@article{nifong_nicholson_shew_lewis_2011, title={Variability for Resistance to Phytophthora nicotianae Within a Collection of Nicotiana rustica Accessions}, volume={95}, ISSN={["1943-7692"]}, DOI={10.1094/pdis-11-10-0862}, abstractNote={ Black shank, caused by Phytophthora nicotianae, is one of the most important diseases affecting tobacco (Nicotiana tabacum) production worldwide. Many current tobacco cultivars possess immunity to race 0 of this pathogen conferred by introgressed dominant genetic factors. Novel alleles conditioning resistance to alternative races are desired. The objective of this research was to evaluate variability for black shank resistance within a collection of N. rustica germplasm using both soilborne disease nurseries and controlled race-specific (race 0 and race 1) inoculations. Nearly all of the 86 accessions studied exhibited very high resistance to race 0, and many displayed levels of race 1 resistance greater than that exhibited by the resistant flue-cured tobacco check, ‘K 346’. Materials found to be highly resistant to race 0 and race 1 in growth-chamber experiments also had the best survivability in field disease nurseries. N. rustica accessions TR 6, TR 12, TR 16, TR 21, TR 20, TR 48, TR 54, TR 57, and TR 69 could be sources of novel alleles with large effects on black shank resistance, and could have value for burley and flue-cured tobacco breeding. }, number={11}, journal={PLANT DISEASE}, author={Nifong, J. M. and Nicholson, J. S. and Shew, H. D. and Lewis, R. S.}, year={2011}, month={Nov}, pages={1443–1447} }
 @article{moon_nicholson_heineman_lion_hoeven_hayes_lewis_2009, title={Changes in Genetic Diversity of US Flue-Cured Tobacco Germplasm over Seven Decades of Cultivar Development}, volume={49}, ISSN={["1435-0653"]}, DOI={10.2135/cropsci2008.05.0253}, abstractNote={Plant breeding methodologies have been applied to flue‐cured tobacco (Nicotiana tabacum L.) for approximately seven decades. As has been observed in several other crops, stringent quality requirements have resulted in use of conservative breeding strategies in the development of new cultivars. The impact of breeding practices on genetic diversity within U.S. flue‐cured tobacco germplasm has not been investigated. In this study, we genotyped 117 tobacco cultivars from eight sequential time periods with 71 microsatellite primer pairs. A total of 294 alleles were scored. Only a fraction (48%) of alleles present in the initial germplasm pool was represented in cultivars released during the 1990s and 2000s. Only 13 and 18 alleles were detected in the 1990s and 2000s, respectively, which were undetected in the initial gene pool. The overall trend was one of gradual reduction in allelic counts at microsatellite loci, indicating a reduction in diversity over time at the gene level. Average genetic similarity was highest among cultivars of the 1990s and 2000s, reflecting a reduction in genetic diversity at the population level. This observed narrowing of the U.S. flue‐cured tobacco germplasm base in combination with low rates of genetic gain for yield in the last 20 years may point to a need for diversification of parental materials used in future breeding crosses. Reported genetic relationships among the group of genotyped cultivars may be valuable for future strategic germplasm choices.}, number={2}, journal={CROP SCIENCE}, author={Moon, H. S. and Nicholson, J. S. and Heineman, A. and Lion, K. and Hoeven, P. and Hayes, A. J. and Lewis, R. S.}, year={2009}, pages={498–508} }
 @article{breitschwerdt_maggi_nicholson_cherry_woods_2008, title={Bartonella sp. Bacteremia in Patients with Neurological and Neurocognitive Dysfunction}, volume={46}, ISSN={0095-1137}, url={http://dx.doi.org/10.1128/JCM.00832-08}, DOI={10.1128/JCM.00832-08}, abstractNote={ABSTRACT}, number={9}, journal={Journal of Clinical Microbiology}, publisher={American Society for Microbiology}, author={Breitschwerdt, E. B. and Maggi, R. G. and Nicholson, W. L. and Cherry, N. A. and Woods, C. W.}, year={2008}, month={Jul}, pages={2856–2861} }
 @article{elliott_lewis_shew_gutierrez_nicholson_2008, title={Evaluation of tobacco germplasm for seedling resistance to stem rot and target spot caused by Thanatephorus cucumeris}, volume={92}, ISSN={["0191-2917"]}, DOI={10.1094/PDIS-92-3-0425}, abstractNote={ Stem rot and target spot of tobacco, caused by Rhizoctonia solani and its teleomorph Thanatephorus cucumeris, respectively, can cause serious problems in production of tobacco (Nicotiana tabacum) seedlings. Previous screens for genetic resistance in tobacco have been limited. The objective of this study was to evaluate 97 genotypes composing several classes of tobacco and related Nicotiana spp. for seedling resistance to stem rot and target spot. Significant differences in disease incidence initially were observed among the genotypes for both stem rot and target spot; however, resistance to target spot was not observed when disease pressure was high. Partial resistance to stem rot was observed in several genotypes in repeated tests. These accessions may be useful as a source of resistance to R. solani in future breeding efforts. }, number={3}, journal={PLANT DISEASE}, author={Elliott, P. E. and Lewis, R. S. and Shew, H. D. and Gutierrez, W. A. and Nicholson, J. S.}, year={2008}, month={Mar}, pages={425–430} }
 @article{moon_nicholson_lewis_2008, title={Use of transferable Nicotiana tabacum L. microsatellite markers for investigating genetic diversity in the genus Nicotiana}, volume={51}, ISSN={["0831-2796"]}, DOI={10.1139/G08-039}, abstractNote={The recent development of microsatellite markers for tobacco, Nicotiana tabacum L., may be valuable for genetic studies within the genus Nicotiana . The first objective was to evaluate transferability of 100 N. tabacum microsatellite primer combinations to 5 diploid species closely related to tobacco. The number of primer combinations that amplified scorable bands in these species ranged from 42 to 56. Additional objectives were to assess levels of genetic diversity amongst available accessions of diploid relatives closely related to tobacco (species of sections Sylvestres and Tomentosae), and to evaluate the efficacy of microsatellite markers for establishing species relationships in comparison with existing phylogenetic reconstructions. A subset of 46 primer combinations was therefore used to genotype 3 synthetic tobaccos and an expanded collection of 51 Nicotiana accessions representing 15 species. The average genetic similarity for 7 diverse accessions of tobacco was greater than the average similarity for N. otophora accessions, but lower than the average genetic similarities for N. sylvestris , N. tomentosa , N. kawakamii , and N. tomentosiformis accessions. A microsatellite-based phylogenetic tree was largely congruent with taxonomic representations based on morphological, cytological, and molecular observations. Results will be useful for selection of parents for creation of diploid mapping populations and for germplasm introgression activities.}, number={8}, journal={GENOME}, author={Moon, H. S. and Nicholson, J. S. and Lewis, R. S.}, year={2008}, month={Aug}, pages={547–559} }
 @article{moon_nicholson_2007, title={AFLP and SCAR markers linked to Tomato spotted wilt virus resistance in tobacco}, volume={47}, ISSN={["1435-0653"]}, DOI={10.2135/cropsci2007.01.0002}, abstractNote={Tomato spotted wilt virus (TSWV) is a serious disease in tobacco (Nicotiana tabacum L.). The breeding line ‘Polalta’ contains a single dominant gene conferring resistance to TSWV that was introgressed from N. alata Link & Otto. The resistance is tightly associated with an abnormal plant type, however, and traditional backcrossing has been ineffective in producing normal plants with TSWV resistance. A potential strategy to overcome this problem is to use molecular markers to select against alien chromatin in backcross progeny. Amplified fragment length polymorphism (AFLP) technology and bulked segregant analysis were applied to identify markers linked to the resistance gene. The DNA bulks from susceptible and resistant doubled haploid lines derived from a cross between susceptible cultivar K326 and Polalta were analyzed to identify linked markers. An F2 population and the doubled haploids were used to construct a 2.5‐cM map of this locus containing 17 coupling phase and seven repulsion phase markers. By selecting for resistant plants with an improved plant type and marker profile in a BC3 population, four plants were identified that were missing 1 to 14 of the AFLP markers associated with the alien chromatin, demonstrating that rare recombination events can be identified. Four AFLP fragments were successfully converted to sequence characterized amplified region markers suitable for large‐scale screening. This approach may facilitate development of TSWV‐resistant tobacco cultivars.}, number={5}, journal={CROP SCIENCE}, author={Moon, H. and Nicholson, J. S.}, year={2007}, pages={1887–1894} }
 @article{azhakanandam_weissinger_nicholson_qu_weissinger_2007, title={Amplicon-plus Targeting Technology (APTT) for rapid production of a highly unstable vaccine protein in tobacco plants (vol 64, pg 619, 2007)}, volume={64}, ISSN={["0167-4412"]}, DOI={10.1007/s11103-007-9168-5}, number={5}, journal={PLANT MOLECULAR BIOLOGY}, author={Azhakanandam, Kasi and Weissinger, Sandra M. and Nicholson, Jennifer S. and Qu, Rongda and Weissinger, Arthur K.}, year={2007}, month={Jul}, pages={619–619} }
 @article{azhakanandam_weissinger_nicholson_qu_weissinger_2007, title={Amplicon-plus targeting technology (APTT) for rapid production of a highly unstable vaccine protein in tobacco plants}, volume={63}, DOI={10.1007/s11103-006-9096-9}, abstractNote={High-level expression of transgenes is essential for cost-effective production of valuable pharmaceutical proteins in plants. However, transgenic proteins often accumulate in plants at low levels. Low levels of protein accumulation can be caused by many factors including post-transcriptional gene silencing (PTGS) and/or rapid turnover of the transgenic proteins. We have developed an Amplicon-plus Targeting Technology (APTT), by using novel combination of known techniques that appears to overcome both of these factors. By using this technology, we have successfully expressed the highly-labile L1 protein of canine oral papillomavirus (COPV L1) by infecting transgenic tobacco plants expressing a suppressor of post-transcriptional gene silencing (PTGS) with a PVX amplicon carrying a gene encoding L1, and targeting the vaccine protein into the chloroplasts. Further, a scalable "wound-and-agrospray" inoculation method has been developed that will permit high-throughput Agrobacterium inoculation of Nicotiana tabacum, and a spray-only method (named "agrospray") for use with N. benthamiana to allow large-scale application of this technology. The good yield and short interval from inoculation to harvest characteristic of APTT, combined with the potential for high-throughput achieved by use of the agrospray inoculation protocol, make this system a very promising technology for producing high value recombinant proteins, especially those known to be highly labile, in plants for a wide range of applications including producing vaccines against rapidly evolving pathogens and for the rapid response needed to meet bio-defense emergencies.}, number={3}, journal={Plant Molecular Biology}, author={Azhakanandam, K. and Weissinger, S. M. and Nicholson, J. S. and Qu, R. D. and Weissinger, A. K.}, year={2007}, pages={393–404} }
 @article{lewis_nicholson_2007, title={Aspects of the evolution of Nicotiana tabacum L. and the status of the United States Nicotiana Germplasm Collection}, volume={54}, ISSN={["1573-5109"]}, DOI={10.1007/s10722-006-0024-2}, number={4}, journal={GENETIC RESOURCES AND CROP EVOLUTION}, author={Lewis, R. S. and Nicholson, J. S.}, year={2007}, month={Jun}, pages={727–740} }