@article{sierra-orozco_smeda_xavier_shekasteband_vallad_hutton_2024, title={Identification of Resistance to Target Spot of Tomato Caused by Corynespora cassiicola in Wild Tomato Accessions}, volume={149}, ISSN={["2327-9788"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85187162143&partnerID=MN8TOARS}, DOI={10.21273/JASHS05345-23}, abstractNote={Tomato (Solanum lycopersicum) is an important vegetable crop and a valuable source of nutrients for the human diet. The southeast is the main fresh market tomato producer of the United States, with much of the production concentrated in Florida. However, production in this region is threatened by plant diseases such as target spot of tomato (TS) caused by Corynespora cassiicola, a multitrophic fungus widely distributed in tropical and subtropical areas. TS can infect foliage and fruit, often resulting in significant yield losses in conductive environments. There are no known TS-resistant cultivars, and control relies entirely on fungicidal sprays. However, several studies have demonstrated that the fungus is developing resistance to commonly used fungicides which further complicates disease management. The objective of this work was to identify sources of resistance to TS from wild Solanum accessions. Initial screens of 83 accessions informed the selection of 24 accessions for a more robust screening in which six diverse C. cassiicola isolates were used for single-isolate inoculation experiments. The results from a broad-sense mixed-model analysis including data from all six experiments demonstrated that all 24 accessions had significantly lower disease severities compared with the susceptible controls, suggesting that all accessions potentially harbor resistance quantitative trait loci (QTLs). Solanum cheesmaniae accession LA0524, S. galapagense accessions LA0483 and LA0532, and S. pimpinellifolium accession LA2093 were among the most resistant accessions tested and may be particularly useful for introgression of resistance into cultivated germplasm and for mapping of TS resistance QTLs.}, number={2}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR HORTICULTURAL SCIENCE}, author={Sierra-Orozco, Edgar and Smeda, John and Xavier, Katia Viana and Shekasteband, Reza and Vallad, Gary E. and Hutton, Samuel F.}, year={2024}, month={Mar}, pages={99–106} }
 @article{lahre_shekasteband_meadows_whitfield_rotenberg_2023, title={First Report of Resistance-Breaking Variants of Tomato Spotted Wilt Virus (TSWV) Infecting Tomatoes with the Sw-5 Resistance Gene in North Carolina}, volume={1}, ISSN={["1943-7692"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85152543677&partnerID=MN8TOARS}, DOI={10.1094/PDIS-11-22-2637-PDN}, abstractNote={Widespread use of tomato cultivars with the Sw-5 resistance gene has led to the emergence of resistance-breaking (RB) strains of tomato spotted wilt virus across the globe. In June of 2022, tomato spotted wilt (TSW) symptoms were observed at two farms (A and B, within 15 miles of each other) in Rowan County, NC on several commercial TSW resistant tomato cultivars (all heterozygous for the Sw-5 gene). At farm A, ~10% of plants had symptomatic foliage with ~30% of fruit with symptoms, while at farm B, up to 50% of plants had symptomatic foliage with ~80% of fruit with symptoms. Visual symptoms included stunting, severe leaf curling and bronzing, necrotic lesions on leaves, petioles and stems, and concentric ring spots on fruit (Supplementary Fig. 1). TSWV ImmunoStrips (AgDia, Elkhart, IN) and reverse-transcription (RT)-PCR with NSm primers (di Rienzo et al 2018) confirmed the presence of TSWV in 12 symptomatic plants sampled across the two farms. Primers designed to detect Impatiens necrotic spot virus, groundnut ringspot virus, tomato chlorotic spot virus, tomato chlorosis virus, alfalfa mosaic virus, and tomato necrotic streak virus (ilarvirus, Badillo et al., 2016) failed to generate amplicons of the expected size from cDNA generated from these field samples. The amplicons from full-length NSm cDNA were sequenced from independent, single-leaflet isolates from the TSWV-positive plants (three from farm A, nine from farm B) with the expectation of finding an amino acid (aa) substitution associated with the Sw-5 RB phenotype identified previously in CA (C118Y, Batuman et al. 2017) or Spain (C118Y and T120N, Lopez et al. 2011). All three nucleotide sequences from farm A contained the NSm C118Y substitution reported in CA. All three sequences were 99% identical (including the C118Y mutation) to NCBI GenBank accession KU179600.1, a TSWV isolate collected from GA in 2014 with no cultivar information reported. The nine nucleotide sequences from farm B contained neither of the two previously reported aa substitutions associated with the RB phenotype. Instead, all contained a D122G substitution within a conserved region of the TSWV NSm protein reported to be involved in direct interaction with the Sw-5 protein (Zhu et al 2017). Likewise, Huang et al (2021) generated a D122A mutation in TSWV-NSm, resulting in failure to elicit a Sw-5 mediated hypersensitive response. Three NSm sequences retrieved from GenBank contained the D122G substitution (AY848921.1, HM015516.1, KU179582.1), however, this mutation was not implicated directly with RB phenotypes (Ciuffo et al., 2005; Lopez et al., 2011; Marshall, 2016). The RB phenotype was confirmed with the NC variants on 'Mountain Merit' (Sw-5) by two means of virus inoculation: mechanical, rub-inoculation with extracted sap from infected plants, and thrips transmission assays with lab colony-maintained, Frankliniella occidentalis, the western flower thrips. Symptomatic leaf tissue obtained from these inoculation assays tested positive for TSWV by DAS-ELISA (AgDia, Elkhart, IN) and RT-PCR with NSm primers, providing definitive evidence of the occurrence of RB-TSWV at both farms, and subsequent sequencing confirmed the C118Y and D122G substitutions. This report warrants further investigation of the putative origins, prevalence and epidemiological implications of RB-TSWV variants in NC tomato production, and the development of new sources of resistance to TSWV.}, number={7}, journal={PLANT DISEASE}, author={Lahre, K. and Shekasteband, R. and Meadows, I. and Whitfield, A. E. and Rotenberg, D.}, year={2023}, month={Jan} }
 @article{oh_ingram_shekasteband_adhikari_louws_dean_2023, title={Tissues and mechanisms associated with Verticillium wilt resistance in tomato using bi-grafted near-isogenic lines}, volume={5}, ISSN={["1460-2431"]}, url={https://doi.org/10.1093/jxb/erad182}, DOI={10.1093/jxb/erad182}, abstractNote={Abstract}, number={15}, journal={JOURNAL OF EXPERIMENTAL BOTANY}, author={Oh, Yeonyee and Ingram, Thomas and Shekasteband, Reza and Adhikari, Tika and Louws, Frank J. and Dean, Ralph A.}, editor={Höfte, MonicaEditor}, year={2023}, month={May} }
 @article{bhandari_shekasteband_lee_2022, title={A Consensus Genetic Map and Linkage Panel for Fresh-market Tomato}, volume={147}, ISSN={["2327-9788"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85123519894&partnerID=MN8TOARS}, DOI={10.21273/JASHS05110-21}, abstractNote={The first consensus genetic map in fresh-market tomato (Solanum lycopersicum) was constructed, combining genetic recombination data from two biparental F2 segregating populations derived from four different fresh-market tomatoes. Each F2 population was nominated by different academic tomato breeding programs located in major fresh-market tomato-producing areas of the United States, and chromosome-wide variation in recombination rates was observed between tomato populations based on the origin of their breeding programs. A consensus map constructed using 335 common single nucleotide polymorphism (SNP) sites found in both populations spanned 737.3 cM across 12 tomato chromosomes, with chromosome 2 containing more than 40% of the total SNPs and chromosomes 4, 5, 7, and 10 together representing less than 10% of the SNPs. There was a high degree of collinearity between the genetic and physical positions of those 335 SNP markers. The integration of 6553 SNP sites that were detected in either of the two populations with 335 common sites resulted in an extended consensus genetic map. The total length of the extended map was estimated to be 1997.9 cM, which was compatible with a previous estimate for large-fruited fresh-market tomato. A linkage panel for fresh-market tomato was also established using the combined dataset of the consensus map of 335 SNP loci and 73 SNP-genotyped core fresh-market tomatoes. An empirical genetic mapping study of the tomato brachytic trait using the linkage panel demonstrated the value of the consensus map and linkage panel for tomato research. The allelic information in the linkage panel will serve as a basis for SNP marker implementation, such as genotyping platforms and genomic association map, in tomato.}, number={1}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR HORTICULTURAL SCIENCE}, author={Bhandari, Prashant and Shekasteband, Reza and Lee, Tong Geon}, year={2022}, month={Jan}, pages={53-+} }
 @article{lee_shekasteband_hutton_lee_2022, title={A mutant allele of the flowering promoting factor 1 gene at the tomato BRACHYTIC locus reduces plant height with high quality fruit}, volume={6}, ISSN={["2475-4455"]}, url={https://doi.org/10.1002/pld3.422}, DOI={10.1002/pld3.422}, abstractNote={Abstract}, number={8}, journal={PLANT DIRECT}, author={Lee, Man Bo and Shekasteband, Reza and Hutton, Samuel F. and Lee, Tong Geon}, year={2022}, month={Aug} }
 @article{sierra-orozco_shekasteband_illa-berenguer_snouffer_knaap_lee_hutton_2021, title={Identification and characterization of GLOBE, a major gene controlling fruit shape and impacting fruit size and marketability in tomato}, volume={8}, ISSN={["2052-7276"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85107449043&partnerID=MN8TOARS}, DOI={10.1038/s41438-021-00574-3}, abstractNote={Abstract}, number={1}, journal={HORTICULTURE RESEARCH}, author={Sierra-Orozco, Edgar and Shekasteband, Reza and Illa-Berenguer, Eudald and Snouffer, Ashley and Knaap, Esther and Lee, Tong Geon and Hutton, Samuel F.}, year={2021}, month={Dec} }
 @article{padmanabhan_ma_shekasteband_stewart_hutton_scott_fei_ling_2019, title={Comprehensive transcriptome analysis and functional characterization of PR-5 for its involvement in tomato Sw-7 resistance to tomato spotted wilt tospovirus}, volume={9}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85066091056&partnerID=MN8TOARS}, DOI={10.1038/s41598-019-44100-x}, abstractNote={Tomato spotted wilt tospovirus (TSWV), one of the most important plant viruses, causes yield losses to many crops including tomato. The current disease management for TSWV is based mainly on breeding tomato cultivars containing the Sw-5 locus. Unfortunately, several Sw-5 resistance-breaking strains of TSWV have been identified. Sw-7 is an alternative locus conferring resistance to a broad range of TSWV strains. In an effort to uncover gene networks that are associated with the Sw-7 resistance, we performed a comparative transcriptome profiling and gene expression analysis between a nearly-isogenic Sw-7 line and its susceptible recurrent parent (Fla. 8059) upon infection by TSWV. A total of 1,244 differentially expressed genes were identified throughout a disease progression process involving networks of host resistance genes, RNA silencing/antiviral defense genes, and crucial transcriptional and translational regulators. Notable induced genes in Sw-7 include those involved in callose accumulation, lignin deposition, proteolysis process, transcriptional activation/repression, and phosphorylation. Finally, we investigated potential involvement of PR-5 in the Sw-7 resistance. Interestingly, PR-5 overexpressed plants conferred enhanced resistance, resulting in delay in virus accumulation and symptom expression. These findings will facilitate breeding and genetic engineering efforts to incorporate this new source of resistance in tomato for protection against TSWV.}, number={1}, journal={Scientific Reports}, publisher={Nature Publishing Group}, author={Padmanabhan, C. and Ma, Q. and Shekasteband, R. and Stewart, K.S. and Hutton, S.F. and Scott, J.W. and Fei, Z. and Ling, K.-S.}, year={2019}, pages={1–17} }
 @article{gill_scott_shekasteband_ogundiwin_schuit_francis_sim_smith_hutton_2019, title={Ty-6, a major begomovirus resistance gene on chromosome 10, is effective against Tomato yellow leaf curl virus and Tomato mottle virus}, volume={132}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85061514068&partnerID=MN8TOARS}, DOI={10.1007/s00122-019-03298-0}, abstractNote={Ty-6 is a major resistance gene on chromosome 10 of tomato that provides resistance against monopartite and bipartite begomoviruses and complements resistance conferred by the known Ty-3 and ty-5 genes. Resistance to monopartite and bipartite begomoviruses is an important breeding objective for cultivated tomato. Several begomovirus resistance genes have been introgressed from related Solanum species and are available for breeding purposes. In the present study, we mapped an additional locus, Ty-6, to chromosome 10 of tomato. Ty-6 is effective against both monopartite Tomato yellow leaf curl virus (TYLCV) and bipartite Tomato mottle virus (ToMoV). Gene action is incomplete dominance, with an intermediate resistance response when Ty-6 is heterozygous. Analysis of populations segregating for Ty-6 along with Ty-3 or ty-5 indicates that the highest level of resistance against TYLCV is attained when Ty-6 is combined with an additional resistance allele. Our results also demonstrate that ty-5 is ineffective against ToMoV. Although multiple SNPs linked to Ty-6 were identified and can be used for breeding purposes, none of these were consistently polymorphic between Ty-6 and ty-6 breeding lines. Further research is underway to generate resequencing data for several Ty-6 inbred lines for the discovery of additional sequence polymorphisms that can be used for fine mapping and characterizing the Ty-6 locus.}, number={5}, journal={Theoretical and Applied Genetics}, publisher={Springer Berlin Heidelberg}, author={Gill, U. and Scott, J.W. and Shekasteband, R. and Ogundiwin, E. and Schuit, C. and Francis, D.M. and Sim, S.-C. and Smith, H. and Hutton, S.F.}, year={2019}, pages={1543–1554} }
 @article{lee_hutton_shekasteband_2018, title={Fine mapping of the brachytic locus on the tomato genome}, volume={143}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85052404493&partnerID=MN8TOARS}, DOI={10.21273/JASHS04423-18}, abstractNote={Mechanization of farm work is increasingly demanded for the current system of fresh-market tomato ( Solanum lycopersicum ) production. One essential element for the adoption of mechanical harvest of fresh-market tomatoes is modification of plant architecture so that the crop can be grown without staking. To address this in the current production system, the stem length should be reduced. The tomato brachytic ( br ) locus has been shown to be a primary source of reducing stem length. To improve the effectiveness of marker-assisted selection (MAS) for the br -mediated trait and to provide resources for cloning this gene, we fine-mapped br to the tomato genome. Fine mapping of br to chromosome 1 was initiated by a survey of genome-wide single-nucleotide polymorphisms (SNPs) shown to be polymorphic between the br phenotype and normal using the tomato array, identifying the interval that harbors br . Genetic markers that flank the locus further permitted saturation of the interval. Twenty-six fixed homozygous recombinant lines were identified together in two different populations and tested with those markers. These efforts resulted in the first report that the br is fine-mapped to a 763-kb physical interval of tomato reference genome. The identified markers close to the br in the present study will be significant resources for MAS and gene cloning research.}, number={4}, journal={Journal of the American Society for Horticultural Science}, publisher={American Society for Horticultural Science}, author={Lee, T.G. and Hutton, S.F. and Shekasteband, R.}, year={2018}, pages={239–247} }
 @article{lee_shekasteband_menda_mueller_hutton_2018, title={Molecular markers to select for the j-2–mediated jointless pedicel in tomato}, volume={53}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85042853983&partnerID=MN8TOARS}, DOI={10.21273/HORTSCI12628-17}, abstractNote={The jointless pedicel trait of tomato conferred by the j-2 gene is widely used in processing markets for stem-free removal of fruit to accommodate mechanized harvest. Although current utilization of j-2 for fresh-market tomato breeding is limited, interest in this trait may increase as breeders seek to address high labor costs through the development of mechanically harvestable cultivars for the fresh market. Yet, the introduction of this trait into new market classes heavily relies on phenotypic selection because there are presently no high-throughput methods available to genotype j-2 . Reliable, high-throughput molecular markers to genotype the presence/absence of j-2 for selective breeding were developed. The molecular markers described here use the high-resolution DNA melting analysis (HRM) genotyping with single-nucleotide polymorphism (SNP) and derived cleaved amplified polymorphic sequence (dCAPS)–based genotyping. Two separate HRM-based markers target the j-2 on chromosome 12 or a linked sequence region 3.5 Mbp apart from the gene, and a dCAPS marker resides on the latter. We demonstrate the association between each marker and the jointless pedicel phenotype using segregating populations of diverse filial generations in multiple genetic backgrounds. These markers provide a useful resource for marker-assisted selection of j-2 in breeding populations.}, number={2}, journal={HortScience}, publisher={American Society for Horticultural Science}, author={Lee, T.G. and Shekasteband, R. and Menda, N. and Mueller, L.A. and Hutton, S.F.}, year={2018}, pages={153–158} }
 @article{lee_hutton_shekasteband_2017, title={Genetics of the Compact Growth Habit Trait}, journal={TOMATO PROCEEDINGS}, author={Lee, Tong Geon and Hutton, Samuel and Shekasteband, Reza}, year={2017}, pages={6} }
 @article{khavarinejad_others_2016, title={The Study of Some Morphological, Physiological and Molecular Parameters in the Chs Mutants of Arabidopsis thaliana}, volume={7}, number={1}, journal={Modares Journal of Biotechnology}, publisher={Modares Journal of Biotechnology}, author={Khavarinejad, Ramazan Ali and others}, year={2016}, pages={1–10} }
 @book{scott_hutton_shekasteband_sim_francis_2015, title={Identification of tomato bacterial spot race T1, T2, T3, T4, and Xanthomonas gardneri resistance QTLs derived from PI 114490 populations selected for race T4}, volume={1069}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84928323948&partnerID=MN8TOARS}, DOI={10.17660/ActaHortic.2015.1069.6}, journal={Acta Horticulturae}, author={Scott, J.W. and Hutton, S.F. and Shekasteband, R. and Sim, S.C. and Francis, D.M.}, year={2015}, pages={53–58} }
 @article{gharari_nejad_band_najafi_nabiuni_irian_2014, title={The role of Mn-SOD and Fe-SOD genes in the response to low temperature in chs mutants of Arabidopsis}, volume={38}, number={1}, journal={Turkish Journal of Botany}, publisher={The Scientific and Technological Research Council of Turkey}, author={Gharari, Zahra and NEJAD, RAMAZANALI KHAVARI and BAND, REZA SHEKASTE and Najafi, Farzane and Nabiuni, Mohammad and Irian, Saeed}, year={2014}, pages={80–88} }
 @inproceedings{hutton_scott_shekasteband_levin_lapidot_2013, title={Combinations of Ty resistance genes generally provide more effective control against begomoviruses than do single genes}, booktitle={IV International Symposium on Tomato Diseases 1069}, author={Hutton, SF and Scott, JW and Shekasteband, R and Levin, I and Lapidot, M}, year={2013}, pages={59–64} }
 @inproceedings{scott_hutton_shekasteband_sim_francis_2013, title={Identification of tomato bacterial spot race T1, T2, T3, T4, and Xanthomonas gardneri resistance QTLs derived from PI 114490 populations selected for race T4}, booktitle={IV International Symposium on Tomato Diseases 1069}, author={Scott, JW and Hutton, SF and Shekasteband, R and Sim, SC and Francis, David M}, year={2013}, pages={53–58} }
 @article{khavari-nejad_band_najafi_nabiuni_gharari_2013, title={The role of Pro-P5C Cycle in chs mutants of Arabidopsis under cold stress}, volume={60}, number={3}, journal={Russian journal of plant physiology}, publisher={Springer}, author={Khavari-Nejad, RA and Band, R Shekaste and Najafi, F and Nabiuni, M and Gharari, Z}, year={2013}, pages={375–382} }
 @inbook{zoldan_band_guy_porat_2012, title={Understanding chilling tolerance traits using Arabidopsis chilling-sensitive mutants}, booktitle={Environmental Adaptations and Stress Tolerance of Plants in the Era of Climate Change}, publisher={Springer}, author={Zoldan, Dana and Band, Reza Shekaste and Guy, Charles L and Porat, Ron}, year={2012}, pages={159–173} }
 @article{reza_heidari_zare_norastehnia_2006, title={Antioxidant response of two salt-stressed barley varieties in the presence or absence of exogenous proline}, volume={32}, number={3-4}, journal={Gen. Appl. Plant Physiol}, author={Reza, S and Heidari, R and Zare, S and Norastehnia, A}, year={2006}, pages={233–251} }
 @article{norastehnia_shekastebandb_nojavan-asghari, title={Auxin and Ethylene Was Decreased in the Germinating Maize (Zea mays) Seeds by Methyl Jasmonate}, author={Norastehnia, Akbar and Shekastebandb, Reza and Nojavan-Asghari, Majid} }
 @article{shekasteband_hutton_scott, title={Designing new DNA markers and determining the effective size of Ph-2 and Ph-3 introgressions for late blight resistance stacking purposes in tomato.}, author={Shekasteband, Reza and Hutton, Samuel F and Scott, Jay W} }
 @article{sierra-orozco_shekasteband_hutton_others, title={Fine-mapping and characterization of a novel fruit shape locus in tomato (Solanum lycopersicum L.)}, author={Sierra-Orozco, Edgar and Shekasteband, Reza and Hutton, Samuel and others} }