@article{panthee_pandey_paudel_2024, title={Multiple Foliar Fungal Disease Management in Tomatoes: A Comprehensive Approach}, url={https://www.mdpi.com/2037-0164/15/1/7}, DOI={10.3390/ijpb15010007}, abstractNote={Foliar diseases are the significant production constraints in tomatoes. Among them, foliar fungal diseases in tomatoes, such as early blight (Alternaria linaria), Septoria leaf spot (Septoria lycopersici), and late blight (Phytophthora infestans), which is oomycetes, have higher economic significance. This paper will discuss the etiology, host range, distribution, symptoms, and disease cycle to help us understand the biology, followed by management approaches emphasizing the resistance breeding approach for these diseases. We provide an analytical review of crop improvement efforts, including conventional and molecular methods for improving these diseases’ resistance. We discuss the importance of modern breeding tools, including genomics, genetic transformation, and genome editing, to improve the resistance to these diseases in the future.}, journal={International Journal of Plant Biology}, author={Panthee, Dilip and Pandey, Anju and Paudel, Rajan}, year={2024}, month={Jan} }
 @article{siddique_silverman_louws_panthee_2024, title={Quantitative Trait Loci Mapping for Bacterial Wilt Resistance and Plant Height in Tomatoes}, volume={13}, ISSN={["2223-7747"]}, url={https://doi.org/10.3390/plants13060876}, DOI={10.3390/plants13060876}, abstractNote={Bacterial wilt (BW) of tomatoes, caused by Ralstonia solanacearum, is a devastating disease that results in large annual yield losses worldwide. Management of BW of tomatoes is difficult due to the soil-borne nature of the pathogen. One of the best ways to mitigate the losses is through breeding for disease resistance. Moreover, plant height (PH) is a crucial element related to plant architecture, which determines nutrient management and mechanical harvesting in tomatoes. An intraspecific F2 segregating population (NC 11212) of tomatoes was developed by crossing NC 84173 (tall, BW susceptible) × CLN1466EA (short, BW resistant). We performed quantitative trait loci (QTL) mapping using single nucleotide polymorphic (SNP) markers and the NC 11212 F2 segregating population. The QTL analysis for BW resistance revealed a total of three QTLs on chromosomes 1, 2, and 3, explaining phenotypic variation (R2) ranging from 3.6% to 14.9%, whereas the QTL analysis for PH also detected three QTLs on chromosomes 1, 8, and 11, explaining R2 ranging from 7.1% to 11%. This work thus provides information to improve BW resistance and plant architecture-related traits in tomatoes.}, number={6}, journal={PLANTS-BASEL}, author={Siddique, Muhammad Irfan and Silverman, Emily and Louws, Frank and Panthee, Dilip R.}, year={2024}, month={Mar} }
 @article{panthee_2023, title={Application of Molecular Markers in Crop Improvement and Beyond}, volume={13}, ISSN={["2073-4395"]}, url={https://www.mdpi.com/2073-4395/13/8/2041}, DOI={10.3390/agronomy13082041}, abstractNote={The application of molecular markers in crop improvement first started in the 1980s [...]}, number={8}, journal={AGRONOMY-BASEL}, author={Panthee, Dilip R.}, year={2023}, month={Aug} }
 @article{adhikari_siddique_louws_panthee_2023, title={Identification of quantitative trait loci associated with bacterial spot race T4 resistance in intra-specific populations of tomato (Solanum lycopersicum L.)}, volume={18}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0295551}, DOI={10.1371/journal.pone.0295551}, abstractNote={Bacterial spot of tomato is a serious disease caused by at least four species and four races of Xanthomonas- X. euvesicatoria (race T1), X. vesicatoria (race T2), X. perforans (race T3 and T4), and X. gardneri, with X. perforans race T4 being predominant in the southeast USA. Practical management of this disease is challenging because of the need for more effective chemicals and commercially resistant cultivars. Identification of genetic resistance is the first step to developing a disease-resistant variety. The objective of this study was to identify quantitative trait loci (QTL) conferring resistance to race T4 in two independent recombinant inbred lines (RILs) populations NC 10204 (intra-specific) and NC 13666 (interspecific) developed by crossing NC 30P x NC22L-1(2008) and NC 1CELBR x PI 270443, respectively. Seven QTLs on chromosomes 2, 6, 7, 11, and 12 were identified in NC 10204. The QTL on chromosome 6 explained the highest percentage of phenotypic variance (up to 21.3%), followed by the QTL on chromosome 12 (up to 8.2%). On the other hand, the QTLs on chromosomes 1, 3, 4, 6, 7, 8, 9, and 11 were detected in NC 13666. The QTLs on chromosomes 6, 7, and 11 were co-located in NC 10204 and NC 13666 populations. The donor of the resistance associated with these QTL in NC 10204 is a released breeding line with superior horticultural traits. Therefore, both the donor parent and the QTL information will be useful in tomato breeding programs as there will be minimal linkage drag associated with the bacterial spot resistance.}, number={12}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Adhikari, Pragya and Siddique, Muhammad Irfan and Louws, Frank J. and Panthee, Dilip R.}, editor={Pandey, Abhay K.Editor}, year={2023}, month={Dec}, pages={e0295551} }
 @article{thies_panthee_2023, title={Identification, development and use of rootstocks to improve pest and disease resistance of vegetable crops}, volume={14}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2023.1320828}, abstractNote={EDITORIAL article Front. Plant Sci., 12 December 2023Sec. Crop and Product Physiology Volume 14 - 2023 | https://doi.org/10.3389/fpls.2023.1320828}, journal={FRONTIERS IN PLANT SCIENCE}, author={Thies, Judy A. and Panthee, Dilip R.}, year={2023}, month={Dec} }
 @article{zhang_panthee_2023, title={Improvements in the detection power of algorithms for analyzing next-generation sequencing based bulked segregant analysis data via estimating thresholds at the genomic region level}, url={https://doi.org/10.1101/2023.03.12.532308}, DOI={10.1101/2023.03.12.532308}, abstractNote={Abstract}, author={Zhang, Jianbo and Panthee, Dilip R}, year={2023}, month={Mar} }
 @article{adhikari_siddique_louws_sim_panthee_2023, title={Molecular mapping of quantitative trait loci for resistance to early blight in tomatoes}, volume={14}, ISSN={1664-462X}, url={http://dx.doi.org/10.3389/fpls.2023.1135884}, DOI={10.3389/fpls.2023.1135884}, abstractNote={Early blight (EB), caused by Alternaria linariae (Neerg.) (syn. A. tomatophila) Simmons, is a disease that affects tomatoes (Solanum lycopersicum L.) throughout the world, with tremendous economic implications. The objective of the present study was to map the quantitative trait loci (QTL) associated with EB resistance in tomatoes. The F2 and F2:3 mapping populations consisting of 174 lines derived from NC 1CELBR (resistant) × Fla. 7775 (susceptible) were evaluated under natural conditions in the field in 2011 and in the greenhouse in 2015 by artificial inoculation. In all, 375 Kompetitive Allele Specific PCR (KASP) assays were used for genotyping parents and the F2 population. The broad-sense heritability estimate for phenotypic data was 28.3%, and 25.3% for 2011, and 2015 disease evaluations, respectively. QTL analysis revealed six QTLs associated with EB resistance on chromosomes 2, 8, and 11 (LOD 4.0 to 9.1), explaining phenotypic variation ranging from 3.8 to 21.0%. These results demonstrate that genetic control of EB resistance in NC 1CELBR is polygenic. This study may facilitate further fine mapping of the EB-resistant QTL and marker-assisted selection (MAS) to transfer EB resistance genes into elite tomato varieties, including broadening the genetic diversity of EB resistance in tomatoes.}, journal={Frontiers in Plant Science}, publisher={Frontiers Media SA}, author={Adhikari, Tika B. and Siddique, Muhammad Irfan and Louws, Frank J. and Sim, Sung-Chur and Panthee, Dilip R.}, year={2023}, month={May} }
 @article{panthee_pandey_paudel_2023, title={Resistance to Multiple Foliar Fungal Diseases in Tomato}, url={https://doi.org/10.20944/preprints202306.1268.v1}, DOI={10.20944/preprints202306.1268.v1}, abstractNote={Foliar fungal diseases in tomatoes include early blight (Alternaria linariae), Septoria leaf spot (Septoria lycopersici), and late blight (Phytophthora infestans) which is oomycetes. These are one of the significant production constraints in tomatoes. We describe the etiology, host range, distribution, symptoms, and disease cycle to understand the biology followed by management practices emphasizing the resistance breeding approach for these diseases.  In crop improvement efforts, we provide an analytical review, including conventional and molecular methods for improving this disease resistance. Modern breeding tools, including genomics, genetic transformation, and genome editing, can be used to improve these traits. There is a good possibility of using these tools in the future to improve these traits.}, author={Panthee, Dilip R. and Pandey, Anju and Paudel, Rajan}, year={2023}, month={Jun} }
 @article{reeves_strayer-scherer_panthee_gardner_meadows_2023, title={Variable Yield Responses among Grafted and Nongrafted Late blight-resistant Tomato (Solanum lycopersicum L.) Hybrids in North Carolina}, volume={58}, ISSN={["2327-9834"]}, DOI={10.21273/HORTSCI17145-23}, abstractNote={Host resistance is an environmentally and economically sustainable disease management strategy that may be especially beneficial to small-scale and organic growers for whom other management tools such as synthetic pesticides are too costly or not permitted. In western North Carolina, the demand for vine-ripened tomatoes (Solanum lycopersicum L.) from local and organic farms has led to the development of cultivars bred for resistance to geographically relevant diseases, including late blight of tomato, which causes rapid defoliation and lesions on fruit. Grafting tomato plants has the potential to increase plant vigor and yield; however, this effect is known to be dependent on multiple factors, including scion and geographic location. In this study, we evaluated the yield response of one determinate (‘Mountain Gem’) and four indeterminate (‘Mountain Heritage’, ‘Mountain Girl’, ‘Mountain Rouge’, and ‘NC10291’) late blight–resistant tomato cultivars, grafted on tomato rootstock ‘Maxifort’ or nongrafted, on a commercial farm and at two research facilities in western North Carolina. Yield of marketable fruit from grafted plants was greater than that from nongrafted plants at one location (P = 0.008); however, yield response of each cultivar, grafted or not grafted, differed by location. Yield was consistently greater from ‘Mountain Gem’ plants than other cultivars, and grafted ‘Mountain Gem’ plants had greater yields later in the season at two locations than nongrafted plants. Because of the late planting date intended to expose cultivars to the late blight pathogen, the full yield potential of the indeterminate cultivars was not realized at all locations. Disease severity caused by Verticillium wilt (Verticillium dahliae Kleb., Verticillium albo-atrum Reinke & Berthold) was lowest for cultivar Mountain Heritage at two of three locations. Results from this study emphasize the importance of conducting evaluations of grafted tomato plants at multiple locations, including on farm, to optimize the benefits associated with their use.}, number={8}, journal={HORTSCIENCE}, author={Reeves, Ella R. and Strayer-Scherer, Amanda and Panthee, Dilip R. and Gardner, Randolph and Meadows, Inga M.}, year={2023}, month={Aug}, pages={943–948} }
 @article{duduit_kosentka_miller_blanco-ulate_lenucci_panthee_perkins-veazie_liu_2022, title={Coordinated transcriptional regulation of the carotenoid biosynthesis contributes to fruit lycopene content in high-lycopene tomato genotypes}, volume={9}, ISSN={2052-7276}, url={http://dx.doi.org/10.1093/hr/uhac084}, DOI={10.1093/hr/uhac084}, abstractNote={Abstract}, journal={Horticulture Research}, publisher={Oxford University Press (OUP)}, author={Duduit, James R and Kosentka, Pawel Z and Miller, Morgan A and Blanco-Ulate, Barbara and Lenucci, Marcello S and Panthee, Dilip R and Perkins-Veazie, Penelope and Liu, Wusheng}, year={2022} }
 @article{planas-marques_kressin_kashyap_panthee_louws_coll_valls_2022, title={Four bottlenecks restrict colonization and invasion by the pathogen Ralstonia solanacearum in resistant tomato (vol 71, pg 2157, 2020)}, volume={3}, ISSN={["1460-2431"]}, url={https://publons.com/wos-op/publon/56007363/}, DOI={10.1093/jxb/erac086}, journal={JOURNAL OF EXPERIMENTAL BOTANY}, author={Planas-Marques, Marc and Kressin, Jonathan P. and Kashyap, Anurag and Panthee, Dilip R. and Louws, Frank J. and Coll, Nuria S. and Valls, Marc}, year={2022}, month={Mar} }
 @inbook{amoroso_panthee_andolfo_ramìrez_ercolano_2022, place={Cham, Switzerland}, title={Genomic Tools for Improving Tomato to Biotic Stress Resistance}, ISBN={9783030977849 9783030977856}, url={http://dx.doi.org/10.1007/978-3-030-97785-6}, DOI={10.1007/978-3-030-97785-6_1}, booktitle={Genomic Designing for Biotic Stress Resistant Vegetable Crops}, publisher={Springer International Publishing}, author={Amoroso, C.G. and Panthee, D.R. and Andolfo, G. and Ramìrez, F.P. and Ercolano, M.R.}, editor={Kole, ChittaranjanEditor}, year={2022}, pages={1–35} }
 @inproceedings{shi_panthee_2022, title={RNA-Seq analysis of tomato genotypes resistant to Bacterial spot (Xanthomonas perforans) race T4}, booktitle={International Horticulture Congress}, author={Shi, R. and Panthee, D.R.}, year={2022} }
 @article{gong_louws_panthee_2022, title={Screening of tomato lines for late blight resistance}, volume={57}, number={9S}, journal={HortScience}, author={Gong, X. and Louws, F.J. and Panthee, D.R.}, year={2022}, pages={S114} }
 @article{panthee_2022, title={Tomato -Vegetable cultivar descriptions for North America, List 28}, volume={57}, number={8}, journal={HortScience}, author={Panthee, D.R.}, editor={Mou, B.Editor}, year={2022}, month={Aug}, pages={949–1040} }
 @article{panthee_gardner_2022, title={‘Mountain Bebe’: Hybrid Grape Tomato and Its Parents NC 7 Grape and NC 8 Grape}, volume={57}, ISSN={0018-5345 2327-9834}, url={http://dx.doi.org/10.21273/HORTSCI16366-21}, DOI={10.21273/HORTSCI16366-21}, abstractNote={and fusarium wilt and The has a compact, indeterminate growth habit short It has total ’}, number={3}, journal={HortScience}, publisher={American Society for Horticultural Science}, author={Panthee, Dilip R. and Gardner, Randy G.}, year={2022}, month={Mar}, pages={444–446} }
 @article{zhang_panthee_2021, title={Development of codominant SCAR markers to detect the
            <i>Pto
            ,
            <i>
              Tm2
              <sup>2
            
            ,
            <i>I3
            and
            <i>Sw5
            genes in tomato (
            <i>Solanum lycopersicum
            )}, volume={140}, ISSN={0179-9541 1439-0523}, url={http://dx.doi.org/10.1111/pbr.12902}, DOI={10.1111/pbr.12902}, abstractNote={Abstract}, number={2}, journal={Plant Breeding}, publisher={Wiley}, author={Zhang, Jianbo and Panthee, Dilip R.}, editor={Pillen, KlausEditor}, year={2021}, month={Feb}, pages={342–348} }
 @article{panthee_zhang_piotrowski_2021, title={Evaluation of tomato breeding lines for Bacterial speck resistance}, volume={56}, number={9S}, journal={HortScience}, author={Panthee, D.R. and Zhang, J. and Piotrowski, A.}, year={2021}, pages={S127} }
 @article{panthee_kressin_piotrowski_2021, title={Identification of potential rootstocks for tomato grafting from bacterial wilt screening trials in North Carolina}, volume={1302}, ISSN={0567-7572 2406-6168}, url={http://dx.doi.org/10.17660/ActaHortic.2021.1302.23}, DOI={10.17660/ActaHortic.2021.1302.23}, number={1302}, journal={Acta Horticulturae}, publisher={International Society for Horticultural Science (ISHS)}, author={Panthee, D.R. and Kressin, J. and Piotrowski, A.}, year={2021}, month={Jan}, pages={169–176} }
 @article{zhang_panthee_2021, title={Next-generation sequencing-based bulked segregant analysis without sequencing the parental genomes}, volume={12}, ISSN={2160-1836}, url={http://dx.doi.org/10.1093/g3journal/jkab400}, DOI={10.1093/g3journal/jkab400}, abstractNote={Abstract}, number={2}, journal={G3 Genes|Genomes|Genetics}, publisher={Oxford University Press (OUP)}, author={Zhang, Jianbo and Panthee, Dilip R}, editor={Lipka, AEditor}, year={2021}, month={Dec} }
 @article{panthee_2021, title={‘Mountain Regina’: Multiple Disease Resistant Fresh-market Hybrid Tomato and Its Parents, NC 1LF and NC 2LF}, volume={56}, ISSN={0018-5345 2327-9834}, url={http://dx.doi.org/10.21273/HORTSCI15824-21}, DOI={10.21273/HORTSCI15824-21}, abstractNote={large-fruited, fresh-market hybrid tomato ( Solanum lycopersicum vine-ripe is resistant to verticillium wilt ( Verticillium dahliae Kleb) race 1 ( Ve gene); fusarium wilt [ Fusarium oxysporum f.sp. lycopersici (Sacc.) Snyd. and Hans.] races 1, 2, and 3 ( I, I-2 , and I-3 genes); root-knot nematodes ( Meloidogyne spp., Mi gene); Tomato mosaic virus ( Tm-2 gene); and Tomato spotted wilt virus ( Sw-5 gene).}, number={6}, journal={HortScience}, publisher={American Society for Horticultural Science}, author={Panthee, Dilip R.}, year={2021}, month={Jun}, pages={736–738} }
 @article{adhikari_adhikari_louws_panthee_2020, title={Advances and Challenges in Bacterial Spot Resistance Breeding in Tomato (Solanum lycopersicum L.)}, volume={21}, ISSN={1422-0067}, url={http://dx.doi.org/10.3390/ijms21051734}, DOI={10.3390/ijms21051734}, abstractNote={Bacterial spot is a serious disease of tomato caused by at least four species of Xanthomonas. These include X. euvesicatoria (race T1), X. vesicatoria (race T2), X. perforans (races T3 and T4), and X. gardneri, with the distinct geographical distribution of each group. Currently, X. gardneri and X. perforans are two major bacterial pathogens of tomato in North America, with X. perforans (race T4) dominating in east-coast while X. gardneri dominating in the Midwest. The disease causes up to 66% yield loss. Management of this disease is challenging due to the lack of useful chemical control measures and commercial resistant cultivars. Although major genes for resistance (R) and quantitative resistance have been identified, breeding tomato for resistance to bacterial spot has been impeded by multiple factors including the emergence of new races of the pathogen that overcome the resistance, multigenic control of the resistance, linkage drag, non-additive components of the resistance and a low correlation between seedling assays and field resistance. Transgenic tomato with Bs2 and EFR genes was effective against multiple races of Xanthomonas. However, it has not been commercialized because of public concerns and complex regulatory processes. The genomics-assisted breeding, effectors-based genomics breeding, and genome editing technology could be novel approaches to achieve durable resistance to bacterial spot in tomato. The main goal of this paper is to understand the current status of bacterial spot of tomato including its distribution and pathogen diversity, challenges in disease management, disease resistance sources, resistance genetics and breeding, and future prospectives with novel breeding approaches.}, number={5}, journal={International Journal of Molecular Sciences}, publisher={MDPI AG}, author={Adhikari, Pragya and Adhikari, Tika B. and Louws, Frank J. and Panthee, Dilip R.}, year={2020}, month={Mar}, pages={1734} }
 @inbook{tiwari_bhandari_thapa_shrestha_subedi_panthee_2020, title={Cereal crop improvement for food sufficiency}, booktitle={Principles and Practices of Food Security: Sustainable, Sufficient, and Food Food for Healthy Living in Nepal}, publisher={Association of Nepalese Agricultural Professionals in Americas (NAPA)}, author={Tiwari, K.R. and Bhandari, H.S. and Thapa, D.B. and Shrestha, J. and Subedi, M. and Panthee, D.R.}, editor={Rasali, D.P. and Bhandari, P.B. and Karki, U. and Parajulee, M.N. and Acharya, R.N. and Adhikari, R.Editors}, year={2020}, pages={166–197} }
 @article{panthee_perkins-veazie_2020, title={Comparison of tomato genotypes grown under conventional and organic production systems for nutrient composition and fruit quality}, volume={55}, number={9S}, journal={HortScience}, author={Panthee, D.R. and Perkins-Veazie, P.}, year={2020}, pages={S414–S415} }
 @inbook{panthee_gotame_shrestha_tiwari_bhandari_2020, title={Current status of fruits and vegetables and their improvements}, booktitle={Principles and Practices of Food Security: Sustainable, Sufficient, and Food for Healthy Living in Nepal}, publisher={Association of Nepalese Agricultural Professionals in Americas (NAPA)}, author={Panthee, D.R. and Gotame, T.P. and Shrestha, S. and Tiwari, K.R. and Bhandari, H.S.}, editor={Rasali, D.P. and Bhandari, P.B. and Karki, U. and Parajulee, M.N. and Acharya, R.N. and Adhikari, R.Editors}, year={2020}, pages={245–269} }
 @article{adhikari_mcnellie_panthee_2020, title={Detection of Quantitative Trait Loci (QTL) Associated with the Fruit Morphology of Tomato}, volume={11}, ISSN={2073-4425}, url={http://dx.doi.org/10.3390/genes11101117}, DOI={10.3390/genes11101117}, abstractNote={Tomato (Solanum lycopersicum L.) is the second most-consumed vegetable in the world. The market value and culinary purpose of tomato are often determined by fruit size and shape, which makes the genetic improvement of these traits a priority for tomato breeders. The main objective of the study was to detect quantitative trait loci (QTL) associated with the tomato fruit shape and size. The use of elite breeding materials in the genetic mapping studies will facilitate the detection of genetic loci of direct relevance to breeders. We performed QTL analysis in an intra-specific population of tomato developed from a cross between two elite breeding lines NC 30P × NC-22L-1(2008) consisting of 110 recombinant inbred lines (RIL). The precision software Tomato Analyzer (TA) was used to measure fruit morphology attributes associated with fruit shape and size traits. The RIL population was genotyped with the SolCAP 7720 SNP array. We identified novel QTL controlling elongated fruit shape on chromosome 10, explaining up to 24% of the phenotypic variance. This information will be useful in improving tomato fruit morphology traits.}, number={10}, journal={Genes}, publisher={MDPI AG}, author={Adhikari, Pragya and McNellie, James and Panthee, Dilip R.}, year={2020}, month={Sep}, pages={1117} }
 @article{myers_panthee_2020, title={Differential gene expression of bacterial wilt (Ralstonia solanacearum) resistance in tomatoes}, volume={55}, number={9S}, journal={HortScience}, author={Myers, J.A. and Panthee, D.R.}, year={2020}, pages={S192–S193} }
 @article{panthee_gotame_2020, title={Improving heat stress tolerance in tomato}, volume={2020}, ISSN={1749-8848}, url={http://dx.doi.org/10.1079/PAVSNNR202015060}, DOI={10.1079/PAVSNNR202015060}, abstractNote={Abstract}, journal={CABI Reviews}, publisher={CABI Publishing}, author={Panthee, Dilip R. and Gotame, Tek P.}, year={2020}, month={Jan} }
 @article{zhang_panthee_2020, title={PyBSASeq: a simple and effective algorithm for bulked segregant analysis with whole-genome sequencing data}, volume={21}, ISSN={["1471-2105"]}, url={https://doi.org/10.1186/s12859-020-3435-8}, DOI={10.1186/s12859-020-3435-8}, abstractNote={Abstract}, number={1}, journal={BMC BIOINFORMATICS}, publisher={Springer Science and Business Media LLC}, author={Zhang, Jianbo and Panthee, Dilip R.}, year={2020}, month={Mar} }
 @article{panthee_piotrowski_louws_2020, title={Screening tomato breeding lines for Bacterial wilt resistance in NC}, volume={55}, number={9S}, journal={HortScience}, author={Panthee, D.R. and Piotrowski, A. and Louws, F.J.}, year={2020}, pages={S108} }
 @inbook{panthee_tiwari_2020, title={The impact of COVID-19 on agriculture research}, booktitle={COVID-19 pandemic and Nepal: Issues and perspectives}, publisher={Asta-Ja}, author={Panthee, D.R. and Tiwari, K.R.}, editor={Sharma, B. and Adhikari, A.P.Editors}, year={2020}, pages={52–60} }
 @article{shi_panthee_2020, title={Transcriptome-Based Analysis of Tomato Genotypes Resistant to Bacterial Spot (Xanthomonas perforans) Race T4}, volume={21}, ISSN={1422-0067}, url={http://dx.doi.org/10.3390/ijms21114070}, DOI={10.3390/ijms21114070}, abstractNote={Bacterial spot (BS) is one of the most devastating foliar bacterial diseases of tomato and is caused by multiple species of Xanthomonas. We performed the RNA sequencing (RNA-Seq) analysis of three tomato lines with different levels of resistance to Xanthomonas perforans race T4 to study the differentially expressed genes (DEGs) and transcript-based sequence variations. Analysis between inoculated and control samples revealed that resistant genotype Solanum pimpinellifolium accession PI 270443 had more DEGs (834), followed by susceptible genotype tomato (S. lycopersicum L) breeding line NC 714 (373), and intermediate genotype tomato breeding line NC 1CELBR (154). Gene ontology (GO) terms revealed that more GO terms (51) were enriched for upregulated DEGs in the resistant genotype PI 270443, and more downregulated DEGs (67) were enriched in the susceptible genotype NC 714. DEGs in the biotic stress pathway showed more upregulated biotic stress pathway DEGs (67) for PI 270443 compared to more downregulated DEGs (125) for the susceptible NC 714 genotype. Resistant genotype PI 270443 has three upregulated DEGs for pathogenesis-related (PR) proteins, and susceptible genotype NC 714 has one downregulated R gene. Sequence variations called from RNA-Seq reads against the reference genome of susceptible Heinz 1706 showed that chr11, which has multiple reported resistance quantitative trait loci (QTLs) to BS race T4, is identical between two resistant lines, PI 270443 and NC 1CELBR, suggesting that these two lines share the same resistance QTLs on this chromosome. Several loci for PR resistance proteins with sequence variation between the resistant and susceptible tomato lines were near the known Rx4 resistance gene on chr11, and additional biotic stress associated DEGs near to the known Rx4 resistance gene were also identified from the susceptible NC 714 line.}, number={11}, journal={International Journal of Molecular Sciences}, publisher={MDPI AG}, author={Shi, Rui and Panthee, Dilip R.}, year={2020}, month={Jun}, pages={4070} }
 @article{panthee_2020, title={‘Mountain Crown’: Late Blight and Tomato mosaic virus-resistant Plum Hybrid Tomato and Its Parent, NC 1 Plum}, volume={55}, ISSN={0018-5345 2327-9834}, url={http://dx.doi.org/10.21273/HORTSCI15416-20}, DOI={10.21273/HORTSCI15416-20}, abstractNote={‘Mountain Crown’ is a fresh-market plum tomato F 1 hybrid ( Solanum lycopersicum L.) developed by crossing NC 30P · NC 1 Plum. It is resistant to verticillium wilt ( Verticillium dahliae Kleb) (race 1) ( Ve/Ve gene), fusarium wilt ( Fusarium oxysporum f.sp. lycopersici (Sacc.) Snyd. and Hans.) (races 1 and 2) ( I/I and I-2/I-2 genes), late blight (LB) ( Ph-2/ph- 2 and Ph-3/ph-3 genes), Tomato mosaic virus (ToMV) ( Tm2/tm2 gene), and Tomato spot- ted wilt virus (TSWV) ( Sw-5/sw-5 gene).}, number={12}, journal={HortScience}, publisher={American Society for Horticultural Science}, author={Panthee, Dilip R.}, year={2020}, month={Dec}, pages={2056–2057} }
 @inproceedings{zhang_panthee_2019, title={Development of co-dominant SCAR markers for detection of the Pto, Tm-22, I-3, and Sw5 genes in tomato}, booktitle={Tomato Breeders Round Table Meeting}, author={Zhang, J. and Panthee, D.R.}, year={2019}, month={Nov} }
 @article{planas-marquès_kressin_kashyap_panthee_louws_coll_valls_2019, title={Four bottlenecks restrict colonization and invasion by the pathogen Ralstonia solanacearum in resistant tomato}, volume={71}, ISSN={0022-0957 1460-2431}, url={http://dx.doi.org/10.1093/jxb/erz562}, DOI={10.1093/jxb/erz562}, abstractNote={Abstract}, number={6}, journal={Journal of Experimental Botany}, publisher={Oxford University Press (OUP)}, author={Planas-Marquès, Marc and Kressin, Jonathan P and Kashyap, Anurag and Panthee, Dilip R and Louws, Frank J and Coll, Nuria S and Valls, Marc}, editor={Bozhkov, PeterEditor}, year={2019}, month={Dec}, pages={2157–2171} }
 @inproceedings{duduit_kosentka_panthee_perkins-veazie_liu_2019, title={Identification of the key carotenoid biosynthesis pathway genes impacting tomato fruit lycopene content}, booktitle={National Association of Plant Breeders Meeting}, author={Duduit, J.R. and Kosentka, P. and Panthee, D.R. and Perkins-Veazie, P. and Liu, W.}, year={2019}, month={Aug} }
 @inproceedings{shreshtha_zhang_panthee_2019, title={Mapping quantitative trait loci (QTL) associated with flavonoid in tomato (Solanum lycopersicum L.)}, booktitle={National Association of Plant Breeders Meeting}, author={Shreshtha, N. and Zhang, J. and Panthee, D.R.}, year={2019}, month={Aug} }
 @inproceedings{panthee_piotroski_2019, title={New tomato hybrids improved for fruit quality and disease resistance at NC State University}, booktitle={Tomato Breeders Round Table Meeting}, author={Panthee, D.R. and Piotroski, A.}, year={2019}, month={Nov} }
 @article{adhikari_adhikari_timilsina_meadows_jones_panthee_louws_2019, title={Phenotypic and Genetic Diversity of Xanthomonas perforans Populations from Tomato in North Carolina}, volume={109}, ISSN={["1943-7684"]}, url={http://dx.doi.org/10.1094/phyto-01-19-0019-r}, DOI={10.1094/PHYTO-01-19-0019-R}, abstractNote={Bacterial spot caused by Xanthomonas spp. is one of the most devastating diseases of tomato in North Carolina (NC). In total, 290 strains of Xanthomonas spp. from tomato in NC collected over 2 years (2015 and 2016) were analyzed for phenotypic and genetic diversity. In vitro copper and streptomycin sensitivity assays revealed that >95% (n = 290) of the strains were copper tolerant in both years, whereas 25% (n = 127) and 46% (n = 163) were streptomycin tolerant in 2016 and 2015, respectively. Using BOX repetitive element PCR assay, fingerprint patterns showed four haplotypes (H1, H2, H3, and H4) among the strains analyzed. The multiplex real-time quantitative PCR on a subset of representative strains (n = 45) targeting the highly conserved hrcN gene identified Xanthomonas strains from tomato in NC that belonged to X. perforans. Race profiling of the representative strains (n = 45) on tomato and pepper differentials confirmed that ∼9 and 91% of strains are tomato races T3 and T4, respectively. Additionally, PCR assays and sequence alignments confirmed that the copL, copA, copB (copLAB copper tolerance gene cluster), and avrXv4 genes are present in the strains analyzed. Phylogenetic and comparative sequence analyses of six genomic regions (elongation factor G [fusA], glyceraldehyde-3-phosphate dehydrogenase A [gapA], citrate synthase [gltA], gyrase subunit B [gyrB], ABC transporter sugar permease [lacF], and GTP binding protein [lepA]) suggested that 13 and 74% of X. perforans strains from NC were genetically similar to races T3 and T4 from Florida, respectively. Our results provide insights that bacterial spot management practices in tomato should focus on deploying resistance genes to combat emerging pathogenic races of X. perforans and overcome the challenges currently posed by intense use of copper-based bactericides.}, number={9}, journal={PHYTOPATHOLOGY}, author={Adhikari, Pragya and Adhikari, Tika B. and Timilsina, Sujan and Meadows, Inga and Jones, Jeffrey B. and Panthee, Dilip R. and Louws, Frank J.}, year={2019}, month={Sep}, pages={1533–1543} }
 @article{panthee_2019, title={Screening tomato (Solanum lycopersicum L.) for heat stress tolerance}, volume={54:S12-S12}, journal={HortScience}, author={Panthee, D.R.}, year={2019} }
 @inproceedings{planas marques_kressin_kashyap_panthee_louws_coll_valls_2019, title={Structural restriction to Ralstonia solanacearum colonization and invasion in resistant tomato varieties}, volume={32}, booktitle={Molecular Plant-Microbe Interactions}, author={Planas Marques, M. and Kressin, J. and Kashyap, A. and Panthee, D.R. and Louws, F.J. and Coll, N.S. and Valls, M}, year={2019}, pages={130–131} }
 @inproceedings{myers_silverman_kressin_panthee_2019, title={Understanding genetic resistance to bacterial wilt in tomatoes}, booktitle={National Association of Plant Breeders Meeting}, author={Myers, J. and Silverman, E.J. and Kressin, J. and Panthee, D.R.}, year={2019}, month={Aug} }
 @inproceedings{kressin_panthee_louws_planas_nuria sanchez-coll_valls_2018, title={4-Dimensional colonization dynamics of the grafted tomato Bacterial wilt pathosystem and their implication for resistance selection}, booktitle={Tomato Breeders Round Table Meeting}, author={Kressin, J.P. and Panthee, D.R. and Louws, F.J. and Planas, M. and Nuria Sanchez-Coll, N. and Valls, M.}, year={2018} }
 @inproceedings{adhikari_louws_ashrafi_arellano_gunter_panthee_2018, title={Bacterial spot of tomato: Pathogen story and our efforts of tomato improvement in NC}, booktitle={Tomato Breeders Round Table Meeting}, author={Adhikari, P. and Louws, F.J. and Ashrafi, H. and Arellano, C. and Gunter, C.C. and Panthee, D.R.}, year={2018} }
 @article{panthee_perkins-veazie_2018, title={Comparison of Tomato Genotypes Grown Under Conventional and Organic Production System for Nutrient Composition and Fruit Quality}, volume={53:S93-S94}, journal={HortScience}, author={Panthee, D.R. and Perkins-Veazie, P.}, year={2018} }
 @article{bhattarai_sharma_panthee_2018, title={Diversity among Modern Tomato Genotypes at Different Levels in Fresh-Market Breeding}, volume={2018}, ISSN={["1687-8167"]}, url={https://doi.org/10.1155/2018/4170432}, DOI={10.1155/2018/4170432}, abstractNote={Cultivated tomato has been in existence for about 400 years and breeding activities have been conducted for only eight decades. However, more than 10,000 tomato cultivars have already been developed. Ninety-one tomato genotypes were characterized for twenty-one morphological traits using developmental, vegetative, and fruit traits. Correlation, principal component, and cluster analysis between the traits were carried out. Higher correlations between fruit traits including fruit shape, fruit size, and fruit types were observed. These correlations indicate that specific fruit types require specific traits like branched inflorescence and a greater number of fruits per inflorescence are beneficial only for smaller fruit sizes like cherry and grape tomatoes. Contrastingly, traits like determinate growth habit and fruit maturity are preferred in all fruit types of tomato for better cultivation practices and longer production duration and hence showed lower correlations. Principal component analysis clustered tomato genotypes into three main clusters with multiple subgroups. Similar tomato genotypes were placed into one or more clusters confirming the results from correlation analysis. Involvement of private breeding programs in cultivar development has increased the competition on introgression of novel and desired traits across new cultivars. Understanding the diversity present in modern cultivars and potential traits identification in related wild species can enhance tomato diversity and improve quality and production.}, journal={INTERNATIONAL JOURNAL OF AGRONOMY}, author={Bhattarai, Krishna and Sharma, Sadikshya and Panthee, Dilip R.}, year={2018} }
 @inproceedings{panthee_veluchamy_zhang_2018, title={Efforts on Breeding for Bacterial Speck Resistance in Tomato in North Carolina}, booktitle={33rd Tomato Disease Workshop}, author={Panthee, D.R. and Veluchamy, S. and Zhang, J.}, year={2018} }
 @article{shi_lewis_panthee_2018, title={Filter paper-based spin column method for cost-efficient DNA or RNA purification}, volume={13}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0203011}, abstractNote={We describe herein a method of recharging used commercial spin columns or assembling homemade spin columns using filter paper as binding material for cost-effective, low throughput nucleic acid purification. The efficiency of filter paper-based spin columns was evaluated for purification of nucleic acids from various sources. Following protocols of commercial kits, we found filter paper to be a useful binding material for purification of nucleic acids, including plant genomic DNA, plant total RNA, PCR products, and DNA from agarose gels. However, filter paper has a weak binding affinity to plasmid DNA in tested miniprep protocols. Protocols for the use of filter paper recharged spin columns or homemade spin columns for low throughput purification of plant genomic DNA and total RNA with unused commercial kit buffers or less expensive homemade buffers are presented.}, number={12}, journal={PLOS ONE}, author={Shi, Rui and Lewis, Ramsey S. and Panthee, Dilip R.}, year={2018}, month={Dec} }
 @inproceedings{kressin_louws_panthee_2018, title={Genetic and phenotypic diversity of tomato germplasm for bacterial wilt (Ralstonia solanacearum) resistance}, booktitle={Annual Conference, Sol Genomics}, author={Kressin, J.P. and Louws, F.J. and Panthee, D.R.}, year={2018}, month={Sep} }
 @article{panthee_kressin_piotrowski_2018, title={Heritability of Flower Number and Fruit Set under Heat Stress in Tomato}, volume={53}, ISSN={0018-5345 2327-9834}, url={http://dx.doi.org/10.21273/hortsci13317-18}, DOI={10.21273/hortsci13317-18}, abstractNote={The growing volatility of the climate, and its potential impact on crop production, has prompted several physiologic and genetic analyses under high-temperature conditions. Tomato is grown in warm temperate, subtropical, and tropical regions of the world, where daytime and nighttime temperatures regularly exceed the optimum temperatures for tomato growth during the summer, exerting stress on tomato production. Recent trends indicate more frequent extreme summer temperatures, which may grow even greater in the future, impacting crop growth. The objective of the current study was to estimate the heritability of flower and fruit set ability of tomato populations under heat stress conditions so that improvement for these traits can be planned. We developed two tomato populations using contrasting parents from the North Carolina State University (NCSU) tomato breeding program and the World Vegetable Center (formerly Asian Vegetable Research and Development Center). The F2 and F2-derived F3 families (F2:3 populations) were grown at the Piedmont Research Station (PRS), Salisbury, NC, where summer growing temperatures are warmer than optimum for tomato production. Heritability estimates of the number of flowers per cluster, the number of fruit per cluster, and fruit set (measured as a percentage) were determined in two populations of tomato—NC10137 (NC714 × CLN-2413A) and NC10418 [230 HS-1(99) × NC 1CS]—by regression analysis using the offspring-on-parents method. Broad-sense heritability across the traits was high (47.2%–100%), whereas narrow-sense heritability was very low (1.4%–22.5%). There was a positive correlation between the number of flowers and the number of fruit per cluster (r = 0.50, P < 0.05), which was in close agreement with previous findings. These findings will be useful in investigating the genetic control of heat stress tolerance in tomato and in facilitating crop improvement in the future.}, number={9}, journal={HortScience}, publisher={American Society for Horticultural Science}, author={Panthee, Dilip R. and Kressin, Jonathan P. and Piotrowski, Ann}, year={2018}, month={Sep}, pages={1294–1299} }
 @article{shrestha_panthee_2018, title={Inheritance and Segregation Analysis of Anthocyanin Content in Backcross Population of Tomato (Solanum lycopersicum L.)}, volume={53}, number={9}, journal={HortScience}, author={Shrestha, N. and Panthee, D.R.}, year={2018}, pages={S379} }
 @article{louws_suchoff_kressin_panthee_driver_gunter_2018, title={Integrating grafting and emerging products to manage soilborne diseases of tomato}, volume={1207}, ISSN={0567-7572 2406-6168}, url={http://dx.doi.org/10.17660/actahortic.2018.1207.34}, DOI={10.17660/ActaHortic.2018.1207.34}, abstractNote={Major soilborne diseases in North Carolina and surrounding states include fusarium wilt (FW) (causal agent Fusarium oxysporum f. sp. lycopersici; all three races), verticillium wilt (VW) (Verticillium dahliae; two races), southern stem blight (SSB) (Sclerotium rolfsii), root-knot nematodes (RKN) (primarily Meloidogyne incognita) and bacterial wilt (BW) (Ralstonia solanacearum race 1), distributed across the subtropical to temperate ecosystems in the state. FW, VW, SSB, and RKN can be well managed using standard fumigants. Alternative management practices are needed in production systems where fumigants are not used or effective, and/or where heirloom tomato cultivars are grown. We are involved in a USA multi-state program to determine the viability of grafting in open-field production systems. Previously published work showed the utility of grafting to manage FW, SSB, RKN, and BW. In complementary work to manage BW, a replicated on-farm field trial demonstrates that fumigants such as Paladin (79% dimethyl disulfide + 21% chloropicrin) and PicClor60 (60% chloropicrin + 40% 1,3-dichloropropene) allow up to 80% plant death, similar to incidence in non-fumigated plots, whereas grafting to resistant rootstock (Seminis 'Cheong Gang') confers 100% control in non-fumigated plots. Another on-farm randomized complete block design experiment demonstrated that three commercially available rootstocks conferred 100% plant stand, whereas non-grafted plants had 80% plant death using a round tomato scion ('Red Mountain') or 15% plant death using a roma tomato ('Picus'). Grafted plants show economic viability in North Carolina, and additional work is needed to optimize this tool in diverse production systems.}, number={1207}, journal={Acta Horticulturae}, publisher={International Society for Horticultural Science (ISHS)}, author={Louws, F.J. and Suchoff, D. and Kressin, J. and Panthee, D. and Driver, J. and Gunter, C.}, year={2018}, month={Jul}, pages={249–254} }
 @article{adhikari_mcnellie_panthee_2018, title={Mapping quantitative trait loci controlling fruit morphology and color parameters in intra-specific RIL population of tomato}, volume={53}, number={9}, journal={HortScience}, author={Adhikari, P. and McNellie, J. and Panthee, D.R.}, year={2018} }
 @inproceedings{panthee_2018, title={Molecular mapping of quantitative trait loci (QTL) for fruit quality in heirloom tomato background}, author={Panthee, D.R.}, year={2018}, month={Sep} }
 @inproceedings{panthee_piotrowski_kressin_2018, title={Tomato improvement for fruit quality and disease resistance at NC State University}, booktitle={Tomato Breeders Round Table Meeting}, author={Panthee, D.R. and Piotrowski, A. and Kressin, J.}, year={2018} }
 @article{shi_panthee_2017, title={A novel plant DNA extraction method using filter paper-based 96-well spin plate}, volume={246}, ISSN={0032-0935 1432-2048}, url={http://dx.doi.org/10.1007/s00425-017-2743-3}, DOI={10.1007/s00425-017-2743-3}, abstractNote={A simple, low cost and safe method using homemade filter paper-based 96-well spin plates and homemade solutions was developed for high throughput plant DNA extraction to use in molecular marker analysis. A low cost and safe method was developed for high throughput extraction of plant DNA for molecular marker analysis. In this method, we describe a simple way to prepare 96-well spin plate using filter paper, a plant material product for DNA binding. Such filter paper-based spin plate can combine with homemade non-toxic buffers for high throughput extraction of plant DNA. We confirmed that filter paper is an efficient solid-phase DNA binding material and comparable to silicon-based glass fiber filters adopted in commercial DNA extraction kits, and that plant DNA extracted by this method can be readily used as template for PCR. The efficacy of this method was also fully demonstrated by molecular marker analysis in segregating populations of tomato. Due to greatly reduced expense compared to commercial kits, this method is of great value for small labs with limited resources.}, number={3}, journal={Planta}, publisher={Springer Nature}, author={Shi, Rui and Panthee, Dilip R.}, year={2017}, month={Jul}, pages={579–584} }
 @article{adhikari_panthee_meadows_adhikari_louws_2017, title={Characterizing pathogen phenotypes and diversity to inform management decisions to control bacterial spot of tomato in North Carolina}, volume={52}, number={9}, journal={HortScience}, author={Adhikari, P. and Panthee, D.R. and Meadows, I. and Adhikari, T. and Louws, F.J.L.}, year={2017}, pages={S410–S411} }
 @article{adhikari_oh_panthee_2017, title={Current Status of Early Blight Resistance in Tomato: An Update}, volume={18}, ISSN={1422-0067}, url={http://dx.doi.org/10.3390/ijms18102019}, DOI={10.3390/ijms18102019}, abstractNote={Early blight (EB) is one of the dreadful diseases of tomato caused by several species of Alternaria including Alternaria linariae (which includes A. solani and A. tomatophila), as well as A. alternata. In some instances, annual economic yield losses due to EB have been estimated at 79%. Alternaria are known only to reproduce asexually, but a highly-virulent isolate has the potential to overcome existing resistance genes. Currently, cultural practices and fungicide applications are employed for the management of EB due to the lack of strong resistant cultivars. Resistance sources have been identified in wild species of tomato; some breeding lines and cultivars with moderate resistance have been developed through conventional breeding methods. Polygenic inheritance of EB resistance, insufficient resistance in cultivated species and the association of EB resistance with undesirable horticultural traits have thwarted the effective breeding of EB resistance in tomato. Several quantitative trait loci (QTL) conferring EB resistance have been detected in the populations derived from different wild species including Solanum habrochaites, Solanum arcanum and S. pimpinellifolium, but none of them could be used in EB resistance breeding due to low individual QTL effects. Pyramiding of those QTLs would provide strong resistance. More research is needed to identify additional sources of useful resistance, to incorporate resistant QTLs into breeding lines through marker-assisted selection (MAS) and to develop resistant cultivars with desirable horticultural traits including high yielding potential and early maturity. This paper will review the current understanding of causal agents of EB of tomato, resistance genetics and breeding, problems associated with breeding and future prospects.}, number={10}, journal={International Journal of Molecular Sciences}, publisher={MDPI AG}, author={Adhikari, Pragya and Oh, Yeonyee and Panthee, Dilip}, year={2017}, month={Sep}, pages={2019} }
 @misc{panthee_kressin_adhikari_2017, title={Developing disease-resistant tomato varieties}, ISBN={9781786760401}, ISSN={2059-6936}, url={http://dx.doi.org/10.19103/as.2016.0007.32}, DOI={10.19103/as.2016.0007.32}, journal={Achieving sustainable cultivation of tomatoes}, publisher={Burleigh Dodds Science Publishing}, author={Panthee, D. R. and Kressin, J. P. and Adhikari, P.}, year={2017}, month={Mar}, pages={449–494} }
 @article{panthee_veluchamy_shi_piotrowski_2017, title={Evaluation of bacterial speck resistance in tomato breeding}, volume={52}, number={9}, journal={HortScience}, author={Panthee, D.R. and Veluchamy, S. and Shi, R. and Piotrowski, A.}, year={2017}, pages={S357–S358} }
 @article{panthee_piotrowski_ibrahim_2017, title={Mapping Quantitative Trait Loci (QTL) for Resistance to Late Blight in Tomato}, volume={18}, ISSN={1422-0067}, url={http://dx.doi.org/10.3390/ijms18071589}, DOI={10.3390/ijms18071589}, abstractNote={Late blight caused by Phytophthora infestans (Montagne, Bary) is a devastating disease of tomato worldwide. There are three known major genes, Ph-1, Ph-2, and Ph-3, conferring resistance to late blight. In addition to these three genes, it is also believed that there are additional factors or quantitative trait loci (QTL) conferring resistance to late blight. Precise molecular mapping of all those major genes and potential QTL is important in the development of suitable molecular markers and hence, marker-assisted selection (MAS). The objective of the present study was to map the genes and QTL associated with late blight resistance in a tomato population derived from intra-specific crosses. To achieve this objective, a population, derived from the crossings of NC 1CELBR × Fla. 7775, consisting of 250 individuals at F2 and F2-derived families, were evaluated in replicated trials. These were conducted at Mountain Horticultural Crops Reseach & Extension Center (MHCREC) at Mills River, NC, and Mountain Research Staion (MRS) at Waynesville, NC in 2011, 2014, and 2015. There were two major QTL associated with late blight resistance located on chromosomes 9 and 10 with likelihood of odd (LOD) scores of more than 42 and 6, explaining 67% and 14% of the total phenotypic variation, respectively. The major QTLs are probably caused by the Ph-2 and Ph-3 genes. Furthermore, there was a minor QTL on chromosomes 12, which has not been reported before. This minor QTL may be novel and may be worth investigating further. Source of resistance to Ph-2, Ph-3, and this minor QTL traces back to line L3707, or Richter’s Wild Tomato. The combination of major genes and minor QTL may provide a durable resistance to late blight in tomato.}, number={7}, journal={International Journal of Molecular Sciences}, publisher={MDPI AG}, author={Panthee, D.R. and Piotrowski, A. and Ibrahim, R.}, year={2017}, month={Jul}, pages={1589} }
 @article{panthee_piotrowski_ibrahem_2017, title={Mapping quantitative trait loci (QTL) for resistance to late blight in tomato}, volume={18}, number={7}, journal={International Journal of Molecular Sciences}, author={Panthee, D. R. and Piotrowski, A. and Ibrahem, R.}, year={2017} }
 @article{bhattarai_louws_williamson_panthee_2017, title={Resistance to Xanthomonas perforans
 race T4 causing bacterial spot in tomato breeding lines}, volume={66}, ISSN={0032-0862}, url={http://dx.doi.org/10.1111/ppa.12656}, DOI={10.1111/ppa.12656}, abstractNote={Tomato (Solanum lycopersicum) is the second most important vegetable crop in the world. Bacterial spot (BS) of tomato, caused by four species of Xanthomonas: X. euvesicatoria, X. vesicatoria, X. perforans and X. gardneri, results in severe loss in yield and quality due to defoliation and formation of lesions on fruits, respectively. Currently management practices do not offer effective control under conditions of high disease pressure. Thus, developing BS resistance is a critical priority for tomato growers in order to minimize crop losses. Sixty‐three advanced tomato breeding lines, heirlooms and wild tomato lines with diverse genetic backgrounds were screened under greenhouse and field conditions for BS resistance using X. perforans race T4, which was found to be a prevalent race in North Carolina. Race T4 isolate 9 was used to inoculate the plants by spraying, and disease severity was measured using the Horsfall–Barratt scale. Tomato lines 74L‐1W(2008), NC2CELBR, 081‐12‐1X‐gsms, NC22L‐1 (2008) and 52LB‐1 showed resistance to BS in the field and/or greenhouse trials. These lines were derived from S. pimpinellifolium L3707. Screening L3707 followed by development of a mapping population and mapping resistance genes might be useful for breeding resistance against BS in future breeding programmes.}, number={7}, journal={Plant Pathology}, publisher={Wiley}, author={Bhattarai, K. and Louws, F. J. and Williamson, J. D. and Panthee, D. R.}, year={2017}, month={Jan}, pages={1103–1109} }
 @inproceedings{alballat_panthee_2016, title={Assessment of tomato genotypes for resistance to bacterial spot}, booktitle={Annual Conference, Sol Genomics}, author={AlBallat, I.A. and Panthee, D.R.}, year={2016} }
 @inproceedings{panthee_2016, title={Bacterial wilt tolerance improvement in tomato}, booktitle={46th Tomato Breeders Round Table Meeting}, author={Panthee, D.R.}, year={2016}, month={Mar} }
 @inproceedings{kressin_panthee_louws_2016, title={Current status of grafted management of tomato bacterial wilt in the NC Mountain region}, booktitle={31st Tomato Disease Workshop}, author={Kressin, J.P. and Panthee, D.R. and Louws, F.J.}, year={2016} }
 @article{bhattarai_louws_williamson_panthee_2016, title={Differential response of tomato genotypes to Xanthomonas-specific pathogen-associated molecular patterns and correlation with bacterial spot (Xanthomonas perforans) resistance}, volume={3}, DOI={10.1038/hortres.2016.35}, abstractNote={Plants depend on innate immune responses to retard the initial spread of pathogens entering through stomata, hydathodes or injuries. These responses are triggered by conserved patterns in pathogen-encoded molecules known as pathogen-associated molecular patterns (PAMPs). Production of reactive oxygen species (ROS) is one of the first responses, and the resulting ‘oxidative burst’ is considered to be a first line of defense. In this study, we conducted association analyses between ROS production and bacterial spot (BS; Xanthomonas spp.) resistance in 63 genotypes of tomato (Solanum lycopersicum L.). A luminol-based assay was performed on leaf tissues that had been treated with a flagellin 22 (flg22), flagellin 28 and a Xanthomonas-specific flg22 (flg22-Xac) peptide, to measure PAMP-induced ROS production in each genotype. These genotypes were also assessed for BS disease response by inoculation with Xanthomonas perforans, race T4. Although there was no consistent relationship between peptides used and host response to the BS, there was a significant negative correlation (r=−0.25, P<0.05) between foliar disease severity and ROS production, when flg22-Xac was used. This response could potentially be used to identify the Xanthomonas-specific PRR allele in tomato, and eventually PAMP-triggered immunity loci could be mapped in a segregating population. This has potential significance in tomato improvement.}, journal={Horticulture Research}, author={Bhattarai, K. and Louws, F. J. and Williamson, J. D. and Panthee, Dilip}, year={2016} }
 @article{bhattarai_louws_williamson_panthee_2016, title={Diversity analysis of tomato genotypes based on morphological traits with commercial breeding significance for fresh market production in eastern USA}, volume={10}, ISSN={1835-2693 1835-2707}, url={http://dx.doi.org/10.21475/ajcs.2016.10.08.p7391}, DOI={10.21475/ajcs.2016.10.08.p7391}, abstractNote={Tomato is one of the most economically important vegetable crops in the world. Objective of this study was to determine the genetic diversity of tomato based on its horticultural traits. Seventy-one tomato genotypes were planted and grown in two replications with randomized complete block design for two years. Diversity analysis produced six distinct clusters based on average-linkage method. Five principal components (PC) explained more than 92% of the phenotypic variation. Clusters produced in this analysis can be of importance for breeding programs developing specific fruit types based on consumer’s demand.}, number={8}, journal={Australian Journal of Crop Science}, publisher={Southern Cross Publishing}, author={Bhattarai, Krishna and Louws, Frank J. and Williamson, John D. and Panthee, Dilip R.}, year={2016}, month={Aug}, pages={1098–1103} }
 @article{touchell_ranney_panthee_gehl_krings_2016, title={Genetic diversity, cytogenetics, and biomass yields among taxa of giant reeds (Arundo species)}, volume={141}, number={3}, journal={Journal of the American Society for Horticultural Science}, author={Touchell, D. H. and Ranney, T. G. and Panthee, D. R. and Gehl, R. J. and Krings, A.}, year={2016}, pages={256–263} }
 @inproceedings{illa-berenguer_hutton_panthee_van der knaap_2016, title={Genetic fruit weight regulation in 3 distinct tomato (Solanum lycopersicum L.) market classes}, booktitle={Plant and Animal Genome XXIV Conference}, author={Illa-Berenguer, E. and Hutton, S. and Panthee, D. and van der Knaap, Esther}, year={2016}, month={Jan} }
 @article{panthee_kressin_piotrowski_2016, title={Heritability analysis for heat stress tolerance in tomato (Solanum lycopersicum L.)}, volume={51}, number={9}, journal={HortScience}, author={Panthee, D.R. and Kressin, J.P. and Piotrowski, A.}, year={2016}, pages={S191} }
 @article{panthee_kressin_2016, title={Heritability analysis for heat stress tolerance in tomato (solanum lycopersicum l)}, volume={51}, journal={HortScience}, author={Panthee, D.R. and Kressin, J.}, year={2016}, pages={S191} }
 @inproceedings{adhikari_panthee_meadows_adhikari_louws_2016, title={Occurrence of Copper and Streptomycin resistant Xanthomonas spp. in tomato in North Carolina}, booktitle={Annual Meeting. National Association of Plant Breeders}, author={Adhikari, P. and Panthee, D.R. and Meadows, I. and Adhikari, T. and Louws, F.J.}, year={2016} }
 @inproceedings{kressin_silverman_panthee_louws_2016, title={Tomato rootstock resistance to bacterial wilt in the Mountain region of North Carolina}, booktitle={6th International Bacterial Wilt Symposium}, author={Kressin, J.P. and Silverman, E.J. and Panthee, D.R. and Louws, F.J.}, year={2016} }
 @article{panthee_perkins-veazie_2015, title={Comparison of tomato genotypes grown under conventional and organic production system for nutrient composition}, volume={50:9}, journal={HortScience}, author={Panthee, D.R. and Perkins-Veazie, P.}, year={2015}, pages={S300–S301} }
 @article{panthee_perkins-veazie_anderson_ibrahem_2015, title={Diallel Analysis for Lycopene Content in the Hybrids Derived from Different Colored Parents in Tomato}, volume={06}, ISSN={2158-2742 2158-2750}, url={http://dx.doi.org/10.4236/ajps.2015.69147}, DOI={10.4236/ajps.2015.69147}, abstractNote={Lycopene is a red pigment in tomato with purported antioxidant properties. As the amount of lycopene has been reported to differ in different colored tomatoes or even absent in non-red tomatoes, the objective of this study was to investigate the inheritance of lycopene content and the color parameters of hybrids using a 10 parent diallel excluding reciprocals. Parents differed in general combining ability (GCA) for lycopene and color parameters. “Chocolate Stripe” (purple and brown striped) had the highest lycopene content followed by NC 1CS (red colored with the crimson gene) with the best general combining ability among parental lines. Hybrids differed in lycopene content and color parameters across two summer and greenhouse experiments, with no interaction between experiments indicating that the lycopene content was consistent. Narrow-sense heritability for lycopene was only 9% whereas broad-sense heritability was estimated to be 25%. The order of dominance for lycopene content was found as purple-brown > red > blue > yellow > green. Heritability estimates for color parameters were close to those for lycopene. This information may be useful in developing specialty type tomatoes or increasing lycopene content in tomatoes.}, number={09}, journal={American Journal of Plant Sciences}, publisher={Scientific Research Publishing, Inc,}, author={Panthee, Dilip R. and Perkins-Veazie, Penelope and Anderson, Candice and Ibrahem, Ragy}, year={2015}, pages={1483–1492} }
 @article{veluchamy_panthee_2015, title={Differential expression analysis of a select list of genes in susceptible and resistant heirloom tomatoes with respect to Pseudomonas syringae pv. tomato}, volume={142}, ISSN={["1573-8469"]}, DOI={10.1007/s10658-015-0621-z}, number={4}, journal={EUROPEAN JOURNAL OF PLANT PATHOLOGY}, author={Veluchamy, Selvakumar and Panthee, Dilip R.}, year={2015}, month={Aug}, pages={653–663} }
 @article{panthee_gardner_ibrahem_anderson_2015, title={Molecular Markers Associated with Ph-3 Gene Conferring Late Blight  Resistance in Tomato}, volume={06}, ISSN={2158-2742 2158-2750}, url={http://dx.doi.org/10.4236/ajps.2015.613216}, DOI={10.4236/ajps.2015.613216}, abstractNote={Late blight (LB), caused by the oomycete Phytophthora infestans, is one of the most devastating diseases of tomato. Three major genes Ph-1, Ph-2 and Ph-3 conferring resistance to LB have been identified and mapped to the chromosomes 7, 10 and 9, respectively. However, PCR-based molecular markers associated with these genes are limited. Molecular markers are extremely useful in the screening and selection of tomato lines for the development of LB resistant genotypes. The objective of this study was to identify molecular markers associated with Ph-3 gene conferring LB resistance in tomato. Four co-dominant markers were found to be associated with Ph-3, all of which were sequence characterized amplified region (SCAR) type. Breeding lines and cultivars were inoculated with a field isolate of Phytophthora infestans to collect phenotypic data on disease resistance. Genotypic data from molecular markers associated with Ph-3 were in close agreement with the phenotypic data for the lines tested. With the verification of genotypic data from novel molecular markers in known genotypes supported by phenotypic data, the novel molecular markers may be useful in screening tomato populations aiming to develop LB resistant genotypes or cloning the LB resistant genes.}, number={13}, journal={American Journal of Plant Sciences}, publisher={Scientific Research Publishing, Inc,}, author={Panthee, Dilip R. and Gardner, Randy G. and Ibrahem, Ragy and Anderson, Candice}, year={2015}, pages={2144–2150} }
 @article{joshi_louws_yencho_sosinski_arellano_panthee_2015, title={Molecular Markers for Septoria Leaf Spot (Septoria lycopersicii Speg.) Resistance in Tomato (Solanum lycopersicum L.)}, volume={3}, ISSN={2467-9313 2091-1130}, url={http://dx.doi.org/10.3126/njb.v3i1.14230}, DOI={10.3126/njb.v3i1.14230}, abstractNote={Marker assisted selection (MAS) has not been initiated in tomato (Solanum lycopersicum L.) for septoria leaf spot (SLS) resistance caused by Septoria lycopersici Speg due to lack of molecular markers. We studied the inheritance of SLS resistance and identified molecular markers linked to SLS resistance using bulked segregant analysis (BSA) in a segregating F2 population. Tomato inbred lines, NC 85L-1W (2007), susceptible to SLS and NC 839-2(2007)-1, resistant to SLS were used to develop the segregating population. A total of 250 F2 plants, and 10 plants each of P1, P2 and F1 were grown at the Mountain Horticultural Crops Research and Extension Center (MHCREC), Mills River NC in the summer of 2009. Disease severity was scored using a scale of 0 to 5, where 0 = no disease and 5 = complete development of disease. DNA was extracted from 2-3 week old plants and parental lines were screened with a total of 197 random amplified polymorphic DNA (RAPD) primers, of which 34 were polymorphic. Two DNA bulks, called resistant bulk (RB) and susceptible bulk (SB) were prepared from the F2 individuals. The RB and SB consisted of 8 individuals each with disease scores of 0, and 4.0 or 4.5, respectively. The segregation ratio of resistant and susceptible plants in F2 generation fit the expected Mendelian ratio of 3:1 for a single dominant gene. Five RAPD markers were linked to the SLS disease reaction, of which two were linked to susceptibility and three to the resistance. Subject to verification in independent populations, these markers may be useful for MAS of SLS resistance in tomato.Nepal Journal of Biotechnology. Dec. 2015 Vol. 3, No. 1: 40-47}, number={1}, journal={Nepal Journal of Biotechnology}, publisher={Nepal Journals Online (JOL)}, author={Joshi, Bal K and Louws, Frank J and Yencho, G Craig and Sosinski, Byron R and Arellano, Consuelo and Panthee, Dilip R}, year={2015}, month={Dec}, pages={40–47} }
 @article{patel_krasnyanski_allen_louws_panthee_williamson_2015, title={Progeny of Selfed Plants from Tomato Breeding Line ‘NC1 Grape’ Overexpressing Mannitol Dehydrogenase (MTD) Have Increased Resistance to the Early Blight Fungus, Alternaria solani}, volume={16}, ISSN={1535-1025}, url={http://dx.doi.org/10.1094/php-rs-15-0022}, DOI={10.1094/php-rs-15-0022}, abstractNote={ Reactive oxygen species (ROS) made by plants in response to pathogen infection not only initiate local and systemic defenses, they are also antimicrobial. A number of fungi are hypothesized to secrete the antioxidant mannitol to protect against this antimicrobial ROS during infection. This hypothesis is supported by reports that overexpression of the mannitol catabolic enzyme mannitol dehydrogenase (MTD) in plants increases resistance to mannitol-secreting pathogens like Botrytis cinerea and Alternaria alternata. To extend this hypothesis and test the general utility of this approach, we overexpressed celery MTD in a tomato breeding line (NC1 Grape) currently used in our program. Although we reported earlier that MTD overexpression provides resistance to Botrytis gray mold in a greenhouse tomato, this is the first report of overexpression in an elite breeding variety providing heritable, whole-plant resistance to A. solani (tomato early blight). In this study, progeny from a high-MTD-expressing line had infection rates <65% those of nontransformed plants, and transformants outgrew infection by 7 days post-inoculation. Finally, our results suggest that screening for higher innate MTD expression in plants, rather than screening solely for the presence of the Mtd gene, might be a more effective way to identify parental lines for use in conventional breeding of early blight resistance. }, number={3}, journal={Plant Health Progress}, publisher={Scientific Societies}, author={Patel, Takshay K. and Krasnyanski, Sergei F. and Allen, George C. and Louws, Frank J. and Panthee, Dilip R. and Williamson, John D.}, year={2015}, month={Jan}, pages={115–117} }
 @inbook{lohar_panthee_joshi_adhikari_2015, place={Kathmandu, Nepal}, title={Role of Plant breeding and biotechnology in sustainable agriculture development in Nepal}, booktitle={Sustainable Livelihood System in Nepal: Principles, Practices and Prospects}, publisher={IUCN-CFFN}, author={Lohar, D.P. and Panthee, D.R. and Joshi, K.D. and Adhikari, K.N.}, editor={Adhikari, A.P. and Dahal, G.P.Editors}, year={2015}, pages={65–86} }
 @article{patel_krasnyanski_allen_louws_panthee_williamson_2015, title={Tomato Plants Overexpressing a Celery Mannitol Dehydrogenase (MTD) Have  Decreased Susceptibility to <i>Botrytis cinerea</i>}, volume={06}, ISSN={2158-2742 2158-2750}, url={http://dx.doi.org/10.4236/ajps.2015.68116}, DOI={10.4236/ajps.2015.68116}, abstractNote={The oxidative burst is a critical early event in plant-pathogen interactions that leads to a localized, programmed cell death (PCD) called the hypersensitive response (HR). The HR and associated PCD retard infection by biotrophic pathogens, but can, in fact, enhance infection by necrotrophic pa- thogens like Botrytis cinerea. In addition to signaling the induction of the HR, reactive oxygen spe- cies (ROS) produced during the oxidative burst are antimicrobial. We hypothesize that pathogens such as B. cinerea survive the antimicrobial effects of ROS, at least partially by secreting the anti- oxidant mannitol during infection. This is supported by the previous observation that overexpres- sion of the catabolic enzyme mannitol dehydrogenase (MTD) can decrease a plants susceptibility to mannitol-secreting pathogens like B. cinerea. To extend the above hypothesis, and test the gen- eral utility of this approach in an important horticultural crop, we overexpressed celery MTD in tomato (Solanum lycopersicum cv. "Moneymaker"). In these studies, we observed a significant in- crease (up to 90%) in resistance to B. cinerea in transgenic tomatoes expressing high amounts of MTD.}, number={08}, journal={American Journal of Plant Sciences}, publisher={Scientific Research Publishing, Inc,}, author={Patel, Takshay K. and Krasnyanski, Sergei F. and Allen, George C. and Louws, Frank J. and Panthee, Dilip R. and Williamson, John D.}, year={2015}, pages={1116–1125} }
 @inproceedings{kressin_silverman_panthee_louws_2015, title={Tomato rootstock resistance to bacterial wilt as modulated by grafting and NC regional isolates}, booktitle={SE Winter Vegetable Conference}, author={Kressin, J.P. and Silverman, E.J. and Panthee, D.R. and Louws, F.J.}, year={2015} }
 @article{panthee_gardner_2014, title={'Mountain Lion': A large-fruited, extended shelf-life hybrid tomato and its parent line, NC 2rinEC}, volume={49}, number={11}, journal={HortScience}, author={Panthee, D. R. and Gardner, R. G.}, year={2014}, pages={1461–1462} }
 @article{panthee_gardner_2014, title={'Mountain Rouge': A pink-fruited, heirloom-type hybrid tomato and its parent line NC 161L}, volume={49}, number={11}, journal={HortScience}, author={Panthee, D. R. and Gardner, R. G.}, year={2014}, pages={1463–1464} }
 @inproceedings{panthee_ibrahem_perkins-veazie_2014, title={Combining fruit quality and late blight resistance in tomato}, booktitle={2014 ASHS Annual Conference}, author={Panthee, D.R. and Ibrahem, R. and Perkins-Veazie, P.}, year={2014} }
 @inproceedings{touchell_ranney_panthee_gehl_krings_2014, title={Genetic diversity, cytogenetics, and biomass yields among Arundo species and accessions (Arundineae)}, booktitle={ASHS Annual Meeting}, author={Touchell, D.H. and Ranney, T.G. and Panthee, D. and Gehl, R. and Krings, A.}, year={2014} }
 @article{sams_panthee_charron_kopsell_barickman_yuan_2014, title={MICROARRAY ANALYSIS REVEALS SELENIUM DOWN-REGULATES GLUCOSINOLATE BIOSYNTHESIS IN ARABIDOPSIS SHOOTS}, volume={6}, ISSN={0567-7572 2406-6168}, url={http://dx.doi.org/10.17660/actahortic.2014.1040.38}, DOI={10.17660/actahortic.2014.1040.38}, number={1040}, journal={Acta Horticulturae}, publisher={International Society for Horticultural Science (ISHS)}, author={Sams, C.E. and Panthee, D.R. and Charron, C.S. and Kopsell, D.A. and Barickman, T.C. and Yuan, J.S.}, year={2014}, month={Jun}, pages={277–279} }
 @inproceedings{silverman_louws_panthee_2014, title={Mapping Bacterial wilt Resistance in a F2 Population of Tomatoes Derived from CLN1466EA X NC84173}, booktitle={45th Tomato Breeders Round Table Meeting}, author={Silverman, E. and Louws, F.J. and Panthee, D.R.}, year={2014} }
 @inproceedings{panthee_ibrahem_2014, title={Mapping QTL associated with late blight resistance}, booktitle={45th Tomato Breeders Round Table Meeting}, author={Panthee, D.R. and Ibrahem, R.}, year={2014} }
 @inproceedings{sams_panthee_charron_kopsell_yuan_2014, title={Microarray analysis reveals selenium down-regulates glucisonolate biosynthesis in Arabidopsis shoots}, booktitle={FAV HEALTH 2009. 3rd International Symposium on Human Health Effects of Fruits and Vegetables}, author={Sams, C.E. and Panthee, D.R. and Charron, C.S. and Kopsell, D.A. and Yuan, J.S.}, year={2014}, pages={192} }
 @article{veluchamy_hind_dunham_martin_panthee_2014, title={Natural Variation for Responsiveness to flg22, flgII-28, and csp22 and Pseudomonas syringae pv. tomato in Heirloom Tomatoes}, volume={9}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0106119}, abstractNote={Tomato (Solanum lycopersicum L.) is susceptible to many diseases including bacterial speck caused by Pseudomonas syringae pv. tomato. Bacterial speck disease is a serious problem worldwide in tomato production areas where moist conditions and cool temperatures occur. To enhance breeding of speck resistant fresh-market tomato cultivars we identified a race 0 field isolate, NC-C3, of P. s. pv. tomato in North Carolina and used it to screen a collection of heirloom tomato lines for speck resistance in the field. We observed statistically significant variation among the heirloom tomatoes for their response to P. s. pv. tomato NC-C3 with two lines showing resistance approaching a cultivar that expresses the Pto resistance gene, although none of the heirloom lines have Pto. Using an assay that measures microbe-associated molecular pattern (MAMP)-induced production of reactive oxygen species (ROS), we investigated whether the heirloom lines showed differential responsiveness to three bacterial-derived peptide MAMPs: flg22 and flgII-28 (from flagellin) and csp22 (from cold shock protein). Significant differences were observed for MAMP responsiveness among the lines, although these differences did not correlate strongly with resistance or susceptibility to bacterial speck disease. The identification of natural variation for MAMP responsiveness opens up the possibility of using a genetic approach to identify the underlying loci and to facilitate breeding of cultivars with enhanced disease resistance. Towards this goal, we discovered that responsiveness to csp22 segregates as a single locus in an F2 population of tomato.}, number={9}, journal={PLOS ONE}, author={Veluchamy, Selvakumar and Hind, Sarah R. and Dunham, Diane M. and Martin, Gregory B. and Panthee, Dilip R.}, year={2014}, month={Sep} }
 @article{patel_williamson_krasnyanski_panthee_allen_desai_2014, title={Overexpression of Celery Mannitol Dehydrogenase (MTD) in Tomato Increases Resistance to the Mannitol Secreting Fungal Pathogen Botrytis cinerea}, volume={49}, journal={HortScience}, author={Patel, T. and Williamson, J.D. and Krasnyanski, S.F. and Panthee, D.R. and Allen, G.C. and Desai, A.}, year={2014}, pages={S22–S22} }
 @inproceedings{bhattarai_louws_williamson_panthee_2014, title={Screening for bacterial spot resistance}, booktitle={45th Tomato Breeders Round Table Meeting}, author={Bhattarai, K. and Louws, F.J. and Williamson, J.D. and Panthee, D.R.}, year={2014} }
 @article{bhattarai_louws_williamson_panthee_2014, title={Screening of tomato (Solanum lycopersicum L.) lines for Bacterial spot (Xanthomonas sp) resistance}, volume={49}, journal={HortScience}, author={Bhattarai, K. and Louws, F.J. and Williamson, J.D. and Panthee, D.R.}, year={2014}, pages={S244–S244} }
 @inproceedings{bhattarai_louws_williamson_panthee_2014, title={Screening of tomato (Solanum lycopersicum L.) lines for bacterial spot (Xanthomonas spp.) resistance}, booktitle={2014 ASHS Annual Conference}, author={Bhattarai, K. and Louws, F.J. and Williamson, J.D. and Panthee, D.R.}, year={2014} }
 @inproceedings{kressin_louws_panthee_2014, title={The influence of temperature on Bacterial Wilt disease (Ralstonia solanacearum Smith), especially as it pertains to tomato (Solanum lycopersicum L.) from a historical perspective}, booktitle={45th Tomato Breeders Round Table Meeting}, author={Kressin, J.P. and Louws, F.J. and Panthee, D.R.}, year={2014} }
 @inproceedings{kressin_silverman_louws_panthee_2014, title={Tomato rootstock resistance to Bacterial wilt (Ralstonia solanacearum): Effects of genotype and cold stress on epidemic profile}, booktitle={2014 ASHS Annual Conference}, author={Kressin, J.P. and Silverman, E.J. and Louws, F.J. and Panthee, D.R.}, year={2014} }
 @article{panthee_gardner_2013, title={'Mountain Honey' hybrid grape tomato and its parent NC 6 Grape breeding line}, volume={48}, number={9}, journal={HortScience}, author={Panthee, D. R. and Gardner, R. G.}, year={2013}, pages={1192–1194} }
 @article{panthee_gardner_2013, title={'Mountain Vineyard' hybrid grape tomato and its parents: NC 4 Grape and NC 5 Grape tomato breeding lines}, volume={48}, number={9}, journal={HortScience}, author={Panthee, D. R. and Gardner, R. G.}, year={2013}, pages={1189–1191} }
 @article{panthee_foolad_2013, title={A reexamination of molecular markers for use in marker-assisted breeding in tomato (Retraction of vol 184, pg 165, 2012)}, volume={194}, number={1}, journal={Euphytica}, author={Panthee, D. R. and Foolad, M. R.}, year={2013}, pages={149–149} }
 @article{silverman_driver_kressin_panthee_louws_2013, title={Evaluating bacterial wilt resistance of tomato rootstocks in North Carolina}, volume={103}, journal={Phytopathology}, author={Silverman, E.J. and Driver, J. and Kressin, J. and Panthee, D. and Louws, F.J.}, year={2013}, pages={134} }
 @article{panthee_labate_robertson_2013, title={Evaluation of tomato accessions for flavour and flavour-contributing components}, volume={11}, ISSN={["1479-263X"]}, DOI={10.1017/s1479262112000421}, abstractNote={Flavour is one of the most highly demanded consumer traits of tomato at present; poor flavour is one of the most commonly heard complaints associated with modern varieties of tomato. In order to combine flavour with other desirable fruit traits in improved cultivars, it is important to determine how much variability exists in the crucial compounds that contribute most to flavour. The objective of the present study was to determine the variability of flavour-contributing components including total soluble solids (TSS) and total titratable acids (TTA) among other subjective traits related to flavour in a core collection of tomato accessions. The core collection was comprised of 173 tomato accessions with a wide genetic background from the United States Department of Agriculture (USDA), Agricultural Research Services (ARS) Plant Genetic Resources Unit repository. The TTA varied from 0.20 to 0.64%, whereas the TSS ranged from 3.4 to 9.0%, indicating the availability of broad variation for these traits. Rinon (PI 118783), Turrialba, Purple Calabash and LA2102 were among the high TTA (>0.45%) containing accessions, whereas those with high TSS (>7.0%) were AVRDC#6, Sponzillo and LA2102. A positive correlation of overall flavour with TTA (r= 0.33; P< 0.05) and TSS (r= 0.37; P< 0.05) indicated that these two components play an important role in determining the overall flavour in tomato. Subjectively measured other traits including fruity odour and fruity flavour had positive correlations with overall flavour. Overall flavour is discussed in the context of other traits including fruit firmness. Information obtained from this study may be useful for tomato breeders aiming to improve tomato flavour.}, number={2}, journal={PLANT GENETIC RESOURCES-CHARACTERIZATION AND UTILIZATION}, author={Panthee, Dilip R. and Labate, Joanne A. and Robertson, Larry D.}, year={2013}, month={Aug}, pages={106–113} }
 @article{ling_li_panthee_gardner_2013, title={First Report of Potato spindle tuber viroid Naturally Infecting Greenhouse Tomatoes in North Carolina}, volume={97}, ISSN={["0191-2917"]}, DOI={10.1094/pdis-07-12-0679-pdn}, abstractNote={ In spring 2012, a severe disease was observed on a limited number of tomato plants (Solanum lycopersicum L.) in a research greenhouse facility in western North Carolina. The first symptoms noted were downward curling of the terminal leaves accompanied by a rough puckered darker green texture. This was followed in time by greater distortion of the leaves with pale green on leaf margins. Older leaves with symptoms developed necrosis, with necrotic spots and streaks appearing on a few fruits. On some of these affected fruits, stems, peduncles, pedicels, and sepals also showed symptoms. Infected plants were badly stunted, and fruits in the upper parts of plants displaying severe symptoms remained very small. In just a few months, the disease spread to other tomato plants inside the greenhouse. A survey in May 2012 showed a disease incidence of 18% (156 symptomatic plants out of a total of 864) in this greenhouse. Initial screenings for possible viruses using ELISA (Agdia, Elkhart, IN), as well as a reverse transcription (RT)-PCR panel of 15 common tomato viruses in our laboratory were negative. Because of the symptoms and negative results for viruses, a viroid infection was suspected. Total plant RNA was prepared using TRIzol reagent (Invitrogen, Carlsbad, CA) from leaf tissues of eight diseased plants and one seed sample. Using real-time RT-PCR developed against Potato spindle tuber viroid (PSTVd) and some related pospiviroids (1), positive signals were observed with a mean Ct = 13.24 for leaf tissues and Ct = 19.91 for the seed sample. To obtain a full viroid genome, RT-PCR using two different sets of primers, one specific for PSTVd (PSTVd-F and PSTVd-R) (2), and a universal primer set for pospiviroids (MTTVd-F and MTTVd-R) (3) was performed. RT-PCR generated amplicons with expected size of ~360 bp from all eight leaf and one seed samples, but not from a healthy control. PCR products were cloned using the TOPO TA cloning kit (Invitrogen, Carlsbad, CA). A total of 22 full genomic sequences were obtained. A multi-sequence alignment generated a consensus sequence of 360 nt, designated as NC12-01 (GenBank Accession No. JX280944). BLASTn search in the NCBI database revealed the highest sequence identity of 96.9% to Australian (AY962324) and UK (AJ583449) isolates of PSTVd and 95.9% identity to the tomato isolate of PSTVd-CA1 (HM753555). Similar disease symptoms were observed on two ‘Rutgers’ tomato plants 2 weeks post mechanical inoculation and the presence of PSTVd was confirmed by real-time RT-PCR (1). A mock-inoculated plant did not show any symptoms. In the U.S., natural infection of PSTVd on tomato was first identified in California in 2010 (3). To our knowledge, this is the first report of a natural occurrence of PSTVd on tomato in the eastern U.S. The diseased plants were contained, properly disposed of, and eradicated in this location. The broader geographic distribution of PSTVd on tomato in the U.S., and the potential latent infection in potato and a number of ornamentals (4), emphasizes the need for better plant and seed health tests for viroids on these plants. }, number={1}, journal={PLANT DISEASE}, author={Ling, K. -S. and Li, R. and Panthee, D. R. and Gardner, R. G.}, year={2013}, month={Jan}, pages={148–149} }
 @article{panthee_labate_mcgrath_breksa_robertson_2013, title={Genotype and environmental interaction for fruit quality traits in vintage tomato varieties}, volume={193}, ISSN={["1573-5060"]}, DOI={10.1007/s10681-013-0895-1}, number={2}, journal={EUPHYTICA}, author={Panthee, Dilip R. and Labate, Joanne A. and McGrath, Margaret T. and Breksa, Andrew P., III and Robertson, Larry D.}, year={2013}, month={Sep}, pages={169–182} }
 @inproceedings{veluchamy_martin_panthee_2013, title={Heirloom tomatoes show differential sensitivity to Flg22, Flg28, and Csp22 and a field isolate of Pseudomonas syringae pv. tomato}, booktitle={The 27th Annual Retreat, Plant Molecular Biology Consortium}, author={Veluchamy, S. and Martin, G.B. and Panthee, D.R.}, year={2013} }
 @article{panthee_perkins-veazie_randall_brown_2013, title={Lycopene Estimation in Tomato Lines Using Infrared Absorbance and Tomato Analyzer}, volume={19}, ISSN={1931-5260 1931-5279}, url={http://dx.doi.org/10.1080/19315260.2012.715324}, DOI={10.1080/19315260.2012.715324}, abstractNote={The color of red tomatoes (Solanum lycopersicum L.) is mostly from the carotenoid pigment lycopene, which is of interest to consumers and the tomato industry because of its purported protective effects against diabetes, cardiovascular events, and some cancers. Lycopene content was measured in at least 179 tomato lines with pink, red, and dark red fruit derived from a diverse genetic background to determine the level of variation for lycopene and to develop prediction models. Two methods (Tomato Analyzer or DigiEye) for quantifying total lycopene and to develop prediction models were tested on tomato fruit to find a high throughput lycopene measurement system suitable for screening hundreds of lines in a breeding program. The tomato lycopene content ranged from 28 to 133 mg•kg−1 of tomato sample, indicating a wide variation in the set of tomato lines. Using this variation, lycopene prediction models were developed. Though a single equation could not be developed using data from the DigiEye or Tomato Analyzer to predict lycopene content of tomato fruit, individual equations within color groups proved useful in predicting lycopene content (r = 0.77, P < 0.05). Our data indicate that rapid analysis of tomato fruit, kept relatively intact, can be done to accurately predict lycopene content in a wide range of fruit colors. Current address for Dan Randall: Shaw Industries Inc., 200 Industrial Blvd., Bainbridge, GA 39817.}, number={3}, journal={International Journal of Vegetable Science}, publisher={Informa UK Limited}, author={Panthee, Dilip R. and Perkins-Veazie, Penelope and Randall, Dan and Brown, Allan F.}, year={2013}, month={Jul}, pages={240–255} }
 @article{panthee_ibrahem_2013, title={New molecular markers associated with the Sw-5 gene conferring resistance to Tomato spotted wilt virus in tomato}, volume={88}, ISSN={["1462-0316"]}, DOI={10.1080/14620316.2013.11512946}, abstractNote={Summary Tomato spotted wilt virus (TSWV) is an important Tospovirus causing significant crop losses in tomato throughout the World. Resistance to TSWV is conferred by the Sw-5 gene. Screening for TSWV resistance under field conditions, and the development of resistant tomato genotypes based on phenotype is not only time-consuming, but also inconclusive because of variable inoculum pressure in the field. The development of molecular markers for marker-assisted selection (MAS) would help to avoid this problem and facilitate the screening of a large number of independent breeding lines. However, for MAS to be successful, the molecular markers must be reliable, easy to use, and highly reproducible. We evaluated four potential PCR-based markers, developed based on Sw-5 locus-specific sequences. All four PCR-based markers were used successfully to identify resistant and susceptible tomato genotypes, consistent with the phenotypic data. Three (NCSw-003, NCSw-007, and NCSw-011) of the four molecular markers were co-dominant, whereas one (NCSw-012) was dominant. Two of the four molecular markers (NCSw-003 and NCSw-012) were sequence-characterised amplified region (SCAR) markers. The other two (NCSw-007 and NCSw-011) were cleaved amplified polymorphic sequence (CAPS) markers. All four markers were 19 kbp from CT 220, a previously reported molecular marker. All four DNA markers were novel and may be useful to tomato breeders wishing to screen for TSWV resistance in segregating populations.}, number={2}, journal={JOURNAL OF HORTICULTURAL SCIENCE & BIOTECHNOLOGY}, author={Panthee, Dilip R. and Ibrahem, Ragy}, year={2013}, month={Mar}, pages={129–134} }
 @article{panthee_brown_yousef_ibrahem_anderson_2013, title={Novel molecular marker associated with Tm2(a) gene conferring resistance to tomato mosaic virus in tomato}, volume={132}, ISSN={["0179-9541"]}, DOI={10.1111/pbr.12076}, abstractNote={Abstract}, number={4}, journal={PLANT BREEDING}, author={Panthee, Dilip R. and Brown, Allan F. and Yousef, Gad G. and Ibrahem, Ragy and Anderson, Candice}, year={2013}, month={Aug}, pages={413–416} }
 @inproceedings{panthee_van deynze_sim_francis_2013, title={QTL analysis for early blight resistance in tomato}, booktitle={ASHS Annual Meetings}, author={Panthee, D.R. and Van Deynze, A. and Sim, S. and Francis, D.M.}, year={2013} }
 @article{joshi_panthee_louws_yencho_sosinski_arellano_2013, title={RAPD Markers Linked to Late Blight Resistance in Tomato}, volume={14}, ISSN={1994-1412}, url={http://dx.doi.org/10.3126/njst.v14i1.8871}, DOI={10.3126/njst.v14i1.8871}, abstractNote={Identification of marker is the prerequisite for marker assisted selection (MAS) and is also very effective for gene pyramiding. Bulked Segregant Analysis (BSA) technique was used to identify RAPD markers linked to the late blight disease (caused by Phytopthora infestans (Mont. de Bary) resistance in tomato using F2 population generated by crossing tomato inbred lines, NC 85L-1W(2007) which is resistant to late blight and NC 839-2(2007)-1 which is susceptible to it. A total of 250 F2 plants, and 10 plants each of the parents and F1 were used for BSA. Transgressive segregation was observed for late blight resistance. The segregation of susceptible and resistance perfectly fit the expected ratio of 3:1, that means resistance is governed by single recessive gene. Only 34 RAPD primers (17.26%) were found polymorphic between parents. Sixteen RAPD primers (47%) out of 34 gave polymorphic bands between resistant and susceptible bulks of the late blight. Four RAPD primers, namely MRTOMR-026, MRTOMR-031, MRTOMR-038 and MRTOMR-046 were identified as linked markers to loci related to late blight disease. Among those, two were linked to susceptible and two to resistance. Because of low reproducibility and dominant nature of RAPD, these markers need to be converted to SCAR markers. Nepal Journal of Science and Technology Vol. 14, No. 1 (2013) 1-14 DOI: http://dx.doi.org/10.3126/njst.v14i1.8871}, number={1}, journal={Nepal Journal of Science and Technology}, publisher={Nepal Journals Online (JOL)}, author={Joshi, Bal K and Panthee, Dilip R and Louws, Frank J and Yencho, G Craig and Sosinski, Bryon and Arellano, Consuelo}, year={2013}, month={Oct}, pages={1–14} }
 @article{panthee_foolad_2013, title={Retraction Note to: A reexamination of molecular markers for use in marker-assisted breeding in tomato}, volume={194}, ISSN={0014-2336 1573-5060}, url={http://dx.doi.org/10.1007/S10681-013-0966-3}, DOI={10.1007/S10681-013-0966-3}, number={1}, journal={Euphytica}, publisher={Springer Science and Business Media LLC}, author={Panthee, Dilip R. and Foolad, Majid R.}, year={2013}, month={Jul}, pages={149–149} }
 @article{gardner_panthee_2012, title={'Mountain Magic': An early blight and late blight-resistant specialty type F-1 hybrid tomato}, volume={47}, number={2}, journal={HortScience}, author={Gardner, R. G. and Panthee, D. R.}, year={2012}, pages={299–300} }
 @article{panthee_foolad_2012, title={A reexamination of molecular markers for use in marker-assisted breeding in tomato (Retracted article. See vol. 194, pg. 149, 2013)}, volume={184}, ISSN={["1573-5060"]}, DOI={10.1007/s10681-011-0544-5}, number={2}, journal={EUPHYTICA}, author={Panthee, Dilip R. and Foolad, Majid R.}, year={2012}, month={Mar}, pages={165–179} }
 @article{joshi_gardner_panthee_2012, title={Diversity Analysis of Tomato Cultivars Based on Coefficient of Parentage and RAPD Molecular Markers}, volume={26}, ISSN={1542-7528 1542-7536}, url={http://dx.doi.org/10.1080/15427528.2011.623264}, DOI={10.1080/15427528.2011.623264}, abstractNote={Genetic diversity analysis provides information on the genetic base of the gene pool of released genotypes. The objectives of this study were to assess the diversity of tomato cultivars and breeding lines released from North Carolina State University based on their coefficient of parentage (COP) and RAPD markers, and to estimate the contribution of ancestors to these tomato cultivars and breeding lines. The COP analysis revealed that a single ancestor Walter constituted 25.17% of the North Carolina tomato gene pool followed by Blazer (11.57%) and Fla. 2153 (6.29%). Walter was used in developing 30 lines, whereas Blazer and Fla. 2153 were used in developing 29 lines each. The highest COP value (0.828) was between Summit and Monte Verde, indicating that they were the most similar lines. Similarity coefficients based on the RAPD molecular markers ranged from 0.461 to 0.935, with an average of 0.77. The similarity coefficient of NC3Grape with NCEBR8 was the lowest (0.461), whereas it was the highest (0.935) between NC1CS and NC946. On the basis of molecular data, first and second principal components accounted for 78% and 3.3% of the total variation, respectively. A significant positive correlation (r = 0.19, p = 0.04) existed between two similarity matrices based on the RAPD and the pedigree. This information may be useful for selecting the parents in breeding programs, particularly to widen the genetic base for designing future breeding strategies.}, number={2}, journal={Journal of Crop Improvement}, publisher={Informa UK Limited}, author={Joshi, Bal K. and Gardner, Randy G. and Panthee, Dilip R.}, year={2012}, month={Mar}, pages={177–196} }
 @inproceedings{panthee_labate_robertson_2012, title={Evaluation of tomato germplasm for flavor and flavor-contributing components}, booktitle={ASHS Annual Meetings}, author={Panthee, D.R. and Labate, J.L. and Robertson, L.D.}, year={2012}, month={Jul} }
 @article{sim_van deynze_stoffel_douches_zarka_ganal_chetelat_hutton_scott_gardner_et al._2012, title={High-Density SNP Genotyping of Tomato (Solanum lycopersicum L.) Reveals Patterns of Genetic Variation Due to Breeding}, volume={7}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0045520}, abstractNote={The effects of selection on genome variation were investigated and visualized in tomato using a high-density single nucleotide polymorphism (SNP) array. 7,720 SNPs were genotyped on a collection of 426 tomato accessions (410 inbreds and 16 hybrids) and over 97% of the markers were polymorphic in the entire collection. Principal component analysis (PCA) and pairwise estimates of F st supported that the inbred accessions represented seven sub-populations including processing, large-fruited fresh market, large-fruited vintage, cultivated cherry, landrace, wild cherry, and S. pimpinellifolium. Further divisions were found within both the contemporary processing and fresh market sub-populations. These sub-populations showed higher levels of genetic diversity relative to the vintage sub-population. The array provided a large number of polymorphic SNP markers across each sub-population, ranging from 3,159 in the vintage accessions to 6,234 in the cultivated cherry accessions. Visualization of minor allele frequency revealed regions of the genome that distinguished three representative sub-populations of cultivated tomato (processing, fresh market, and vintage), particularly on chromosomes 2, 4, 5, 6, and 11. The PCA loadings and F st outlier analysis between these three sub-populations identified a large number of candidate loci under positive selection on chromosomes 4, 5, and 11. The extent of linkage disequilibrium (LD) was examined within each chromosome for these sub-populations. LD decay varied between chromosomes and sub-populations, with large differences reflective of breeding history. For example, on chromosome 11, decay occurred over 0.8 cM for processing accessions and over 19.7 cM for fresh market accessions. The observed SNP variation and LD decay suggest that different patterns of genetic variation in cultivated tomato are due to introgression from wild species and selection for market specialization.}, number={9}, journal={PLOS ONE}, author={Sim, Sung-Chur and Van Deynze, Allen and Stoffel, Kevin and Douches, David S. and Zarka, Daniel and Ganal, Martin W. and Chetelat, Roger T. and Hutton, Samuel F. and Scott, John W. and Gardner, Randolph G. and et al.}, year={2012}, month={Sep} }
 @inproceedings{ling_li_panthee_gardner_2012, title={Identification of Potato spindle tuber viroid naturally infecting greenhouse tomatoes in North Carolina and its potential in seed transmission}, booktitle={27th Annual Tomato Disease Workshop}, author={Ling, K.S. and Li, R. and Panthee, D.R. and Gardner, R.G.}, year={2012} }
 @article{panthee_cao_debenport_rodriguez_labate_robertson_breksa_knaap_gardener_2012, title={Magnitude of Genotype x Environment Interactions Affecting Tomato Fruit Quality}, volume={47}, ISSN={["2327-9834"]}, DOI={10.21273/hortsci.47.6.721}, abstractNote={There is a growing interest by consumers to purchase fresh tomatoes with improved quality traits including lycopene, total soluble solids (TSS), vitamin C, and total titratable acid (TTA) content. As a result, there are considerable efforts by tomato breeders to improve tomato for these traits. However, suitable varieties developed for one location may not perform the same in different locations. This causes a problem for plant breeders because it is too labor-intensive to develop varieties for each specific location. The objective of this study was to determine the extent of genotype × environment (G×E) interaction that influences tomato fruit quality. To achieve this objective, we grew a set of 42 diverse tomato genotypes with different fruit shapes in replicated trials in three locations: North Carolina, New York, and Ohio. Fruits were harvested at the red ripe stage and analyzed for lycopene, TSS, vitamin C, and TTA. Analysis of variance (ANOVA) revealed that there were significant differences (P < 0.05) among tomato genotypes, locations, and their interaction. Further analysis of quality traits from individual locations revealed that there was as much as 211% change in performance of some genotypes in a certain location compared with the average performance of a genotype. Lycopene was found to be most influenced by the environment, whereas TTA was the least influenced. This was in agreement with heritability estimates observed in the study for these quality traits, because heritability estimate for lycopene was 16%, whereas that for TTA was 87%. The extent of G×E interaction found for the fruit quality traits in the tomato varieties included in this study may be useful in identifying optimal locations for future field trials by tomato breeders aiming to improve tomato fruit quality.}, number={6}, journal={HORTSCIENCE}, author={Panthee, Dilip R. and Cao, Chunxue and Debenport, Spencer J. and Rodriguez, Gustavo R. and Labate, Joanne A. and Robertson, Larry D. and Breksa, Andrew P., III and Knaap, Esther and Gardener, Brian B. McSpadden}, year={2012}, month={Jun}, pages={721–726} }
 @misc{foolad_panthee_2012, title={Marker-Assisted Selection in Tomato Breeding}, volume={31}, ISSN={["1549-7836"]}, DOI={10.1080/07352689.2011.616057}, abstractNote={The cultivated tomato, Solanum lycopersicum L., is the second most consumed vegetable crop after potato and unquestionably the most popular garden crop in the world. There are more varieties of tomato sold worldwide than any other vegetable crop. Most of the commercial cultivars of tomato have been developed through phenotypic selection and traditional breeding. However, with the advent of molecular markers and marker-assisted selection (MAS) technology, tomato genetics and breeding research has entered into a new and exciting era. Molecular markers have been used extensively for genetic mapping as well as identification and characterization of genes and QTLs for many agriculturally important traits in tomato, including disease and insect resistance, abiotic stress tolerance, and flower- and fruit-related characteristics. The technology also has been utilized for marker-assisted breeding for several economically important traits, in particular disease resistance. However, the extent to which MAS has been employed in public and private tomato breeding programs has not been clearly determined. The objectives of this study were to review the publically-available molecular markers for major disease resistance traits in tomato and assess their current and potential use in public and private tomato breeding programs. A review of the literature indicated that although markers have been identified for most disease resistance traits in tomato, not all of them have been verified or are readily applicable in breeding programs. For example, many markers are not validated across tomato genotypes or are not polymorphic within tomato breeding populations, thus greatly reducing their utility in crop improvement programs. However, there seems to be a considerable use of markers, particularly in the private sector, for various purposes, including testing hybrid purity, screening breeding populations for disease resistance, and marker assisted backcross breeding. Here we provide a summary of molecular markers available for major disease resistance traits in tomato and discuss their actual use in tomato breeding programs. It appears that many of the available markers may need to be further refined or examined for trait association and presence of polymorphism in breeding populations. However, with the recent advances in tomato genome and transcriptome sequencing, it is becoming increasingly possible to develop new and more informative PCR-based markers, including single nucleotide polymorphisms (SNPs), to further facilitate the use of markers in tomato breeding. It is also expected that more markers will become available via the emerging technology of genotyping by sequencing (GBS).}, number={2}, journal={CRITICAL REVIEWS IN PLANT SCIENCES}, author={Foolad, Majid R. and Panthee, Dilip R.}, year={2012}, pages={93–123} }
 @article{gardner_panthee_2012, title={Tomato spotted wilt virus-resistant fresh-market tomato breeding lines: NC 58S, NC 123S, NC 127S, and NC 132S}, volume={47}, number={4}, journal={HortScience}, author={Gardner, R. G. and Panthee, D. R.}, year={2012}, pages={531–532} }
 @article{panthee_gardner_2011, title={'Mountain Majesty': A tomato spotted wilt virus-resistant fresh-market hybrid tomato and Its parents NC 714 and NC 1CS}, volume={46}, number={9}, journal={HortScience}, author={Panthee, D. R. and Gardner, R. G.}, year={2011}, pages={1321–1323} }
 @inproceedings{panthee_perkins-veazie_2011, title={Breeding tomato for pigments}, booktitle={43rd Tomato Breeders’ Round Table Meeting}, author={Panthee, D.R. and Perkins-Veazie, P.}, year={2011}, month={Oct} }
 @article{panthee_kopsell_sams_2011, title={Diversity Analysis of Arabidopsis thaliana (L.) Heynh Ecotypes for Glucosinolates in Shoots and Seeds}, volume={46}, ISSN={0018-5345 2327-9834}, url={http://dx.doi.org/10.21273/hortsci.46.7.968}, DOI={10.21273/hortsci.46.7.968}, abstractNote={Glucosinolates (GS) are important secondary plant metabolites present in several plant species, including Arabidopsis thaliana (L.) Heynh. Although genotypic differences among a limited number of samples from a limited geographical range have been reported, there have been few studies exploring the variation from a wider genetic base. The objective of this study was to explore the genetic variation for GS in A. thaliana collected throughout the world. We screened 58 A. thaliana ecotypes collected from the geographic area of lat. 15° N to lat. 59° N and long. 137° E to long. 123° W. Elevation in these areas ranged from sea level to over 480 m. We believe that this study has covered a large geographical region and captured most of the available genetic variation in A. thaliana for GS. There was no geographical trend in A. thaliana shoot or seed tissue for GS concentration. Total shoot GS ranged from 1.1 to 52.8 μmol·g−1 dry weight (DW), averaging 9.3 μmol·g−1 DW among all ecotypes. Total seed GS ranged from 1.6 to 41.8 μmol·g−1 DW with an average of 16.8 μmol·g−1 DW among all ecotypes. Low and high GS-accumulating A. thaliana ecotypes identified in this study may provide a basis for further genetic analysis for GS metabolism. Information provided may also prove useful for improving concentrations of nutritionally beneficial GS in vegetable Brassicas.}, number={7}, journal={HortScience}, publisher={American Society for Horticultural Science}, author={Panthee, Dilip R. and Kopsell, Dean A. and Sams, Carl E.}, year={2011}, month={Jul}, pages={968–974} }
 @article{joshi_gardner_panthee_2011, title={GGE Biplot Analysis of Tomato F1Hybrids Evaluated Across Years for Marketable Fruit Yield}, volume={25}, ISSN={1542-7528 1542-7536}, url={http://dx.doi.org/10.1080/15427528.2011.587138}, DOI={10.1080/15427528.2011.587138}, abstractNote={Genotypes are generally evaluated in multi-environments to determine their consistent performance across locations and years. Several techniques are available to conduct such valuations. We used GGE biplot technique to understand the genotypic and genotype × year interaction in tomato (Solanum lycopersicum L.). Five F1 hybrids of tomato were evaluated from 2003 to 2008 in North Carolina for total marketable fruit yield. Significant (P < 0.05) genotype × year interaction indicated the necessity of further analysis to select the genotype that had high yield and stability across years. ‘Mountain Fresh’ was the best hybrid as far as yield and stability across years were concerned, followed by ‘Crista’; ‘Mountain Glory’ was highly unstable for marketable fruit yield. We concluded that ‘Mountain Fresh’ could be considered an ideal hybrid that can also be used as control for evaluation of other F1 hybrids. Close association between field performance and GGE biplot findings indicated that GGE biplot is a useful tool to graphically visualize the high-yielding and stable genotypes across years.}, number={5}, journal={Journal of Crop Improvement}, publisher={Informa UK Limited}, author={Joshi, Bal K. and Gardner, Randy G. and Panthee, Dilip R.}, year={2011}, month={Sep}, pages={488–496} }
 @article{panthee_gardner_2011, title={Genetic Improvement of Fresh Market Tomatoes for Yield and Fruit Quality Over 35 Years in North Carolina: A Review}, volume={17}, ISSN={1931-5260 1931-5279}, url={http://dx.doi.org/10.1080/19315260.2010.545867}, DOI={10.1080/19315260.2010.545867}, abstractNote={Improving tomatoes (Solanum lycopersicum L.) for higher yield, disease resistance, and better quality is required to make the tomato industry more attractive for tomato growers. Advanced breeding lines and hybrids of fresh market tomatoes were developed and evaluated in replicated yield trials with the objective of identifying superior inbred lines and hybrids in North Carolina. Numerous breeding lines and hybrids have been released from the North Carolina State University tomato breeding program. The objective of this review was to estimate the genetic gain achieved through breeding fresh market tomatoes for fruit yield and quality traits over the period from 1975 through 2009. No review on genetic gain has been performed for a fresh market tomato breeding program. This review describes the current status of fresh market tomato breeding and provides a foundation for future studies. Analysis of the data from replicated yield trials revealed that, although there was no genetic gain for total yield, a significant genetic gain in early marketable yield at the rate of 227 kg·ha−1 per year has been made. Average genetic gain of 3.1 g fruit weight/year increased until 2009. Total yield data indicated that fruit yield improvement potential may have reached a plateau, but there is potential to improve quality traits and disease resistance.}, number={3}, journal={International Journal of Vegetable Science}, publisher={Informa UK Limited}, author={Panthee, Dilip R. and Gardner, Randy G.}, year={2011}, month={Jul}, pages={259–273} }
 @article{joshi_touchell_panthee_ranney_2011, title={Genotype, media and temperature influence regeneration of tomato cultivars from anthers}, volume={47}, journal={Vitro Cellular & Developmental Biology-Animal}, author={Joshi, B.K. and Touchell, D.H. and Panthee, D.R. and Ranney, T.G.}, year={2011}, pages={S65} }
 @article{shi_vierling_grazzini_chen_caton_panthee_2011, title={Identification of molecular markers for Sw-5 gene of tomato spotted wilt virus resistance}, volume={1}, journal={American Journal of Biotechnology and Molecular Sciences}, author={Shi, A. and Vierling, R. and Grazzini, R. and Chen, P. and Caton, H. and Panthee, D.R.}, year={2011}, pages={8–16} }
 @inproceedings{panthee_2011, title={Identification of useful source of bacterial wilt resistance in tomato}, booktitle={26th Annual Tomato Disease Workshop}, author={Panthee, D.R.}, year={2011}, month={Oct} }
 @article{joshi_panthee_2011, title={Information Theory and Multivariate Techniques for Analyzing DNA Sequence Data: An Example from Tomato Genes}, volume={1}, ISSN={2467-9313 2091-1130}, url={http://dx.doi.org/10.3126/njb.v1i1.3867}, DOI={10.3126/njb.v1i1.3867}, abstractNote={  DNA and amino acid sequences are alphabetic symbols having no underlying metric. Use of information theory is one of the solutions for sequence metric problems. The reflection of DNA sequence complexity in phenotype stability might be useful for crop improvement. Shannon-Weaver index (Shannon Entropy, H') and mutual information (MI) index were estimated from DNA sequences of 22 genes, consisted of two gene families of tomato, namely disease resistance and fruit quality. Main objective was use of information theory and multivariate techniques to understand diversity among genes and relate the sequence complexity with phenotypes. The normalized H' value ranged from 0.429 to 0.461. The highest diversity was observed in the gene Crtr-B (beta carotene hydroxylase). Two principal components which accounted for 36.65% variation placed these genes into four groups. Groupings of these genes by both principal component and cluster analyses showed clearly the similarity at phenotypes levels within cluster. Sequences similarity among genes was observed within a family. Diversity assessment of genes applying information theory should link to understand the sequences complexity with respect to gene stability for example stability of resistance gene.Key words: Diversity analysis; DNA sequences; principal component analysis; tomato genesNepal Journal of Biotechnology, 2011, Vol. 1, No. 1 pp.1-9}, number={1}, journal={Nepal Journal of Biotechnology}, publisher={Nepal Journals Online (JOL)}, author={Joshi, Bal K. and Panthee, Dilip R.}, year={2011}, pages={1–9} }
 @article{panthee_perkins-veazie_randall_brown_ducharme_gunter_2011, title={Lycopene content profiling in tomato lines derived from diverse genetic background by colorimetry and infra-red absorbance methods}, volume={46}, number={9}, journal={Hortscience}, author={Panthee, D.R. and Perkins-Veazie, P. and Randall, D. and Brown, A.F. and Ducharme, D. and Gunter, C.C.}, year={2011}, pages={S183–S194} }
 @inproceedings{cao_debenport_rodriguez_labate_panthee_francis_van der knaap_mcspadden-gardener_2011, title={Magnitude of genotype x environment interactions affecting tomato fruit morphology}, number={7538}, booktitle={Plant Biology and Botany Annual Meeting}, author={Cao, C. and Debenport, S.J. and Rodriguez, G.R. and Labate, J.A. and Panthee, D.R. and Francis, D.M. and Van der Knaap, E.K.M. and McSpadden-Gardener, B.B.}, year={2011} }
 @article{shi_vierling_grazzini_chen_caton_panthee_2011, title={Molecular Markers for Tm-2 Alleles of Tomato Mosaic Virus Resistance in Tomato}, volume={02}, ISSN={2158-2742 2158-2750}, url={http://dx.doi.org/10.4236/ajps.2011.22020}, DOI={10.4236/ajps.2011.22020}, abstractNote={Tomato mosaic virus (ToMV) is one of the most infectious virus diseases in tomato (Solanum lycopersicum L). The practical and effective method of controlling this disease is through genetic control by using major resistance genes. So far, three genes Tm-1, Tm-2 and Tm-22 conferring resistance to ToMV have been reported and utilized in tomato culti-var development. Marker assisted selection (MAS) has become very important and useful tool in selection of ToMV re-sistant tomato lines or hybrids. The objective of this research was to identify allele-specific PCR-based, cleaved ampli-fied polymorphic sequence (CAPS), and allele-derived single nucleotide polymorphism (SNP) markers for Tm-2 loci. Four allele-specific PCR-based markers were identified: one for Tm-2, one for Tm-22, and two for the susceptible allele tm-2. Three allele-derived CAPS markers were identified, which can identify and distinguish three alleles, tm-2, Tm-2 and Tm-22 in tomato germplasm. Three SNP markers were developed specific for Tm-2 locus. These markers will pro-vide breeders with a tool in selection of Tm-2 and Tm-22 resistance genes in tomato breeding program.}, number={02}, journal={American Journal of Plant Sciences}, publisher={Scientific Research Publishing, Inc,}, author={Shi, Ainong and Vierling, Richard and Grazzini, Richard and Chen, Pengyin and Caton, Homer and Panthee, Dilip}, year={2011}, pages={180–189} }
 @inproceedings{labate_panthee_mcgrath_francis_breksa_robertson_2011, title={Phenotypic and molecular variation in 44 vintage tomato varieties}, booktitle={43rd Tomato Breeders’ Round Table Meeting}, author={Labate, J.A. and Panthee, D.R. and McGrath, M.T. and Francis, D.M. and Breksa, A. and Robertson, L.D.}, year={2011}, month={Oct} }
 @article{sams_panthee_charron_kopsell_yuan_2011, title={Selenium Regulates Gene Expression for Glucosinolate and Carotenoid Biosynthesis in Arabidopsis}, volume={136}, ISSN={0003-1062 2327-9788}, url={http://dx.doi.org/10.21273/jashs.136.1.23}, DOI={10.21273/jashs.136.1.23}, abstractNote={Glucosinolates (GSs) and carotenoids are important plant secondary metabolites present in several plant species, including arabidopsis (Arabidopsis thaliana). Although genotypic and environmental regulation of GSs and carotenoid compounds has been reported, few studies present data on their regulation at the molecular level. Therefore, the objective of this study was to explore differential expression of genes associated with GSs and carotenoids in arabidopsis in response to selenium fertilization, shown previously to impact accumulations of both classes of metabolites in Brassica species. Arabidopsis was grown under 0.0 or 10.0 μM Na2SeO4 in hydroponic culture. Shoot and root tissue samples were collected before anthesis to measure GSs and carotenoid compounds and conduct gene expression analysis. Gene expression was determined using arabidopsis oligonucleotide chips containing more than 31,000 genes. There were 1274 differentially expressed genes in response to selenium (Se), of which 516 genes were upregulated. Ontology analysis partitioned differentially expressed genes into 20 classes. Biosynthesis pathway analysis using AraCyc revealed that four GSs, one carotenoid, and one chlorophyll biosynthesis pathways were invoked by the differentially expressed genes. Involvement of the same gene in more than one biosynthesis pathway indicated that the same enzyme may be involved in multiple GS biosynthesis pathways. The decrease in carotenoid biosynthesis under Se treatment occurred through the downregulation of phytoene synthase at the beginning of the carotenoid biosynthesis pathway. These findings may be useful to modify the GS and carotenoid levels in arabidopsis and may lead to modification in agriculturally important plant species.}, number={1}, journal={Journal of the American Society for Horticultural Science}, publisher={American Society for Horticultural Science}, author={Sams, Carl E. and Panthee, Dilip R. and Charron, Craig S. and Kopsell, Dean A. and Yuan, Joshua S.}, year={2011}, month={Jan}, pages={23–34} }
 @article{panthee_gardner_2010, title={'Mountain Merit': A late blight-resistant large-fruited tomato hybrid}, volume={45}, number={10}, journal={HortScience}, author={Panthee, D. R. and Gardner, R. G.}, year={2010}, pages={1547–1548} }
 @article{gardner_panthee_2010, title={'Plum Regal' fresh-market plum tomato hybrid and Its parents, NC 25P and NC 30P}, volume={45}, number={5}, journal={HortScience}, author={Gardner, R. G. and Panthee, D. R.}, year={2010}, pages={824–825} }
 @misc{katam_panthee_bhattacharya_basha_kole_2010, title={Arabidopsis}, ISBN={9783642148705 9783642148712}, url={http://dx.doi.org/10.1007/978-3-642-14871-2_1}, DOI={10.1007/978-3-642-14871-2_1}, journal={Wild Crop Relatives: Genomic and Breeding Resources}, publisher={Springer Berlin Heidelberg}, author={Katam, Ramesh and Panthee, Dilip R. and Bhattacharya, Anjanabha and Basha, Sheikh M. and Kole, Chittaranjan}, year={2010}, month={Sep}, pages={1–16} }
 @misc{katam_panthee_basenko_bandopadhyay_basha_eswaran_kole_2010, title={Arabidopsis Genome Initiative}, url={http://dx.doi.org/10.1201/9781439845523-7}, DOI={10.1201/9781439845523-7}, journal={Principles and Practices of Plant Genomics, Volume 3}, publisher={Science Publishers}, author={Katam, Ramesh and Panthee, Dilip and Basenko, Evelina and Bandopadhyay, Rajib and Basha, Sheikh and Eswaran, Kokiladevi and Kole, Chittaranjan}, year={2010}, month={Aug}, pages={175–204} }
 @article{labate_francis_mcgrath_panthee_robertson_2010, title={Diversity in a collection of heirloom tomato varieties}, volume={45}, number={8}, journal={HortScience}, author={Labate, J.A. and Francis, D. and McGrath, M.T. and Panthee, D.R. and Robertson, L.D.}, year={2010}, pages={S145} }
 @article{miles_inglis_gundersen_kreider_roozen_horneburg_panthee_2010, title={Evaluation of late blight on tomato cultivars grown in the field, 2009}, volume={4}, journal={Plant Disease Management Reports}, author={Miles, C. and Inglis, D. and Gundersen, B. and Kreider, P. and Roozen, J. and Horneburg, B. and Panthee, D.}, year={2010}, pages={126} }
 @article{panthee_chen_2010, title={Genomics of Fungal Disease Resistance in Tomato}, volume={11}, ISSN={["1875-5488"]}, DOI={10.2174/138920210790217927}, abstractNote={Tomato (Solanum lycopersicum) is an important vegetable crop worldwide. Often times, its production is hindered by fungal diseases. Important fungal diseases limiting tomato production are late blight, caused by Phytophthora infestans, early blight, caused by Alternaria solanii, and septoria leaf spot, caused by Septoria lycopersici, fusarium wilt caused by Fusarium oxysporium fsp. oxysporium, and verticilium wilt caused by Verticilium dahlea. The Phytophthora infestans is the same fungus that caused the devastating loss of potato in Europe in 1845. A similar magnitude of crop loss in tomato has not occurred but Phytophthora infestans has caused the complete loss of tomato crops around the world on a small scale. Several attempts have been made through conventional breeding and the molecular biological approaches to understand the biology of host-pathogen interaction so that the disease can be managed and crop loss prevented. In this review, we present a comprehensive analysis of information produced by molecular genetic and genomic experiments on host-pathogen interactions of late blight, early blight, septoria leaf spot, verticilim wilt and fusarium wilt in tomato. Furthermore, approaches adopted to manage these diseases in tomato including genetic transformation are presented. Attempts made to link molecular markers with putative genes and their use in crop improvement are discussed.}, number={1}, journal={CURRENT GENOMICS}, author={Panthee, Dilip R. and Chen, Feng}, year={2010}, month={Mar}, pages={30–39} }
 @article{gardner_panthee_2010, title={Grape tomato breeding lines: NC 1 Grape, NC 2 Grape, and NC 3 Grape}, volume={45}, number={12}, journal={HortScience}, author={Gardner, R. G. and Panthee, D. R.}, year={2010}, pages={1887–1888} }
 @inproceedings{panthee_gardner_2010, title={Identification of useful source of resistance for bacterial wilt in tomato: A challenge}, booktitle={25th Annual Tomato Disease Workshop}, author={Panthee, D.R. and Gardner, R.G.}, year={2010} }
 @article{robbins_masud_panthee_gardner_francis_stevens_2010, title={Marker-assisted selection for coupling phase resistance to tomato spotted wilt virus and phytophthora infestans (late blight) in tomato}, volume={45}, number={10}, journal={HortScience}, author={Robbins, M. D. and Masud, M. A. T. and Panthee, D. R. and Gardner, R. G. and Francis, D. M. and Stevens, M. R.}, year={2010}, pages={1424–1428} }
 @article{gardner_panthee_2010, title={NC 1 CELBR and NC 2 CELBR: Early blight and late blight-resistant fresh market tomato breeding lines}, volume={45}, number={6}, journal={HortScience}, author={Gardner, R. G. and Panthee, D. R.}, year={2010}, pages={975–976} }
 @misc{shrivastava_rogers_wszelaki_panthee_chen_2010, title={Plant Volatiles-based Insect Pest Management in Organic Farming}, volume={29}, ISSN={["1549-7836"]}, DOI={10.1080/07352681003617483}, abstractNote={Organic agriculture is increasing in popularity worldwide due to the rapidly growing market for organic products. In organic production, insects present a major pest challenge that negatively impacts crop health and yield. To successfully manage an organic farmland, an effective insect pest management program is key. In this review, we first describe the approaches currently used for pest management in organic farming. Next, we review natural plant defense mechanisms, especially those based on plant volatile organic compounds. Chemically complex, plant volatiles have multiple ecological roles in plant-insect interactions including attracting pollinators, acting as cues for foraging herbivores as well as functioning as direct defense, indirect defense, or interplant priming. Based on the ecological roles of plant volatiles, we then discuss in-depth how pest management may be improved through a variety of strategies including using resistant cultivars, polyculture, using beneficial microorganisms such as mycorrhizal fungi and endophytes, and using plant-derived pesticides, all of which are reviewed in the context of plant volatiles. Lastly, integration of these different strategies based on the trait of plant volatiles for a successful and sustainable pest management program in organic farming is discussed.}, number={2}, journal={CRITICAL REVIEWS IN PLANT SCIENCES}, author={Shrivastava, Gitika and Rogers, Mary and Wszelaki, Annette and Panthee, Dilip R. and Chen, Feng}, year={2010}, pages={123–133} }
 @article{panthee_davis_2010, title={Screening tomato lines for late blight (Phytophthora infestans) resistance under conventional and organic systems}, volume={45}, number={8}, journal={Hortscience}, author={Panthee, D.R. and Davis, J.M.}, year={2010}, pages={S144} }
 @misc{panthee_2010, title={Varietal improvement in soybean.}, url={http://dx.doi.org/10.1079/9781845936440.0092}, DOI={10.1079/9781845936440.0092}, abstractNote={Abstract}, journal={The soybean: botany, production and uses}, publisher={CABI}, author={Panthee, D. R.}, year={2010}, pages={92–112} }
 @inproceedings{panthee_2009, title={Current status of grape and plum tomato breeding at NC State University}, booktitle={42nd Tomato Breeders’ Round Table Meeting}, author={Panthee, D.R.}, year={2009}, month={Jun} }
 @article{panthee_marois_wright_narvaez_yuan_stewart_2009, title={Differential expression of genes in soybean in response to the causal agent of Asian soybean rust (Phakopsora pachyrhizi Sydow) is soybean growth stage-specific}, volume={118}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-008-0905-1}, abstractNote={Understanding plant host response to a pathogen such as Phakopsora pachyrhizi, the causal agent of Asian soybean rust (ASR), under different environmental conditions and growth stages is crucial for developing a resistant plant variety. The main objective of this study was to perform global transcriptome profiling of P. pachyrhizi-exposed soybean (Glycine max) with susceptible reaction to the pathogen from two distinct developmental growth stages using whole genome Affymetrix microarrays of soybean followed by confirmation using a resistant genotype. Soybean cv. 5601T (susceptible to ASR) at the V(4) and R(1) growth stages and Glycine tomentella (resistant to ASR) plants were inoculated with P. pachyrhizi and leaf samples were collected after 72 h of inoculation for microarray analysis. Upon analyzing the data using Array Assist software at 5% false discovery rate (FDR), a total of 5,056 genes were found significantly differentially expressed at V(4) growth stage, of which 2,401 were up-regulated, whereas 579 were found differentially expressed at R(1) growth stage, of which 264 were up-regulated. There were 333 differentially expressed common genes between the V(4) and R(1) growth stages, of which 125 were up-regulated. A large difference in number of differentially expressed genes between the two growth stages indicates that the gene expression is growth-stage-specific. We performed real-time RT-PCR analysis on nine of these genes from both growth stages and both plant species and found results to be congruent with those from the microarray analysis.}, number={2}, journal={THEORETICAL AND APPLIED GENETICS}, author={Panthee, Dilip R. and Marois, James J. and Wright, David L. and Narvaez, Dario and Yuan, Joshua S. and Stewart, C. Neal, Jr.}, year={2009}, month={Jan}, pages={359–370} }
 @book{davis_panthee_gardner_2009, place={Raleigh, NC}, title={Opportunities with Organic and Heirloom Tomatoes}, journal={Farm Prosperity Project}, institution={Department of Horticultural Science, NC State University}, author={Davis, J.M. and Panthee, D.R. and Gardner, R.G.}, year={2009} }
 @article{abercrombie_anderson_baldwin_bang_beldade_bernardi_boubou_branca_bretagnolle_bruford_et al._2009, title={Permanent Genetic Resources added to Molecular Ecology Resources database 1 January 2009-30 April 2009}, volume={9}, ISSN={1755-098X 1755-0998}, url={http://dx.doi.org/10.1111/j.1755-0998.2009.02746.x}, DOI={10.1111/j.1755-0998.2009.02746.x}, abstractNote={Abstract}, number={5}, journal={Molecular Ecology Resources}, publisher={Wiley}, author={Abercrombie, L. G. and Anderson, C. M. and Baldwin, B. G. and Bang, I. C. and Beldade, R. and Bernardi, G. and Boubou, A. and Branca, A. and Bretagnolle, F. and Bruford, M. W. and et al.}, year={2009}, month={Sep}, pages={1375–1379} }
 @inproceedings{panthee_2009, title={Potential tomato hybrids with improved fruit quality and disease resistance}, author={Panthee, D.R.}, year={2009}, month={Dec} }
 @article{panthee_davis_albela_sams_2009, title={Tomato flavor affected by variety and production system}, volume={44}, number={4}, journal={HortScience}, author={Panthee, D.R. and Davis, J.M. and Albela, L.P. and Sams, C.E.}, year={2009}, month={Jul}, pages={1156} }
 @inproceedings{panthee_charron_kopsell_yuan_sams_2008, title={Identification of differentially expressed genes in Arabidopsis shoots in response to selenium}, volume={43}, number={4}, booktitle={HortScience}, author={Panthee, D.R. and Charron, C.S. and Kopsell, D. and Yuan, J. and Sams, C.E.}, year={2008}, month={Jul}, pages={1289} }
 @article{panthee_kopsell_sams_2008, title={Screening of Arabidopsis ecotypes for Glucosinolates accumulated in shoots and seeds}, volume={43}, number={4}, journal={HortScience}, author={Panthee, D.R. and Kopsell, D. and Sams, C.E.}, year={2008}, month={Jul}, pages={1288} }
 @article{delwiche_pordesimo_panthee_pantalone_2007, title={Assessing Glycinin (11S) and β-Conglycinin (7S) Fractions of Soybean Storage Protein by Near-Infrared Spectroscopy}, volume={84}, ISSN={0003-021X 1558-9331}, url={http://dx.doi.org/10.1007/s11746-007-1144-3}, DOI={10.1007/s11746-007-1144-3}, abstractNote={Abstract}, number={12}, journal={Journal of the American Oil Chemists' Society}, publisher={Wiley}, author={Delwiche, Stephen R. and Pordesimo, Lester O. and Panthee, Dilip R. and Pantalone, Vincent R.}, year={2007}, month={Oct}, pages={1107–1115} }
 @inproceedings{panthee_yuan_wright_marois_stewart_2007, title={Differential expression of genes in soybean in response to Asian soybean rust (Phakopsora pachyrhizi Sydow) is specific to the soybean growth stage}, booktitle={Plant Biology}, author={Panthee, D.R. and Yuan, J. and Wright, D.L. and Marois, J. and Stewart, C.N.}, year={2007} }
 @article{panthee_yuan_wright_marois_mailhot_stewart_2007, title={Gene expression analysis in soybean in response to the causal agent of Asian soybean rust (Phakopsora pachyrhizi Sydow) in an early growth stage}, volume={7}, ISSN={1438-793X 1438-7948}, url={http://dx.doi.org/10.1007/s10142-007-0045-8}, DOI={10.1007/s10142-007-0045-8}, abstractNote={Asian soybean rust (ASR) caused by Phakopsora pachyrhizi Sydow is a potentially devastating disease posing a serious threat to the soybean industry. Understanding plant host response at the molecular level is certainly important for control of the disease. The main objective of this study was to perform a transcriptome profiling of P. pachyrhizi-exposed young soybean plants (V2 growth stage) using whole genome Affymetrix microarrays of soybean. Three-week-old soybean cv. 5601 T plants at the V2 growth stage were inoculated with P. pachyrhizi, and leaf samples were collected 72 h post inoculation with subsequent microarray analysis performed. A total of 112 genes were found to be differentially expressed from P. pachyrhizi exposure, of which 46 were upregulated, and 66 were downregulated. Most of the differentially expressed genes were general defense and stress-related genes, and 34 of these were unknown. Confirmational real-time reverse transcription-polymerase chain reaction was performed on a subset of 5 out of 112 differentially expressed genes. These results were congruent with the microarray analysis. Our results indicated that low and nonspecific innate response to the pathogen may account for the failure to develop rust resistance in the soybean variety studied. To our knowledge, this is the first microarray analysis of soybean in response to ASR.}, number={4}, journal={Functional & Integrative Genomics}, publisher={Springer Science and Business Media LLC}, author={Panthee, D. R. and Yuan, J. S. and Wright, D. L. and Marois, J. J. and Mailhot, D. and Stewart, C. N., Jr.}, year={2007}, month={Feb}, pages={291–301} }
 @inproceedings{panthee_yuan_wright_marois_stewart_2007, title={Growth stage specificity for differential gene expression in soybean in response to Phakopsora pachyrhizi Sydow}, booktitle={Third International Plant Pathology Conference}, author={Panthee, D.R. and Yuan, J. and Wright, D.L. and Marois, J. and Stewart, C.N.}, year={2007}, month={Nov} }
 @article{panthee_pantalone_saxton_west_sams_2007, title={Quantitative trait loci for agronomic traits in soybean}, volume={126}, ISSN={0179-9541 1439-0523}, url={http://dx.doi.org/10.1111/j.1439-0523.2006.01305.x}, DOI={10.1111/j.1439-0523.2006.01305.x}, abstractNote={Abstract}, number={1}, journal={Plant Breeding}, publisher={Wiley}, author={Panthee, D. R. and Pantalone, V. R. and Saxton, A. M. and West, D. R. and Sams, C. E.}, year={2007}, month={Feb}, pages={51–57} }
 @inproceedings{panthee_pantalone_saxton_west_sams_2007, title={Quantitative trait loci for agronomic traits in soybean}, booktitle={Agronomy Abstracts}, author={Panthee, D.R. and Pantalone, V.R. and Saxton, A.M. and West, D.R. and Sams, C.E.}, year={2007} }
 @article{panthee_kc_regmi_subedi_bhattarai_dhakal_2006, title={Diversity Analysis of Garlic (Allium sativum L.) Germplasms Available in Nepal Based on Morphological Characters}, volume={53}, ISSN={0925-9864 1573-5109}, url={http://dx.doi.org/10.1007/s10722-004-6690-z}, DOI={10.1007/s10722-004-6690-z}, number={1}, journal={Genetic Resources and Crop Evolution}, publisher={Springer Nature}, author={Panthee, D. R. and Kc, R. B. and Regmi, H. N. and Subedi, P. P. and Bhattarai, S. and Dhakal, J.}, year={2006}, month={Feb}, pages={205–212} }
 @article{panthee_pantalone_saxton_west_sams_2006, title={Genomic Regions Associated with Amino Acid Composition in Soybean}, volume={17}, ISSN={1380-3743 1572-9788}, url={http://dx.doi.org/10.1007/s11032-005-2519-5}, DOI={10.1007/s11032-005-2519-5}, number={1}, journal={Molecular Breeding}, publisher={Springer Nature}, author={Panthee, D. R. and Pantalone, V. R. and Saxton, A. M. and West, D. R. and Sams, C. E.}, year={2006}, month={Jan}, pages={79–89} }
 @article{panthee_yuan_wright_marois_mailhot_stewart_2006, title={Global gene expression analysis in soybean in response to the causal agent of Asian soybean rust (Phakopsora pachyrhizi Sydow)}, ISSN={0375-5495}, number={1735a}, journal={Agronomy Abstracts}, author={Panthee, D.R. and Yuan, J. and Wright, D.L. and Marois, J. and Mailhot, D. and Stewart, N.}, year={2006} }
 @article{panthee_pantalone_saxton_2006, title={Modifier QTL for fatty acid composition in soybean oil}, volume={152}, ISSN={0014-2336 1573-5060}, url={http://dx.doi.org/10.1007/s10681-006-9179-3}, DOI={10.1007/s10681-006-9179-3}, number={1}, journal={Euphytica}, publisher={Springer Nature}, author={Panthee, D. R. and Pantalone, V. R. and Saxton, A. M.}, year={2006}, month={Sep}, pages={67–73} }
 @article{panthee_pantalone_2006, title={Registration of Soybean Germplasm Lines TN03–350 and TN04–5321 with Improved Protein Concentration and Quality}, volume={46}, ISSN={1435-0653}, url={http://dx.doi.org/10.2135/cropsci2005.11.0437}, DOI={10.2135/cropsci2005.11.0437}, abstractNote={Crop ScienceVolume 46, Issue 5 p. 2328-2329 Registrations of Germplasms Registration of Soybean Germplasm Lines TN03–350 and TN04–5321 with Improved Protein Concentration and Quality D.R. Panthee, D.R. Panthee Dep. of Plant Sciences, Univ. of Tennessee, 2431 Joe Johnson Dr., Knoxville, TN, 37996-4561Search for more papers by this authorV.R. Pantalone, Corresponding Author V.R. Pantalone [email protected] Dep. of Plant Sciences, Univ. of Tennessee, 2431 Joe Johnson Dr., Knoxville, TN, 37996-4561Corresponding author ([email protected])Search for more papers by this author D.R. Panthee, D.R. Panthee Dep. of Plant Sciences, Univ. of Tennessee, 2431 Joe Johnson Dr., Knoxville, TN, 37996-4561Search for more papers by this authorV.R. Pantalone, Corresponding Author V.R. Pantalone [email protected] Dep. of Plant Sciences, Univ. of Tennessee, 2431 Joe Johnson Dr., Knoxville, TN, 37996-4561Corresponding author ([email protected])Search for more papers by this author First published: 01 September 2006 https://doi.org/10.2135/cropsci2005.11.0437Citations: 12 Registration by CSSA. Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onEmailFacebookTwitterLinkedInRedditWechat No abstract is available for this article. REFERENCES Brim, C.A. 1966. A modified pedigree method of selection in soybeans. Crop Sci. 6: 220. Burton, J.W., T.E. Carter and R.F. Wilson. 1999. Registration of Prolina soybean. Crop Sci. 39: 294–295. George, A.A. and B.O. de Lumen. 1991. A novel methionine-rich protein in soybean seed: Identification, amino acid composition, and N-terminal sequence. J. Agric. Food Chem. 39: 224–227. Pantalone, V.R., F.L. Allen and D. Landau-Ellis. 2003a. Registration of ‘TN93-99’ Soybean germplasm. Crop Sci. 43: 1137. Pantalone, V.R., F.L. Allen and D. Landau-Ellis. 2003b. Registration of ‘5601T’. Soybean. Crop Sci. 43: 1123–1124. Pantalone, V.R., F.L. Allen and D. Landau-Ellis. 2004. Registration of ‘5002T’. Soybean. Crop Sci. 44: 1483–1484. Paris, B. 2003. Uniform Soybean Test: Southern States 2003. USDA-ARS, Stoneville, MS. Citing Literature Volume46, Issue5September–October 2006Pages 2328-2329 ReferencesRelatedInformation}, number={5}, journal={Crop Science}, publisher={Crop Science Society of America}, author={Panthee, D.R. and Pantalone, V.R.}, year={2006}, pages={2328} }
 @article{pantalone_panthee_sams_saxton_west_2005, title={Genomic regions governing soybean sulfur containing amino acids}, volume={35}, journal={AOCS Abstracts}, author={Pantalone, V.R. and Panthee, D.R. and Sams, C.E. and Saxton, A.M. and West, D.R.}, year={2005} }
 @article{panthee_pantalone_west_saxton_sams_2005, title={Quantitative Trait Loci for Seed Protein and Oil Concentration, and Seed Size in Soybean}, volume={45}, ISSN={1435-0653}, url={http://dx.doi.org/10.2135/cropsci2004.0720}, DOI={10.2135/cropsci2004.0720}, abstractNote={Soybean [Glycine max (L.) Merr.] is an important crop because of its high oil and protein concentration. However, there is an inverse relationship between seed protein and oil concentration, making it difficult to improve both traits simultaneously. Molecular breeding may be helpful to facilitate a balanced accumulation of desirable alleles. The objective of this study was to identify quantitative trait loci (QTL) governing soybean protein, oil and seed size. To achieve this objective, 101 F6–derived recombinant inbred lines (RIL) from a population developed from a cross of N87‐984‐16 × TN93‐99 were used. Heritability estimates on an entry mean basis for protein and oil concentrations, and seed size were 0.66, 0.54, and 0.71, respectively. A total of 585 simple sequence repeat (SSR) molecular genetic markers were screened and 94 were polymorphic in the RIL. Single factor ANOVA was used to identify candidate QTL, which were then confirmed by composite interval mapping. One novel molecular marker (Satt570) on molecular linkage group (MLG) G associated with a protein QTL was detected. Novel molecular markers (Satt274, Satt420, and Satt479) located on MLG D1b, O, and O respectively and a previously reported marker (Satt317) located on MLG H were associated with oil QTL in this study. Molecular markers Satt002 (MLG D2) and Satt184 (MLG D1a) associated with seed size QTL were verified whereas Satt147 (MLG D1a) was novel. The individual QTL explained 20.2, 9.4‐15, and 10 to 16.5% of the phenotypic variation for protein and oil concentrations, and seed size, respectively. Thus, we identified major loci for improving soybean seed quality.}, number={5}, journal={Crop Science}, publisher={Crop Science Society of America}, author={Panthee, D. R. and Pantalone, V. R. and West, D. R. and Saxton, A. M. and Sams, C. E.}, year={2005}, pages={2015} }
 @article{panthee_pantalone_sams_saxton_west_orf_killam_2005, title={Quantitative trait loci controlling sulfur containing amino acids, methionine and cysteine, in soybean seeds}, volume={112}, ISSN={0040-5752 1432-2242}, url={http://dx.doi.org/10.1007/s00122-005-0161-6}, DOI={10.1007/s00122-005-0161-6}, abstractNote={Soybean [Glycine max (L.) Merr.] is the single largest source of protein in animal feed. However, a major limitation of soy proteins is their deficiency in sulfur-containing amino acids, methionine (Met) and cysteine (Cys). The objective of this study was to identify quantitative trait loci (QTL) associated with Met and Cys concentration in soybean seed. To achieve this objective, 101 F(6)-derived recombinant inbred lines (RIL) from a population developed from a cross of N87-984-16 x TN93-99 were used. Ground soybean seed samples were analyzed for Met and Cys concentration using a near infrared spectroscopy instrument. Data were analyzed using SAS software and QTL Cartographer. RIL differed (P<0.01) in Met and Cys concentrations, with a range of 5.1-7.3 (g kg(-1) seed dry weight) for Cys and 4.4-8.8 (g kg(-1) seed dry weight) for Met. Heritability estimates on an entry mean basis were 0.14 and 0.57 for Cys and Met, respectively. A total of 94 polymorphic simple sequence repeat molecular genetic markers were screened in the RIL. Single factor ANOVA was used to identify candidate QTL, which were confirmed by composite interval mapping using QTL Cartographer. Four QTL linked to molecular markers Satt235, Satt252, Satt427 and Satt436 distributed on three molecular linkage groups (MLG) D1a, F and G were associated with Cys and three QTL linked to molecular markers Satt252, Satt564 and Satt590 distributed on MLG F, G and M were associated with Met concentration in soybean seed. QTL associated with Met and Cys in soybean seed will provide important information to breeders targeting improvements in the nutritional quality of soybean.}, number={3}, journal={Theoretical and Applied Genetics}, publisher={Springer Science and Business Media LLC}, author={Panthee, D. R. and Pantalone, V. R. and Sams, C. E. and Saxton, A. M. and West, D. R. and Orf, J. H. and Killam, A. S.}, year={2005}, month={Dec}, pages={546–553} }
 @inproceedings{panthee_pantalone_sams_saxton_west_2004, title={Cysteine and Methionine QTL in soybean}, author={Panthee, D.R. and Pantalone, V.R. and Sams, C.E. and Saxton, A.M. and West, D.R.}, year={2004} }
 @article{panthee_pantalone_sams_saxton_west_rayford_2004, title={Genomic regions governing soybean seed nitrogen accumulation}, volume={81}, ISSN={0003-021X}, url={http://dx.doi.org/10.1007/s11746-004-0860-4}, DOI={10.1007/s11746-004-0860-4}, abstractNote={Abstract}, number={1}, journal={Journal of the American Oil Chemists' Society}, publisher={Wiley}, author={Panthee, D. R. and Pantalone, V. R. and Sams, C. E. and Saxton, A. M. and West, D. R. and Rayford, W. E.}, year={2004}, month={Jan}, pages={77–81} }
 @article{panthee_kwanyuen_sams_west_saxton_pantalone_2004, title={Quantitative trait loci for β-conglycinin (7S) and glycinin (11S) fractions of soybean storage protein}, volume={81}, ISSN={0003-021X}, url={http://dx.doi.org/10.1007/s11746-004-1014-4}, DOI={10.1007/s11746-004-1014-4}, abstractNote={Abstract}, number={11}, journal={Journal of the American Oil Chemists' Society}, publisher={Wiley}, author={Panthee, D. R. and Kwanyuen, P. and Sams, C. E. and West, D. R. and Saxton, A. M. and Pantalone, V. R.}, year={2004}, month={Nov}, pages={1005–1012} }
 @inproceedings{panthee_kwanyuen_sams_west_saxton_pantalone_2004, title={Quantitative trait loci for -conglycinin (7S) and glycinin (11S) fractions of soybean storage protein}, booktitle={10th Biennial Conference of the Cellular and Molecular Biology of the Soybean}, author={Panthee, D.R. and Kwanyuen, P. and Sams, C.E. and West, D.R. and Saxton, A.M. and Pantalone, V.R.}, year={2004} }
 @inproceedings{panthee_sams_saxton_west_pantalone_2004, title={Soybean molecular markers for seed nitrogen accumulation}, author={Panthee, D.R. and Sams, C.E. and Saxton, A.M. and West, D.R. and Pantalone, V.R.}, year={2004} }
 @article{panthee_wetten_caligari_2003, title={Expression and Inheritance of a Transgene for Salinity Tolerance in Tomato}, ISSN={0000-0000}, url={http://dx.doi.org/10.3126/jiaas.v24i0.372}, DOI={10.3126/jiaas.v24i0.372}, abstractNote={The study was conducted to investigate the expression and inheritance of the transgene, oxalate oxidase, conferring salinity tolerance in transgenic lines of tomato ( Lycopersicon esculentum Mill.). R 2 seeds from different lines were assessed for oxalate oxidase, and first back-crosses were planted in the glasshouse with two levels of salt treatments (0% and 1.5%) to determine the level of enzyme expression. A qualitative assessment of R 2 seeds for oxalate oxidase revealed that the gene was inherited in a normal Mendelian fashion as a single dominant gene producing a 3:1 ratio (84%) and 16% produced distinct 15:1 ratios indicating the possibility of presence of two copies of the oxalate oxidase gene in the tomato genome. A quantitative assessment of the tomato leaf extract for oxalate oxidase at different growth stages revealed that the enzyme activity was as low as 0.36 nM H 2 O 2 /min/mg protein in the control genotype to as high as 115 nM H 2 O 2 /min/mg protein in transgenic lines, but there were no significant differences between transgenic lines. Salt treated plants had higher enzyme activity than untreated. There were no differences between young and old leaves for enzyme expression. There was a decreasing trend of enzyme activity with the age of the plant. 
 
 Keywords: Inheritance, Lycopersicon esculentum , oxalate oxidase, salinity, transgene 
 
J. Inst. Agric. Anim. Sci. 2003 24:43-50}, number={24}, journal={Journal of the Institute of Agriculture and Animal Science}, publisher={Nepal Journals Online (JOL)}, author={Panthee, D.R. and Wetten, A. and Caligari, P.D.S.}, year={2003}, pages={43–50} }
 @inproceedings{panthee_pantalone_sams_west_saxton_2003, title={Genomic regions controlling the amino acid composition in soybean}, booktitle={Agronomy Abstracts}, author={Panthee, D.R. and Pantalone, V.R. and Sams, C.E. and West, D.R. and Saxton, A.M.}, year={2003} }
 @inproceedings{panthee_pantalone_sams_west_saxton_rayford_2003, title={Genomic regions governing soybean seed nitrogen accumulation}, booktitle={AOCS Abstracts}, author={Panthee, D.R. and Pantalone, V.R. and Sams, C.E. and West, D.R. and Saxton, A.M. and Rayford, W.E.}, year={2003}, pages={33} }
 @article{panthee_2003, title={Precision agriculture: Its relevance with Nepalese agriculture}, volume={1}, journal={Agri-Link Newsletter}, author={Panthee, D.R.}, year={2003}, pages={3–4} }
 @inproceedings{panthee_wetten_caligari_2000, title={Expression and inheritance of a transgene for salinity tolerance in tomato}, booktitle={3rd International Conference on Biotechnology and Biodiversity}, author={Panthee, D.R. and Wetten, A. and Caligari, P.D.S.}, year={2000}, pages={14–16} }
 @article{panthee_1999, title={Studies on seed dormancy of broad leaf mustard and garden cress}, volume={3}, journal={Nepalese Horticulture}, author={Panthee, D.R.}, year={1999}, pages={30–35} }
 @article{panthee_newbury_1998, title={Effect of genotype, medium and explant on callus production and in vitro regeneration of tomato (Lycopersicon esculentum Mill.)}, volume={2}, journal={Nepal Agriculture Research Journal}, author={Panthee, D.R. and Newbury, H.J.}, year={1998}, pages={20–26} }
 @book{panthee_subedi_1998, place={Nepal}, title={Effect of threshing, cleaning and drying period on onion seed viability}, number={98/18}, institution={Lumle Agricultural Research Centre}, author={Panthee, D.R. and Subedi, P.P.}, year={1998} }
 @article{panthee_newbury_1998, title={Evaluating the performance of tomato (Lycopersicon esculentum Mill.) cultivars for genetic transformation}, volume={2}, journal={Nepal Agriculture Research Journal}, author={Panthee, D.R. and Newbury, H.J.}, year={1998}, pages={48–54} }
 @book{panthee_bhattarai_1998, place={Nepal}, title={Identification of the parents for the production of bacterial wilt tolerant and high yielding hybrids of tomato (Lycopersicon esculentum}, number={98/23}, institution={Lumle Agricultural Research Center}, author={Panthee, D.R. and Bhattarai, S.P.}, year={1998} }
 @book{panthee_bhandari_sah_1998, place={Nepal}, title={Rice varietal improvement research for low-hills carried out at LARC during 1995}, number={98/11}, institution={Lumle Agricultural Research Center}, author={Panthee, D.R. and Bhandari, H.S. and Sah, R.P.}, year={1998} }
 @book{panthee_dhital_budhathoki_1998, place={Nepal}, title={Stability analysis of potato varieties}, number={98/13}, institution={Lumle Agricultural Research Center}, author={Panthee, D.R. and Dhital, B.K. and Budhathoki, C.B.}, year={1998} }
 @article{panthee_1998, title={Storage life of onion seeds in relation to the methods of threshing and cleaning, and drying period}, volume={2}, journal={Nepalese Horticulture}, author={Panthee, D.R.}, year={1998}, pages={31–36} }
 @book{panthee_1998, place={Nepal}, title={Study on morphological characteristics of rice, wheat, oil seed rape, onion, broad leaf mustard and radish varieties, 1996}, number={98/2}, institution={Lumle Agricultural Research Centre}, author={Panthee, D.R.}, year={1998} }
 @article{panthee_1996, title={Efficacy of six different indigenous pesticides for wheat seed storage}, volume={17-18}, journal={Journal of Institute of Agriculture and Animal Sciences}, author={Panthee, D.R.}, year={1996}, pages={69–74} }
 @article{panthee_1996, title={Identification of a suitable indigenous storage structures for wheat seed storage}, volume={17-18}, journal={Journal of Institute of Agriculture and Animal Sciences}, author={Panthee, D.R.}, year={1996}, pages={54–62} }
 @book{panthee_1995, place={Nepal}, title={Change in seed quality under farmers' seed storage system}, number={95/22}, institution={Lumle Agricultural Research Center}, author={Panthee, D.R.}, year={1995} }
 @book{panthee_lohar_shreshtha_subedi_1995, place={Nepal}, title={Constraints and potentialities of vegetable seed privatization in Nepal}, number={95/7}, institution={Lumle Agricultural Research Center}, author={Panthee, D.R. and Lohar, D.P. and Shreshtha, P.K. and Subedi, P.P.}, year={1995} }
 @book{panthee_1995, place={Nepal}, title={Dormancy behavior of radish, broad leaf mustard, cress and cauliflower seeds}, number={95/20}, institution={Lumle Agricultural Research Center}, author={Panthee, D.R.}, year={1995} }
 @book{panthee_1995, place={Nepal}, title={Effect of post-harvest operations on onion seeds viability}, number={95/16}, institution={Lumle Agricultural Research Center}, author={Panthee, D.R.}, year={1995} }
 @book{panthee_1995, place={Nepal}, title={Seed production, quality control, and marketing and distribution system in Nepal}, number={95/1}, institution={Lumle Agricultural Research Center}, author={Panthee, D.R.}, year={1995} }
 @book{panthee_1995, place={Nepal}, title={Study on morphological characteristics of wheat, oil seed rape, onion, broad leaf mustard and radish varieties, 1994/95}, number={95/44}, institution={Lumle Agricultural Research Center}, author={Panthee, D.R.}, year={1995} }