Genome mapping in trees We study the organization of genes and chromosomes in trees through genetic linkage mapping and molecular cytogenetics.  In collaboration with tree breeders, we are using such genetic maps to identify quantitative trait loci that govern growth, pest resistance, and wood quality in important forest tree species such as Douglas-fir, white spruce, chestnut, and northern red oak.

Molecular analysis of genetic diversity in forests
Genetic diversity among natural populations forms the foundation for biodiversity.  We use DNA markers in the nuclear, mitochondrial and chloroplast genomes to study genetic variability within and among populations of forest trees and associated wildlife.  We wish to better understand and conserve the various genetic mechanisms that species have evolved to adapt to their natural surroundings.

Christmas tree biotechnology
We are developing techniques for more efficiently propagating Christmas tree species such as Fraser fir, Douglas-fir, and Scotch pine.  This research may provide opportunities to develop new varieties with environmentally friendly resistance to insect pests and other stresses.

Environmental tree biotechnology
Research is being conducted on the molecular basis of lignin synthesis and the response of trees to environmental pollutants.  This may lead to improved genotypes of trees for environmentally friendly pulp and paper production and for use in remediation of contaminated soils.

Morse AM, Peterson dg, M. Islam-Faridi n, Smith KE, Garcia SA, Kubisiak TL, Amerson HV, Carlson JE, Nelson CD, Davis JM, 2009. Evolution of Genome Size and Complexity in Pinus. PLoS ONE 4(2): e4332.

Swanson J-D, Carlson JE, Guiltinan MJ. 2008. Flower development and floral gene expression in Theobroma cacao. International Journal of Plant Sciences, 169(9):1187–1199.

Frost CJ, Mescher MC, Dervinis C, Davis JM, Carlson JE, De Moraes CM. 2008. Priming defense genes and metabolites in hybrid poplar by the green leaf volatile cis-3-hexenyl acetate. New Phytologist, 180(3): 722-734.

Geib SM, Filley T, Hatcher P, Hoover K, Carlson J, del Mar Jimenez-Gasco M, Nakagawa-Izumi A, Sleighter R, Tien M. 2008. Lignin degradation in wood-feeding insects. Proc Natl Acad Sci USA 105(35): 12932 – 12937.

Liang H, Frost CJ, Wei X, Brown NR, Carlson JE, Tien M. 2008. A novel approach toward lignin modification to facilitate cellulosic ethanol production: introducing a tyrosine-rich cell wall peptide gene in poplar. Clean 36(8): 662-668.

Liang H, Carlson JE, Leebens-Mack JH, Wall PK, Mueller LA, BuzgoM, Landherr LL, Hu Y, DiLoreto DS, Ilut DC, Field D, Tanksley SD, Ma H, dePamphilis CW. 2008. An EST Database for Liriodendron tulipifera L. floral buds: the first EST resource for functional and comparative genomics in Liriodendron. Tree Genetics & Genomes 4(3): 419-433.

Soltis DE, Albert VA, Leebens-Mack J, Palmer J, Wing R, dePamphilis C, Ma H, Carlson JE, Altman N, Kim S, Wall PK, Zuccolo A, Soltis P. 2008. The Amborella Genome: An Evolutionary Reference for Plant Biology. Genome Biology 9:402, 6 pages.

Frost CJ, Mescher MC, Carlson JE, De Moraes CM. 2008. Plant defense priming against herbivores: getting ready for a different battle. Plant Physiology 146: 818–824.

Barakat A, Wall PK, DiLoreto S, dePamphilis CW, Carlson JE. 2007. Conservation and divergence of microRNAs in Populus. BMC Genomics 8:481.

Frost CJ, Appel HM, Carlson JE, DeMoraes C, Mescher MC, Schultz JC. 2007. Within-plant signaling via volatiles overcomes vascular constraints on systemic signaling and primes responses against herbivores. Ecology Letters 10(6): 490-498.

Gilbert MTP, Binladen J, Miller W, Wiuf C, Willerslev E, Poinar H, Carlson JE, Leebens-Mack JH, Schuster S. 2007. Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis. Nucleic Acids Research 35:1-10.

Liang H, Fang EG, Tomkins JP, Luo M, Kudrna D, Arumuganathan K, Zhao S, Schlarbaum SE, Banks JA, dePamphilis CW, Mandoli DF, Wing RA, Carlson JE. 2007. Development of a BAC library resource for yellow poplar (Liriodendron tulipifera) and the identification of genomic regions associated with flower development and lignin biosynthesis. Tree Genetics & Genomes 3(3): 215 - 225.

Cai Z, Penaflor C, Kuehl JV, Leebens-Mack J, Carlson J, dePamphilis CW, Boore JL, Jansen RK. 2006. Complete chloroplast genome sequences of Drimys, Liriodendron, and Piper: Implications for the phylogeny of magnoliids and the evolution of GC content. BMC Evolutionary Biology 6:77, 20 pp.

Tuskan GA, et al. 2006. The Genome of Western Black Cottonwood, Populus trichocarpa (Torr. & Gray ex Brayshaw). Science 313: 1596-1604. (Sept 15, 2006).

Cui L, Wall PK, Leebens-Mack JH, Lindsay BG, Soltis D, Doyle JJ, Soltis P, Carlson JE, Arumuganathan K, Barakat A, Albert V, Ma H, dePamphilis CW. 2006. Widespread genome duplications throughout the history of flowering plants. Genome Research 16: 738 - 749.

St. Clair S, Carlson JE, Lynch J. 2005. Evidence for Oxidative Stress in Sugar Maple Stands Growing on Acidic, Nutrient Imbalanced Forest Soils. Oecologia 145: 258 – 269.