichment at a temperate forest. Global Change Biology. 26(4): 2519-2533. https://doi.org/10.1111/gcb.14971.
  • Kobziar, Leda N.; Pingree, Melissa R. A.; Watts, Adam C.; Nelson, Kellen N.; Dreaden, Tyler J.; Ridout, Mary. 2019. Accessing the life in smoke: A new application of unmanned aircraft systems (UAS) to sample wildland fire bioaerosol emissions and their environment. Fire. 2(4): 56-. https://doi.org/10.3390/fire2040056.
  • Li, Xiaoshu; Holmes, Thomas P.; Boyle, Kevin J.; Crocker, Ellen V.; Nelson, C. Dana. 2019. Hedonic analysis of forest pest invasion: the Case of emerald ash borer. Forests. 10(9): 820-. https://doi.org/10.3390/f10090820.
  • Müller, Markus; Nelson, C. Dana; Gailing, Oliver. 2018. Analysis of Environment-Marker Associations in American Chestnut. Forests. 9(11): 695-. https://doi.org/10.3390/f9110695.
  • Piculell, B.J., P.J. Martínez-García, C.D. Nelson, and J.D Hoeksema. 2018. Association mapping of ectomycorrhizal traits in loblolly pine (Pinus taeda). Molecular Ecology (accepted, pending revisions).
  • Sakhanokho, Hamidou F.; Islam-Faridi, Nurul; Babiker, Ebrahiem M.; Nelson, Charles D.; Stringer, Stephen J.; Adamczyk, John J. 2020. Determination of nuclear DNA content, ploidy, and FISH location of ribosomal DNA in Hibiscus hamabo. Scientia Horticulturae. 264: 109167-. https://doi.org/10.1016/j.scienta.2019.109167.
  • Sena, Kenton L.; Yang, Jian; Kohlbrand, Alysia J.; Dreaden, Tyler J.; Barton, Christopher D. 2019. Landscape variables influence Phytophthora cinnamomi distribution within a forested Kentucky watershed. Forest Ecology and Management. 436: 39-44. https://doi.org/10.1016/j.foreco.2019.01.008.
  • Sena, Kenton; Dreaden, Tyler J.; Crocker, Ellen; Barton, Chris. 2018. Detection of Phytophthora cinnamomi in forest soils by PCR on DNA extracted from leaf disc baits . Plant Health Progress. 19(3): 193-200. 8 p.  https://doi.org/10.1094/PHP-01-18-0004-RS.
  • Staton, Margaret; Addo-Quaye, Charles; Cannon, Nathaniel; Yu, Jiali; Zhebentyayeva, Tetyana; Huff, Matthew; Islam-Faridi, Nurul; Fan, Shenghua; Georgi, Laura L.; Nelson, C. Dana; Bellis, Emily; Fitzsimmons, Sara; Henry, Nathan; Drautz-Moses, Daniela; Noorai, Rooksana E.; Ficklin, Stephen; Saski, Christopher; Mandal, Mihir; Wagner, Tyler K.; Zembower, Nicole; Bodénès, Catherine; Holliday, Jason; Westbrook, Jared; Lasky, Jesse; Hebard, Frederick V.; Schuster, Stephan C.; Abbott, Albert G.; Carlson, John E. 2020. A reference genome assembly and adaptive trait analysis of Castanea mollissima ⿿Vanuxem,⿿ a source of resistance to chestnut blight in restoration breeding. Tree Genetics & Genomes. 16(4): 1392-. https://doi.org/10.1007/s11295-020-01454-y.
  • Zhebentyayeva, Tetyana N.; Sisco, Paul H.; Georgi, Laura L.; Jeffers, Steven N.; Perkins, M. Taylor; James, Joseph B.; Hebard, Frederick V.; Saski, Christopher; Nelson, C. Dana; Abbott, Albert G. 2019. Dissecting resistance to Phytophthora cinnamomi in interspecific hybrid chestnut crosses using sequence-based genotyping and QTL mapping . Phytopathology. : PHYTO-11-18-042-. https://doi.org/10.1094/PHYTO-11-18-0425-R.


Progress 10/01/16 to 09/30/17

Outputs
OUTPUTS: Amerson, Henry V.; Nelson, C. Dana; Kubisiak, Thomas L.; Kuhlman, E.George; Garcia, Saul 2015. Identification of nine pathotype-specific genes conferring resistance to fusiform rust in loblolly pine (Pinus taeda L.). Forests. 6(8): 2739-2761. 23 p. DOI: 10.3390/f6082739 Butnor, John R.; Samuelson, Lisa J.; Johnsen, Kurt H.; Anderson, Peter H.; Gonz??lez Benecke, Carlos A.; Boot, Claudia M.; Cotrufo, M. Francesca; Heckman, Katherine A.; Jackson, Jason A.; Stokes, Thomas A.; Zarnoch, Stanley J. 2017. Vertical distribution and persistence of soil organic carbon in fire-adapted longleaf pine forests. Forest Ecology and Management, Vol. 390: 12 pages.: 15-26. 10.1016/j.foreco.2017.01.014 Dalgleish, Harmony; Nelson, C.; Scrivani, John; Jacobs, Douglass 2015. Consequences of shifts in abundance and distribution of American chestnut for restoration of a foundation forest tree. Forests, Vol. 7(1): 4-. 9 p. doi:10.3390/f7010004 Gailing, Oliver; Nelson, C. Dana 2017. Genetic variation patterns of American chestnut populations at EST-SSRs. Botany. 95(8): 799-807. 9 p. https://doi.org/10.1139/cjb-2016-0323. Lu, Mengmeng; Krutovsky, Konstantin V.; Nelson, C. Dana; Koralewski, Tomasz E.; Byram, Thomas D.; Loopstra, Carol A. 2016.Exome genotyping, linkage disequilibrium and population structure in loblolly pine (Pinus taeda L.). BMC Genomics. 17(1): 421-. https://doi.org/10.1186/s12864-016-3081-8. Lu, Mengmeng; Krutovsky, Konstantin V.; Nelson, C. Dana; West, Jason B.; Reilly, Nathalie A.; Loopstra, Carol A. 2017. Association genetics of growth and adaptive traits in loblolly pine (Pinus taeda L.) using whole-exome-discovered polymorphisms. Tree Genetics & Genomes. 13(3): 199-216. 18 p. https://doi.org/10.1007/s11295-017-1140-1. Nelson, C. Dana; Boyd, Gwendolyn; Rousseau, Randall J.; Crane, Barbara S.; Echt, Craig S.; Johnsen, Kurt H. 2015. Participatory genetic improvement: longleaf pine. In Proceedings of the 17th biennial southern silvicultural research conference. e⿿Gen. Tech. Rep. SRS⿿203. Asheville, NC: U.S. Department of Agriculture, Forest Service, Southern Research Station. 4 p. Stewart, John F.; Will, Rodney E.; Crane, Barbara S.; Nelson, C. Dana 2016.The genetics of shortleaf pine (Pinus echinata mill.) with implications for restoration and management. Tree Genetics & Genomes. 12(5): 31-. https://doi.org/10.1007/s11295-016-1052-5. Stewart, John F.; Will, Rodney; Crane, Barbara S.; Nelson, C. Dana 2017.Occurrence of Shortleaf ÿ Loblolly Pine Hybrids in Shortleaf Pine Orchards: Implications for Ecosystem Restoration. Forest Science. 63(2): 225-231. https://doi.org/10.5849/forsci.15-167. Stewart, John F; Will, Rodney E; Robertson, Kevin M; Nelson, Dana 2014. Frequent fire protects shortleaf pine (Pinus echinata) from introgression by loblolly pine (P. taeda). Conservation Genetics October 2014. Springer Netherlands. 5 p. Westbrook, Jared W.; Chhatre, Vikram E.; Wu, Le-Shin; Chamala, Srikar; Neves, Leandro Gomide; Munoz,Patricio; Martinez-Garcia, Pedro J.; Neale,David B.; Kirst, Matias; Mockaitis, Keithanne; Nelson, C. Dana; Peter, Gary F.; Davis, John M.; Echt, Craig S. 2015 A consensus genetic map for Pinus taeda and Pinus elliottii and extent of linkage disequilibrium in two genotype-phenotype discovery populations of Pinua taeda. G3.Genes/Genomes/Genetics Vol 5.1685-1694 10 p. Will, Rodney E.; Lilly, Curtis J.; Stewart, John F.; Nelson, C. Dana; Taue, Charles G. 2015. Is there a morphological or physiological explanation for the dramatic increase in hybridization between loblolly and shortleaf pine?. In Proceedings of the 17th biennial southern silvicultural research conference. e⿿Gen. Tech. Rep. SRS⿿203. Asheville, NC: U.S. Department of Agriculture, Forest Service, Southern Research Station. 1 p.

Impacts
(N/A)

Publications

  • Amerson, Henry V.; Nelson, C. Dana; Kubisiak, Thomas L.; Kuhlman, E.George; Garcia, Saul 2015. Identification of nine pathotype-specific genes conferring resistance to fusiform rust in loblolly pine (Pinus taeda L.). Forests. 6(8): 2739-2761. 23 p. DOI: 10.3390/f6082739
  • Nelson, C. Dana; Boyd, Gwendolyn; Rousseau, Randall J.; Crane, Barbara S.; Echt, Craig S.; Johnsen, Kurt H. 2015. Participatory genetic improvement: longleaf pine. In Proceedings of the 17th biennial southern silvicultural research conference. e⿿Gen. Tech. Rep. SRS⿿203. Asheville, NC: U.S. Department of Agriculture, Forest Service, Southern Research Station. 4 p.
  • Stewart, John F.; Will, Rodney E.; Crane, Barbara S.; Nelson, C. Dana 2016.The genetics of shortleaf pine (Pinus echinata mill.) with implications for restoration and management. Tree Genetics & Genomes. 12(5): 31-. https://doi.org/10.1007/s11295-016-1052-5.
  • Stewart, John F.; Will, Rodney; Crane, Barbara S.; Nelson, C. Dana 2017.Occurrence of Shortleaf ÿ Loblolly Pine Hybrids in Shortleaf Pine Orchards: Implications for Ecosystem Restoration. Forest Science. 63(2): 225-231. https://doi.org/10.5849/forsci.15-167.
  • Stewart, John F; Will, Rodney E; Robertson, Kevin M; Nelson, Dana 2014. Frequent fire protects shortleaf pine (Pinus echinata) from introgression by loblolly pine (P. taeda). Conservation Genetics October 2014. Springer Netherlands. 5 p.
  • Westbrook, Jared W.; Chhatre, Vikram E.; Wu, Le-Shin; Chamala, Srikar; Neves, Leandro Gomide; Munoz,Patricio; Martinez-Garcia, Pedro J.; Neale,David B.; Kirst, Matias; Mockaitis, Keithanne; Nelson, C. Dana; Peter, Gary F.; Davis, John M.; Echt, Craig S. 2015 A consensus genetic map for Pinus taeda and Pinus elliottii and extent of linkage disequilibrium in two genotype-phenotype discovery populations of Pinua taeda. G3.Genes/Genomes/Genetics Vol 5.1685-1694 10 p.
  • Will, Rodney E.; Lilly, Curtis J.; Stewart, John F.; Nelson, C. Dana; Taue, Charles G. 2015. Is there a morphological or physiological explanation for the dramatic increase in hybridization between loblolly and shortleaf pine?. In Proceedings of the 17th biennial southern silvicultural research conference. e⿿Gen. Tech. Rep. SRS⿿203. Asheville, NC: U.S. Department of Agriculture, Forest Service, Southern Research Station. 1 p.
  • Butnor, John R.; Samuelson, Lisa J.; Johnsen, Kurt H.; Anderson, Peter H.; Gonz??lez Benecke, Carlos A.; Boot, Claudia M.; Cotrufo, M. Francesca; Heckman, Katherine A.; Jackson, Jason A.; Stokes, Thomas A.; Zarnoch, Stanley J. 2017. Vertical distribution and persistence of soil organic carbon in fire-adapted longleaf pine forests. Forest Ecology and Management, Vol. 390: 12 pages.: 15-26. 10.1016/j.foreco.2017.01.014
  • Dalgleish, Harmony; Nelson, C.; Scrivani, John; Jacobs, Douglass 2015. Consequences of shifts in abundance and distribution of American chestnut for restoration of a foundation forest tree. Forests, Vol. 7(1): 4-. 9 p.  doi:10.3390/f7010004
  • Gailing, Oliver; Nelson, C. Dana 2017. Genetic variation patterns of American chestnut populations at EST-SSRs. Botany. 95(8): 799-807. 9 p. https://doi.org/10.1139/cjb-2016-0323.
  • Lu, Mengmeng; Krutovsky, Konstantin V.; Nelson, C. Dana; Koralewski, Tomasz E.; Byram, Thomas D.; Loopstra, Carol A. 2016.Exome genotyping, linkage disequilibrium and population structure in loblolly pine (Pinus taeda L.). BMC Genomics. 17(1): 421-. https://doi.org/10.1186/s12864-016-3081-8.
  • Lu, Mengmeng; Krutovsky, Konstantin V.; Nelson, C. Dana; West, Jason B.; Reilly, Nathalie A.; Loopstra, Carol A. 2017. Association genetics of growth and adaptive traits in loblolly pine (Pinus taeda L.) using whole-exome-discovered polymorphisms. Tree Genetics & Genomes. 13(3): 199-216. 18 p.  https://doi.org/10.1007/s11295-017-1140-1.


Progress 10/01/13 to 09/30/14

Outputs
OUTPUTS: Research in this problem area was focused in three major areas: pine genomics with genetic mapping, cytogenetics of chestnut, population genetics applied to conservation issues, and genetics of host-pest interaction. A comprehensive, fully gene-annotated genetic map was developed for loblolly pine. This is the first such map for a pine species and should prove valuable for our continuing efforts in fully characterizing the pine genome. An important problem in inter-species hybridization of chestnut was investigated revealing structural differences between the American and Chinese chestnut. Implications for these differences to the backcross breeding program are being explored. Population structure of the true firs of the eastern U.S. were studied with microsatellite DNA markers revealing differentiation among populations but no clear differences between species. Genetic interactions of disease and insect interactions were studied including fusiform rust on loblolly pine, chestnut blight and ink disease in chestnut and beech bark scale in American beech. PARTICIPANTS: Northern Research Station, NC State University, University of Florida, Mississippi State University, The Citadel, Clemson University, Texas A&M University, The American Chestnut Foundation TARGET AUDIENCES: Forest managers, tree breeders, climate change modelers, research community

Impacts
Research results were published that: 1) provided cytogenetic evidence for structural differences at the rDNA sites between American and Chinese chestnuts; 2) summarized our successful research approach for dissecting the gene-gene interaction in the fusiform rust pathosystem; 3) quantified the genetic variation in American beech to beech bark scale infestation; 4) discussed the social context for renewed public investment in plant and tree breeding; 5) quantified the genetic differentiation between true fir populations sampled across the range of balsam fir and its related species.

Publications

  • Nelson, C.D., Powell, W.A., Maynard, C.A., Baier, K.M., Newhouse, A., Merkle, S.A., Nairn, C.J., Kong, L., Carlson, J.E., Addo-Quaye, C., Staton, M.E., Hebard, F.V., Georgi, L.L., Abbott, A.G., Olukolu, B.A., and Zhebentyayeva, T. (2013) The Forest Health Initiative, American chestnut (Castanea dentata) as a model for forest tree restoration: Biological Research Program. Acta Hort 1019:179-189. (refereed)
  • Nelson, C.D., W.A. Powell, S.A. Merkle, J.E. Carlson, F.V. Hebard, N. Islam-Faridi, M.E. Staton, L. Georgi. 2014. Chestnut. In: K. Ramawat, editor, Tree Biotechnology, Chapter 1, CRC Press, pp. 3-35 (April 2014). Nelson was invited to lead the preparation of this chapter by co-author Powell and the Book Editor.
  • Pendleton, A.L., Smith, K.E., Feau, N., Martin, F.M., Grigoriev, I.V., Hamelin, R., Nelson, C.D., Burleigh, J.G., Davis, J.M. 2014. Duplications and losses in gene families of rust pathogens highlight putative effectors. Frontiers in Plant Science 5:(299), 1-13.
  • Quesada, Tania, M.F.R. Resende Jr., P. Muñoz, J.L. Wegrzyn, D.B. Neale, M. Kirst, G.F. Peter, S.A. Gezan, C.D. Nelson, J.M. Davis. 2014. Mapping fusiform rust resistance genes within a complex mating design of loblolly pine. Forests (in press).
  • Sakhanokho, H. F., M. N. Islam-Faridi, E. K. Blythe, B. J. Smith, K. Rajasekaran, and MA Majid. 2014. Morphological and cytomolecular assessment of intraspecific variability in scarlet eggplant (Solanum aethiopicum L.). J. Crop Improv. 28:437-445.
  • Westbrook, J.W., M.F.R. Resende Jr., P. Munoz, A.R. Walker, D.B. Neale, J.L. Wegrzyn, C.D. Nelson, M. Kirst, D.A. Huber, S.A. Gezan, G.F. Peter, J.M. Davis. 2013. Association genetics of oleoresin flow in loblolly pine: discovering genes and predicting phenotype for improved resistance to bark beetles and bioenergy potential, New Phytologist 199:89-100.
  • Zhebentyayeva, T., Chandra, A., Abbott, A.G., Staton, M.E., Olukolu, B.A., Hebard, F.V., Georgi, L.L., Jeffers, S.N., Sisco, P.H., James, J.B., and Nelson, C.D. 2013. Genetic and genomic resources for mapping resistance to Phytophthora cinnamomi in chestnut. Acta Hort 1019:263-270.
  • Zhixin Zhao; Cheng Guo; Sreeskandarajan Sutharzan; Pei Li; Craig S. Echt; Jie Zhang; Chun Liang (2014 Genome-wide analysis of tandem repeats in plants and green algae. G3 - Genes, Genomes, Genetics, 4:67-78, doi:10.1534/g3.113.008524, http://www.g3journal.org/content/4/1/67.full.pdf+html
  • Bartlett, B.D., J.H. Roberds, J.A. Smith, D.G. Peterson, C.D. Nelson. 2014. TOWARDS A GENOME SEQUENCE OF THE BROWN SPOT NEEDLE BLIGHT PATHOGEN (Mycosphaerella dearnessii) INFECTING LONGLEAF PINE. In: Cunningham, M.W. (ed) Proceedings 32nd Southern Forest Tree Improvement Conference, 10-13 June 2013, Clemson, SC, pp. 12-14.
  • Chhatre VE, Resende MFR, Munoz P, Peter GF, Davis JM, Kirst MM, Echt CS, Krutovsky KV, and Nelson CD (2013). Multiple pedigrees allow construction of a densely populated reference linkage map in loblolly pine (Pinus taeda L.). Southern Forest Tree Improvement Conference, June 10, 2013, Clemson University, Clemson, SC, pp. 53.
  • Chhatre, VE (2013). Population structure, association mapping of economic traits and landscape genomics of east Texas loblolly pine (Pinus taeda L.) Doctoral Dissertation, Texas A&M University, May 2013.
  • Georgi, L.L., F.V. Hebard, M.E. Staton, B.A. Olukolu, AG. Abbott, C.D. Nelson. 2013. Adapting Chestnut Single Nucleotide Polymorphisms for Use in Breeding. Acta Hort 1019:105-112.
  • Keith Batesole; Kokulapalan Wimalanathan; Lin Liu; Fan Zhang; Craig Echt; Chun Liang 2014. YouGenMap: A web service for dynamic multi-comparative mapping and visualization of genetic maps. Front. Genet., 5:183, doi: 10.3389/fgene.2014.00183.
  • Nelson, C. D. and Roberds, J. H. 2013. Harrison Experimental Forest. p. 265 In: Long-term trends in ecological systems: A basis for understanding responses to global change. Peters, D.P.C., Laney, C. M., Collins S. L. , Driscoll, C. T., Groffman, P. M., Grove, J. M., Knapp, A. K., Kratz, T. K., Ohman, M. D. Waide, R. B., and Yao, J. Agricultural Research Service Technical Bulletin No. 1931.
  • Nelson, C.D., G.F. Peter, S.E. McKeand, E.J. Jokela, R.B. Rummer, L.H. Groom, and K.H. Johnsen. 2013. Pines. P. 427-459, In: B.P. Singh, editor, Biofuel Crops: Production, Physiology and Genetics, Chapter 20, CABI


Progress 10/01/12 to 09/30/13

Outputs
OUTPUTS: Research in this problem area was focused in three major areas: pine genomics with genetic mapping, cytogenetics of chestnut, population genetics applied to conservation issues, and genetics of host-pest interaction. A comprehensive, fully gene-annotated genetic map was developed for loblolly pine. This is the first such map for a pine species and should prove valuable for our continuing efforts in fully characterizing the pine genome. An important problem in inter-species hybridization of chestnut was investigated revealing structural differences between the American and Chinese chestnut. Implications for these differences to the backcross breeding program are being explored. Population structure of the true firs of the eastern U.S. were studied with microsatellite DNA markers revealing differentiation among populations but no clear differences between species. Genetic interactions of disease and insect interactions were studied including fusiform rust on loblolly pine, chestnut blight and ink disease in chestnut and beech bark scale in American beech. PARTICIPANTS: Northern Research Station, NC State University, University of Florida, Mississippi State University, The Citadel, Clemson University, Texas A&M University, The American Chestnut Foundation TARGET AUDIENCES: Forest managers, tree breeders, climate change modelers, research community

Impacts
Research results were published that: 1) provided cytogenetic evidence for structural differences at the rDNA sites between American and Chinese chestnuts; 2) summarized our successful research approach for dissecting the gene-gene interaction in the fusiform rust pathosystem; 3) quantified the genetic variation in American beech to beech bark scale infestation; 4) discussed the social context for renewed public investment in plant and tree breeding; 5) quantified the genetic differentiation between true fir populations sampled across the range of balsam fir and its related species.

Publications

  • Nelson, C. Dana; Peter, Gary F.; McKeand, Steven E.; Jokela, Eric J.; Rummer, Robert B.; Groom, Leslie H.; and Johnsen, Kurt H. 2013. Pines. In: B.P. Singh, editor, Biofuel Crops: Production, Physiology and Genetics, Chapter 20, CABI Wallingford, UK. pp. 427-459.


Progress 10/01/09 to 09/30/10

Outputs
OUTPUTS: Research in this problem area was focused in three major areas: pine genomics with genetic mapping, cytogenetics of chestnut, population genetics applied to conservation issues, and genetics of host-pest interaction. A comprehensive, fully gene-annotated genetic map was developed for loblolly pine. This is the first such map for a pine species and should prove valuable for our continuing efforts in fully characterizing the pine genome. An important problem in inter-species hybridization of chestnut was investigated revealing structural differences between the American and Chinese chestnut. Implications for these differences to the backcross breeding program are being explored. Population structure of the true firs of the eastern U.S. were studied with microsatellite DNA markers revealing differentiation among populations but no clear differences between species. Genetic interactions of disease and insect interactions were studied including fusiform rust on loblolly pine, chestnut blight and ink disease in chestnut and beech bark scale in American beech. PARTICIPANTS: Northern Research Station, NC State University, University of Florida, Mississippi State University, The Citadel, Clemson University, Texas A&M University, The American Chestnut Foundation TARGET AUDIENCES: Forest managers, tree breeders, climate change modelers, research community

Impacts
Research results were published that: 1) provided cytogenetic evidence for structural differences at the rDNA sites between American and Chinese chestnuts; 2) summarized our successful research approach for dissecting the gene-gene interaction in the fusiform rust pathosystem; 3) quantified the genetic variation in American beech to beech bark scale infestation; 4) discussed the social context for renewed public investment in plant and tree breeding; 5) quantified the genetic differentiation between true fir populations sampled across the range of balsam fir and its related species.

Publications

  • Barakat, A; Carlson, J; Staton, M; Kubisiak, T; Smith, C; DiLoreto, S; Baier, K; Atkins, M; Blackmon, B; Ficklin, S; Hebard, F; Sisco, P; Powell, W; Anahnostakis, S; Nielsen, D; Abbott, A; Wheeler, N; Sederoff, R 2010. Analyses of the transcriptome of the Fagaceae species..
  • Carlson, J.E.; Abbott, A.G.; Anagnostakis, S.; Baier, K; Barakat, A; James, J.B.; Islam-Faridi, N; Ficklin, S; Hebard, F; Kubisiak, T; Maynard, C; Merkel, S.M.; Miller, W; Nairn, C.J.; Powell, W; Schuster, S.C.; Tomsho, L.P.; Wagner, T.K.; Nelson, C.D. 2010. Forest Health Initiative for American chestnut restoration.. Proceedings of Plant and Aniimal Genome XVIII Meeting, San Diego, CA: p523-null.
  • Koch, Jennifer L.; Carey, David W.; Mason, Mary E.; Nelson, C. Dana 2010. Assessment of beech scale resistance in full- and half-sibling American beech families. Canadian Journal of Forest Research 40:265-272.
  • Kubisiak, T.L.; Anderson, C; Amerson, H; Smith, J; Davis, J; Nelson, C.D. 2010. Genetic and genomic resources for the fusiform rust fungus Cronartiium quercuum f.sp.fusiforme (Cqf).. Fourth IUFRO International Rusts of Forest Trees Working Pry Conference, May 3-6, 2010, Florence, Italy.: 17-17.
  • Nelson, CD; Kubisiak, TL; Amerson, HV 2010. Unravelling and managing fusiform rust disease: a model approach for coevolved forest tree pathosystems. Forest Pathology 40:64-72.
  • Potter, Kevin M.; Frampton, John; Josserand, Sedley A.; Nelson, C. Dana 2010. Evolutionary history of two endemic Appalachian conifers revealed using microsatellite markers. Conserv Genet 11:1499-1513.
  • Sederoff, R; Wheeler, N; Carlson, J; Barakat, A; Powell, W; Baier, K; Kubisiak, T; Sisco, P; Hebard, F; Anagnostakis, S.L.; Tomkins, J; Abbott, A; Staton, M; Smith, C; Nielsen, D; Ficklin, S 2010. A genome platform for chestnut.. Proceedings of Plant and Animal Genome XVIII meeting, San Diego, CAlifornia, January 9-13, 2010: 253-null.
  • Sisco, P.H.; Sederoff, R.R.; Tompkins, J.P.; Carlson, J.E.; Kubisiak, T.L.; Staton, M.E.; Hebard, F.V.; Anagnostakis, S.L.; Powell, W.A.; Smith, C.P. 2010. The United States National Science foundation project on developing tools for the study of the Fagaceae:castanea, Quercus, and Fagus.. Acta Hort. (ISHS) , Vol. 844: 8 pages.: 267-274.
  • Woeste, KE; Blanche, SB; Moldenhauer, KA; Nelson, CD 2010. Plant breeding and rural development in the United States. Crop Science 50:1-8.