@article{adhikari_gao_ingram_louws_2020, title={Pathogenomics Characterization of an Emerging Fungal Pathogen,Fusarium oxysporumf. sp.lycopersiciin Greenhouse Tomato Production Systems}, volume={11}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2020.01995}, abstractNote={In recent years, greenhouse-grown tomato (Solanum lycopersicum) plants showing vascular wilt and yellowing symptoms have been observed between 2015 and 2018 in North Carolina (NC) and considered as an emerging threat to profitability. In total, 38 putative isolates were collected from symptomatic tomatoes in 12 grower greenhouses and characterized to infer pathogenic and genomic diversity, and mating-type (MAT) idiomorphs distribution. Morphology and polymerase chain reaction (PCR) markers confirmed that all isolates were Fusarium oxysporum f. sp. lycopersici (FOL) and most of them were race 3. Virulence analysis on four different tomato cultivars revealed that virulence among isolates, resistance in tomato cultivars, and the interaction between the isolates and cultivars differed significantly (P < 0.001). Cultivar ‘Happy Root’ (I-1, I-2, and I-3 genes for resistance) was highly resistant to FOL isolates tested. We sequenced and examined for the presence of 15 pathogenicity genes from different classes (Fmk1, Fow1, Ftf1, Orx1, Pda1, PelA, PelD, Pep1, Pep2, eIF-3, Rho1, Scd1, Snf1, Ste12, and Sge1), and 14 Secreted In Xylem (SIX) genes to use as genetic markers to identify and differentiate pathogenic isolates of FOL. Sequence data analysis showed that five pathogenicity genes, Fmk1, PelA, Rho1, Sge1, and Ste12 were present in all isolates while Fow1, Ftf1, Orx1, Peda1, Pep1, eIF-3, Scd1, and Snf1 genes were dispersed among isolates. Two genes, Pep2 and PelD, were absent in all isolates. Of the 14 SIX genes assessed, SIX1, SIX3, SIX5, SIX6, SIX7, SIX8, SIX12, and SIX14 were identified in most isolates while the remaining SIX genes varied among isolates. All isolates harbored one of the two mating-type (MAT-1 or MAT-2) idiomorphs, but not both. The SIX4 gene was present only in race 1 isolates. Diversity assessments based on sequences of the effector SIX3- and the translation elongation factor 1-α encoding genes SIX3 and tef1-α, respectively were the most informative to differentiate pathogenic races of FOL and resulted in race 1, forming a monophyletic clade while race 3 comprised multiple clades. Furthermore, phylogeny-based on SIX3- and tef1-α gene sequences showed that the predominant race 3 from greenhouse production systems significantly overlapped with previously designated race 3 isolates from various regions of the globe.}, journal={FRONTIERS IN MICROBIOLOGY}, author={Adhikari, Tika B. and Gao, Anne and Ingram, Thomas and Louws, Frank J.}, year={2020}, month={Aug} }
 @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}, publisher={Scientific Societies}, 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{jacobs_adhikari_pattison_yencho_fernandez_louws_2019, title={Inheritance of Resistance to Colletotrichum gloeosporioides and C. acutatum in Strawberry}, volume={109}, ISSN={0031-949X 1943-7684}, url={http://dx.doi.org/10.1094/PHYTO-08-18-0283-R}, DOI={10.1094/PHYTO-08-18-0283-R}, abstractNote={ Information on the inheritance of resistance to Colletotrichum gloeosporioides and C. acutatum hemibiotrophic infections (HBI) in strawberry leaf tissue and the genetic control of anthracnose crown rot (ACR) in crown tissue are relatively unknown. Six parental genotypes were crossed in a half-diallel mating design to generate 15 full-sib families. HBI and ACR experiments were conducted concurrently. Both seedlings and parental clones were inoculated with 1 × 106 conidia/ml of C. gloeosporioides or C. acutatum. Percent sporulating leaf area, wilt symptoms, and relative area under the disease progress curve were calculated to characterize resistance among genotypes and full-sib families. Low dominance/additive variance ratios for C. acutatum HBI (0.13) and C. gloeosporioides ACR (0.20) were observed, indicating additive genetic control of resistance to these traits. Heritability estimates were low for C. acutatum HBI (0.25) and C. gloeosporioides HBI (0.16) but moderate for C. gloeosporioides ACR (0.61). A high genetic correlation (rA = 0.98) between resistance to C. acutatum HBI and C. gloeosporioides HBI was observed, suggesting that resistance to these two Colletotrichum spp. may be controlled by common genes in strawberry leaf tissue. In contrast, negative genetic correlations between ACR and both HBI traits (rA = −0.85 and −0.61) suggest that resistance in crown tissue is inherited independently of resistance in leaf tissue in the populations tested. Overall, these findings provide valuable insight into the genetic basis of resistance, and the evaluation and deployment of resistance to HBIs and ACR in strawberry breeding programs. }, number={3}, journal={Phytopathology}, publisher={Scientific Societies}, author={Jacobs, Raymond L. and Adhikari, Tika B. and Pattison, Jeremy and Yencho, G. Craig and Fernandez, Gina E. and Louws, Frank J.}, year={2019}, month={Mar}, pages={428–435} }
 @article{adhikari_mamidi_gurung_bonman_2015, title={Mapping of new quantitative trait loci (QTL) for resistance to Septoria tritici blotch in spring wheat (Triticum aestivum L.)}, volume={205}, number={3}, journal={Euphytica}, author={Adhikari, T. B. and Mamidi, S. and Gurung, S. and Bonman, J. M.}, year={2015}, pages={699–706} }
 @article{gurung_mamidi_bonman_xiong_brown-guedira_adhikari_2014, title={Genome-Wide Association Study Reveals Novel Quantitative Trait Loci Associated with Resistance to Multiple Leaf Spot Diseases of Spring Wheat}, volume={9}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0108179}, abstractNote={Accelerated wheat development and deployment of high-yielding, climate resilient, and disease resistant cultivars can contribute to enhanced food security and sustainable intensification. To facilitate gene discovery, we assembled an association mapping panel of 528 spring wheat landraces of diverse geographic origin for a genome-wide association study (GWAS). All accessions were genotyped using an Illumina Infinium 9K wheat single nucleotide polymorphism (SNP) chip and 4781 polymorphic SNPs were used for analysis. To identify loci underlying resistance to the major leaf spot diseases and to better understand the genomic patterns, we quantified population structure, allelic diversity, and linkage disequilibrium. Our results showed 32 loci were significantly associated with resistance to the major leaf spot diseases. Further analysis identified QTL effective against major leaf spot diseases of wheat which appeared to be novel and others that were previously identified by association analysis using Diversity Arrays Technology (DArT) and bi-parental mapping. In addition, several identified SNPs co-localized with genes that have been implicated in plant disease resistance. Future work could aim to select the putative novel loci and pyramid them in locally adapted wheat cultivars to develop broad-spectrum resistance to multiple leaf spot diseases of wheat via marker-assisted selection (MAS).}, number={9}, journal={PLOS ONE}, author={Gurung, Suraj and Mamidi, Sujan and Bonman, J. Michael and Xiong, Mai and Brown-Guedira, Gina and Adhikari, Tika B.}, year={2014}, month={Sep} }
 @article{adhikari_hodges_louws_2013, title={First Report of Cylindrocarpon sp Associated with Root Rot Disease of Strawberry in North Carolina}, volume={97}, ISSN={["0191-2917"]}, DOI={10.1094/pdis-01-13-0116-pdn}, abstractNote={ Strawberry (Fragaria × ananassa Duchesne) is an economically important fruit crop in North Carolina for domestic consumption and export. In April 2012, outbreaks of a destructive root disease were observed in strawberry cv. Chandler in Buncombe, New Hanover, and Roman counties, North Carolina. Samples from Rowan (ID 13175) and Buncombe (ID 13193) counties submitted to the Plant Disease and Insect Clinic of the Department of Plant Pathology, North Carolina State University, exhibited yellowing and wilting of leaves and extensive root necrosis, and disease severity based on field symptoms ranged from 20 to 30%. To identify the pathogen, five small pieces of necrotic crown and root tissues were taken from each sample, surface disinfested for 1 min in a 1.5% sodium hypochlorite solution, and plated onto potato dextrose agar (PDA) with 0.5 g liter–1 of streptomycin sulfate. Colonies developing from the tissue samples were transferred to PDA. Colonies from both samples were identical, grew relatively slowly, and gradually turned yellowish to partially brownish. After about 7 days, abundant conidia were formed. These were hyaline, mostly straight with both ends rounded, predominantly three septate, and 40 to 50 × 5 to 10 μm. Based on morphological characteristics, these isolates were identified as a species of Cylindrocarpon (1) To confirm the original identification of the fungus as a species of Cylindrocarpon, genomic DNA of both isolates was extracted from mycelia using DNeasy Plant Mini Kit (Qiagen Inc., Valencia, CA) and analyzed using PCR (2). The internal transcribed spacers (ITS)1 and (ITS)2 flanking the 5.8S rRNA regions were amplified and sequenced using universal primers ITS1 (forward) and ITS4 (reverse). The sequences of the 421 bp (GenBank KC847090 and KC847091) of both isolates were identical. Furthermore, a BLASTn search of these sequences showed homology of 99% with the sequences of Cylidrocarpon species (AB369421.1, AM419069.1, AM419074.1, AY295332.1, JN031017.1, JN253505.1, and JQ886422.1), To fulfill Koch's postulates, inoculum of each isolate was prepared and adjusted to 1.5 × 107 conidia/ml using a hemacytometer. ‘Chandler’ strawberry plants were grown in 25-cm diameter plastic pots (one seedling per pot) in the greenhouse and five 6-week-old plants were injected with conidia of each isolate into the base of crown using a 5-ml syringe. The plants were covered with clear plastic for 24 h and left on the greenhouse bench with a 16-h photoperiod and 25/20°C day/night temperatures and assessed for disease development 14 days after inoculation. The inoculated plants exhibited wilting and root necrosis, consistent with the symptoms observed on strawberry plants in the field. Control plants treated with distilled water remained healthy. Isolations were made from the inoculated plants and the fungus used for inoculation was recovered from all plants. The morphology of these isolates was in agreement with published descriptions of Cylindrocarpon (1). To our knowledge, this is the first report of a Cylindrocarpon sp. causing crown and root rot on strawberry in North Carolina and effective disease management strategies need to be explored.  References: (1) C. D. Booth. Mycol. Pap. (CMI) 104:1, 1996. (2) T. J. White et al. Page 315 in: PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego, CA, 1990. }, number={9}, journal={PLANT DISEASE}, publisher={Scientific Societies}, author={Adhikari, T. B. and Hodges, C. S. and Louws, F. J.}, year={2013}, month={Sep}, pages={1251–1251} }
 @article{gurung_short_adhikari_2013, title={Global population structure and migration patterns suggest significant population differentiation among isolates of Pyrenophora tritici-repentis}, volume={52}, journal={Fungal Genetics and Biology}, author={Gurung, S. and Short, D. P. G. and Adhikari, T. B.}, year={2013}, pages={32–41} }
 @article{patel_mamidi_bonman_adhikari_2013, title={Identification of QTL in spring wheat associated with resistance to a novel isolate of Pyrenophora tritici-repentis}, volume={53}, number={3}, journal={Crop Science}, author={Patel, J. S. and Mamidi, S. and Bonman, J. M. and Adhikari, T. B.}, year={2013}, pages={842–852} }
 @article{gurung_mahto_gyawali_adhikari_2013, title={Phenotypic and molecular diversity of Cochliobolus sativus populations from wheat}, volume={97}, number={1}, journal={Plant Disease}, author={Gurung, S. and Mahto, B. N. and Gyawali, S. and Adhikari, T. B.}, year={2013}, pages={62–73} }
 @article{gurung_hansen_bonman_gironella_adhikari_2012, title={Multiple Disease Resistance to Four Leaf Spot Diseases in Winter Wheat Accessions from the USDA National Small Grains Collection}, volume={52}, number={4}, journal={Crop Science}, author={Gurung, S. and Hansen, J. M. and Bonman, J. M. and Gironella, A. I. N. and Adhikari, T. B.}, year={2012}, pages={1640–1650} }