@article{shi_hubert_dexter-boone_zeng_kernodle_lewis_2019, title={Identification and validation of SNP markers associated with Wz-mediated Phytophthora nicotianae resistance in Nicotiana tabacum L.}, volume={39}, ISSN={["1572-9788"]}, DOI={10.1007/s11032-019-1015-2}, number={7}, journal={MOLECULAR BREEDING}, author={Shi, Rui and Hubert, Hannah and Dexter-Boone, Abigail and Zeng, Jianmin and Kernodle, Sheri P. and Lewis, Ramsey S.}, year={2019}, month={Jul} }
 @article{edwards_fernandez-pozo_drake-stowe_humphry_evans_bombarely_allen_hurst_white_kernodle_et al._2017, title={A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency}, volume={18}, ISSN={["1471-2164"]}, DOI={10.1186/s12864-017-3791-6}, abstractNote={Tobacco (Nicotiana tabacum) is an important plant model system that has played a key role in the early development of molecular plant biology. The tobacco genome is large and its characterisation challenging because it is an allotetraploid, likely arising from hybridisation between diploid N. sylvestris and N. tomentosiformis ancestors. A draft assembly was recently published for N. tabacum, but because of the aforementioned genome complexities it was of limited utility due to a high level of fragmentation.Here we report an improved tobacco genome assembly, which, aided by the application of optical mapping, achieves an N50 size of 2.17 Mb and enables anchoring of 64% of the genome to pseudomolecules; a significant increase from the previous value of 19%. We use this assembly to identify two homeologous genes that explain the differentiation of the burley tobacco market class, with potential for greater understanding of Nitrogen Utilization Efficiency and Nitrogen Use Efficiency in plants; an important trait for future sustainability of agricultural production.Development of an improved genome assembly for N. tabacum enables what we believe to be the first successful map-based gene discovery for the species, and demonstrates the value of an improved assembly for future research in this model and commercially-important species.}, journal={BMC GENOMICS}, author={Edwards, K. D. and Fernandez-Pozo, N. and Drake-Stowe, K. and Humphry, M. and Evans, A. D. and Bombarely, A. and Allen, F. and Hurst, R. and White, B. and Kernodle, S. P. and et al.}, year={2017}, month={Jun} }
 @article{steede_ma_eickholt_drake-stowe_kernodle_shew_danehower_lewis_2017, title={The Tobacco Trichome Exudate Z-abienol and Its Relationship With Plant Resistance to Phytophthora nicotianae}, volume={101}, ISSN={["1943-7692"]}, DOI={10.1094/pdis-10-16-1512-re}, abstractNote={ In previous research, we discovered a favorable quantitative trait locus (QTL) in cigar tobacco cultivar ‘Beinhart 1000’ designated as Phn15.1, which provides a high level of partial resistance to the black shank disease caused by Phytophthora nicotianae. A very close genetic association was also found between Phn15.1 and the ability to biosynthesize Z-abienol, a labdanoid diterpene exuded by the trichomes onto above-ground plant parts, and that imparts flavor and aroma characteristics to Oriental and some cigar tobacco types. Because accumulation of Z-abienol is considered to be undesirable for cultivars of other tobacco types, we herein describe a series of experiments to gain insight on whether this close association is due to genetic linkage or pleiotropy. First, in an in vitro bioassay, we observed Z-abienol and related diterpenes to inhibit hyphal growth of P. nicotianae at concentrations between 0.01 and 100 ppm. Secondly, we field-tested transgenic versions of Beinhart 1000 carrying RNAi constructs for downregulating NtCPS2 or NtABS, two genes involved in the biosynthesis of Z-abienol. Thirdly, we also field tested a recombinant inbred line population segregating for a truncation mutation in NtCPS2 leading to an interrupted Z-abienol pathway. We observed no correlation between field resistance to P. nicotianae and the ability to accumulate Z-abienol in either the transgenic materials or the mapping population. Results suggest that, although Z-abienol may affect P. nicotianae when applied at high concentrations in in vitro assays, the compound has little effect on black shank disease development under natural field conditions. Thus, it should be possible to disassociate Phn15.1-mediated black shank resistance identified in cigar tobacco cultivar Beinhart 1000 from the ability to accumulate Z-abienol, an undesirable secondary metabolite for burley and flue-cured tobacco cultivars. }, number={7}, journal={PLANT DISEASE}, author={Steede, William T. and Ma, Justin M. and Eickholt, David P. and Drake-Stowe, Katherine E. and Kernodle, Sheri P. and Shew, H. David and Danehower, David A. and Lewis, Ramsey S.}, year={2017}, month={Jul}, pages={1214–1221} }
 @article{hancock_kuraparthy_kernodle_lewis_2015, title={Identification of maternal haploids of Nicotiana tabacum aided by transgenic expression of green fluorescent protein: evidence for chromosome elimination in the N-tabacum x N-africana interspecific cross}, volume={35}, ISSN={["1572-9788"]}, DOI={10.1007/s11032-015-0372-8}, number={9}, journal={MOLECULAR BREEDING}, author={Hancock, Wesley G. and Kuraparthy, Vasu and Kernodle, Sheri P. and Lewis, Ramsey S.}, year={2015}, month={Sep} }
 @article{lewis_kernodle_2009, title={A method for accelerated trait conversion in plant breeding}, volume={118}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-009-0998-1}, abstractNote={Backcrossing is often used in cultivar development to transfer one or a few genes to desired genetic backgrounds. The duration necessary to complete such 'trait conversions' is largely dependent upon generation times. Constitutive overexpression of the Arabidopsis thaliana gene FT (FLOWERING LOCUS T) induces early-flowering in many plants. Here, we used tobacco (Nicotiana tabacum L.) as a model system to propose and examine aspects of a modified backcross procedure where transgenic FT overexpression is used to reduce generation time and accelerate gene transfer. In this method, the breeder would select for an FT transgene insertion and the trait(s) of interest at each backcross generation except the last. In the final generation, selection would be conducted for the trait(s) of interest, but against FT, to generate the backcross-derived trait conversion. We demonstrate here that constitutive FT overexpression functions to dramatically reduce days-to-flower similarly in diverse tobacco genetic backgrounds. FT-containing plants flowered in an average of 39 days, in comparison with 87-138 days for non-FT plants. Two FT transgene insertions were found to segregate independently of several disease resistance genes often the focus of backcrossing in tobacco. In addition, no undesirable epigenetic effects on flowering time were observed once FT was segregated away. The proposed system would reduce the time required to complete a trait conversion in tobacco by nearly one-half. These features suggest the possible value of this modified backcrossing system for tobacco or other crop species where long generation times or photoperiod sensitivity may impede timely trait conversion.}, number={8}, journal={THEORETICAL AND APPLIED GENETICS}, author={Lewis, Ramsey S. and Kernodle, S. P.}, year={2009}, month={May}, pages={1499–1508} }
 @article{lewis_milla_kernodle_2007, title={Analysis of an introgressed Nicotiana tomentosa genomic region affecting leaf number and correlated traits in Nicotiana tabacum}, volume={114}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-006-0482-0}, abstractNote={Germplasm from closely related diploid relatives of tobacco (Nicotiana tabacum L.) could be of value for continued genetic modification of this species and for mapping quantitative trait loci (QTLs). We examined near isogenic tobacco lines and hybrids differing for an introgressed genomic region from N. tomentosa Ruiz and Pavon designated as Many Leaves that exhibits a large influence on leaf number and correlated traits. Within a 'Red Russian' genetic background, the region acted in an additive to partially dominant fashion to delay flowering time, and increase leaf number, plant height, and green leaf yield. Evidence of epistasis was observed as the region affected these traits to varying degrees in diverse near isogenic hybrids. Fifteen amplified fragment length polymorphism (AFLP) markers of N. tomentosa origin were mapped within a single linkage group of 34.5 cM using a population of 207 BC(1)F(1) individuals segregating for Many Leaves. Composite interval mapping produced 2-LOD confidence intervals for likely QTL positions influencing leaf number (3.1 cM region), plant height (2.9 cM region), and days to flowering (3.3 cM region). These intervals were overlapping. Results demonstrate that genomic regions with large genetic effects can be transferred to tobacco from closely related diploid relatives, and that sufficient recombination within these regions may permit mapping of genes controlling quantitative traits. Materials and results described here may be useful in future research to gain insight on the genetic control of the transition from vegetative to reproductive development in Nicotiana.}, number={5}, journal={THEORETICAL AND APPLIED GENETICS}, publisher={Springer Science \mathplus Business Media}, author={Lewis, R. S. and Milla, S. R. and Kernodle, S. P.}, year={2007}, month={Mar}, pages={841–854} }
 @article{eifert_curtis_bazaco_meinersmann_berrang_kernodle_stam_jaykus_kathariou_2005, title={Molecular characterization of Listeria monocytogenes of the serotype 4b complex (4b, 4d, 4e) from two turkey processing plants}, volume={2}, ISSN={["1556-7125"]}, DOI={10.1089/fpd.2005.2.192}, abstractNote={Most foodborne outbreaks of listeriosis have been found to involve a small number of closely related strains of Listeria monocytogenes serotype 4b. The ecology of these organisms and their reservoirs in nature or in the processing plant environment, however, remain poorly understood. Surveys of environmental samples from two turkey processing plants in the United States indicated presence of L. monocytogenes of the serotype 4b complex (serotype 4b and the closely related serotypes 4d and 4e). In addition, environmental and raw product samples from one plant repeatedly yielded isolates with genetic markers typical of two major serotype 4b epidemic clonal groups, ECI and ECII. The pulsed field gel electrophoresis (PFGE) profiles of these isolates, however, were clearly distinct from those of confirmed epidemic-associated strains. Furthermore, we observed minor but consistent differences in PFGE profiles of isolates that harbored ECI- or ECII-specific genetic markers, and that were obtained at different sampling times from the same plant. The findings suggest processing plant persistence (or repeated introductions) and genomic diversification of L. monocytogenes serotype 4b isolates that harbor ECI- or ECII-specific genetic markers. Such diversification would need to be taken into consideration in further efforts to elucidate the evolution and epidemiology of these organisms.}, number={3}, journal={FOODBORNE PATHOGENS AND DISEASE}, author={Eifert, J. D. and Curtis, P. A. and Bazaco, M. C. and Meinersmann, R. J. and Berrang, M. E. and Kernodle, S. and Stam, C. and Jaykus, L. -A. and Kathariou, S.}, year={2005}, pages={192–200} }
 @article{menezes-benavente_kernodle_margis-pinheiro_scandalios_2004, title={Salt-induced antioxidant metabolism defenses in maize (Zea mays L.) seedlings}, volume={9}, ISSN={["1743-2928"]}, DOI={10.1179/135100004225003888}, abstractNote={Abstract Salinity alters general metabolic processes and enzymatic activities, causing increased production of reactive oxygen species (ROS). Expression of antioxidant defense genes would, in turn, be triggered to defend the cell against oxidative damage. We report that salt disturbed antioxidant metabolism in maize seedlings, causing detrimental effects on the growth and development of maize plantlets, increased hydrogen peroxide production and altered antioxidant activities and transcripts profiles. Excessive ROS levels were accompanied by increased catalase (CAT) activity in photosynthesizing shoots, along with induction of mRNA accumulation. Increased accumulation of superoxide dismutase (SOD) transcripts was also observed although no significant changes in total SOD enzymatic activity and isozyme profiles were detected. Higher salt concentrations (above 0.25 M NaCl) were highly detrimental to the plants, causing arrested growth and severe wilting, among other effects. Histochemical detection of H2O2 by 3,3-diaminobenzidine (DAB) staining indicated a collapse of the leaf veins, with hydrogen peroxide leaking to neighboring cells. In agreement to these observations, Sod1, Sod2, Sod4, Sod4A, as well as all Cat transcripts were severely inhibited in plants exposed to high salt concentrations.}, number={1}, journal={REDOX REPORT}, author={Menezes-Benavente, L and Kernodle, SP and Margis-Pinheiro, M and Scandalios, JG}, year={2004}, pages={29–36} }
 @article{jung_kernodle_scandalios_2001, title={Differential antioxidant responses to norflurazon-induced oxidative stress in maize}, volume={6}, ISSN={["1743-2928"]}, DOI={10.1179/135100001101536454}, abstractNote={Abstract This study examined the contribution of catalase (CAT) and superoxide dismutase (SOD) in the overall antioxidant response to norflurazon (NF)-induced oxidative stress in leaves, mesocotyls and scutella of maize (Zea mays). Maize catalase null mutants were used to provide insights into the role(s) of these isozymes. A substantial increase in Cat1 and Cat2 transcript levels occurred in NF-treated leaves in all maize lines examined. However, these two transcripts did not show a particular pattern of change in NF-treated scutella from 5-day postimbibition (dpi) and 18-day postpollination (dpp) maize. The NF-induced increase in Cat1 appeared to be dependent on excessive light energy caused by a lack of photoprotectant carotenoids, especially in leaves. In NF-treated leaves, the chloroplastic Cu/Zn-SOD-1 isozyme responded strongly compared to the cytosolic Cu/Zn-SOD and mitochondrial Mn-SOD-3 isozymes, suggesting the critical role of SOD-1 as a major component in chloroplastic antioxidant defenses. All SOD isozymes in the NF-treated scutella of various maize lines were consistent in their response to NF. The most significant increase was observed with Sod1 in NF-treated leaves; however, no significant Sod1 changes were observed in similarly treated scutella at 5 dpi and 18 dpp. These results suggest that the response of the Cat and Sod genes to NF is likely developmental and tissue-specific.}, number={5}, journal={REDOX REPORT}, author={Jung, S and Kernodle, SP and Scandalios, JG}, year={2001}, pages={311–317} }
 @article{kernodle_scandalios_2001, title={Structural organization, regulation, and expression of the chloroplastic superoxide dismutase Sod1 gene in maize}, volume={391}, ISSN={["1096-0384"]}, DOI={10.1006/abbi.2001.2397}, abstractNote={A cDNA and genomic clone encoding maize chloroplastic Cu/Zn superoxide dismutase Sod1 were isolated. Southern blot analysis indicated little homology between the chloroplastic (Sod1) and the cytosolic (Sod2, Sod4, Sod4A) cDNAs. Sequence analysis of the genomic clone revealed a promoter, transit peptide, and partial coding sequence. The promoter contained several response elements (e.g., for light, cold temperature, xenobiotics) that may be involved in the regulation of the Sod1 gene. Sod1 expression during development and in response to physiological and chemical stressors such as temperature, xenobiotics (paraquat), and light were examined.}, number={1}, journal={ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS}, author={Kernodle, SP and Scandalios, JG}, year={2001}, month={Jul}, pages={137–147} }
 @article{kernodle_scandalios_1996, title={A comparison of the structure and function of the highly homologous maize antioxidant Cu/Zn superoxide dismutase genes, Sod4 and Sod4A}, volume={144}, number={1}, journal={Genetics}, author={Kernodle, S. P. and Scandalios, J. G.}, year={1996}, pages={317} }