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Anderson TA, Sudermann MA, DeJong DM, Francis DM, Smart CD, Mutschler MA. Detection of trait donors and QTL boundaries for early blight resistance using local ancestry inference in a library of genomic sequences for tomato. Plant J 2024; 117:404-415. [PMID: 37856521 DOI: 10.1111/tpj.16495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 09/12/2023] [Accepted: 09/27/2023] [Indexed: 10/21/2023]
Abstract
By conducting hierarchical clustering along a sliding window, we generated haplotypes across hundreds of re-sequenced genomes in a few hours. We leveraged our method to define cryptic introgressions underlying disease resistance in tomato (Solanum lycopersicum L.) and to discover resistant germplasm in the tomato seed bank. The genomes of 9 accessions with early blight (Alternaria linariae) disease resistance were newly sequenced and analyzed together with published sequences for 770 tomato and wild species accessions, most of which are available in germplasm collections. Identification of common ancestral haplotypes among resistant germplasm enabled rapid fine mapping of recently discovered quantitative trait loci (QTL) conferring resistance and the identification of possible causal variants. The source of the early blight QTL EB-9 was traced to a vintage tomato named 'Devon Surprise'. Another QTL, EB-5, as well as resistance to bacterial spot disease (Xanthomonas spp.), was traced to Hawaii 7998. A genomic survey of all accessions forecasted EB-9-derived resistance in several heirloom tomatoes, accessions of S. lycopersicum var. cerasiforme, and S. pimpinellifolium PI 37009. Our haplotype-based predictions were validated by screening the accessions against the causal pathogen. There was little evidence of EB-5 prevalence in surveyed contemporary germplasm, presenting an opportunity to bolster tomato disease resistance by adding this rare locus. Our work demonstrates practical insights that can be derived from the efficient processing of large genome-scale datasets, including rapid functional prediction of disease resistance QTL in diverse genetic backgrounds. Finally, our work finds more efficient ways to leverage public genetic resources for crop improvement.
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Affiliation(s)
- Taylor A Anderson
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, 245 Emerson Hall, Ithaca, NY, 14853, USA
| | - Martha A Sudermann
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 630 West North Street, Geneva, NY, 14456, USA
| | - Darlene M DeJong
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, 245 Emerson Hall, Ithaca, NY, 14853, USA
| | - David M Francis
- Department of Horticulture and Crop Science, The Ohio State University, 1680 Madison Avenue, Wooster, OH, 44691, USA
| | - Christine D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 630 West North Street, Geneva, NY, 14456, USA
| | - Martha A Mutschler
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, 245 Emerson Hall, Ithaca, NY, 14853, USA
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Stack GM, Cala AR, Quade MA, Toth JA, Monserrate LA, Wilkerson DG, Carlson CH, Mamerto A, Michael TP, Crawford S, Smart CD, Smart LB. Genetic Mapping, Identification, and Characterization of a Candidate Susceptibility Gene for Powdery Mildew in Cannabis sativa. Mol Plant Microbe Interact 2024; 37:51-61. [PMID: 37750850 DOI: 10.1094/mpmi-04-23-0043-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Powdery mildew (PM) in Cannabis sativa is most frequently caused by the biotrophic fungus Golovinomyces ambrosiae. Based on previously characterized variation in susceptibility to PM, biparental populations were developed by crossing the most resistant cultivar evaluated, 'FL 58', with a susceptible cultivar, 'TJ's CBD'. F1 progeny were evaluated and displayed a range of susceptibility, and two were self-pollinated to generate two F2 populations. In 2021, the F2 populations (n = 706) were inoculated with PM and surveyed for disease severity. In both F2 populations, 25% of the progeny were resistant, while the remaining 75% showed a range of susceptibility. The F2 populations, as well as selected F1 progeny and the parents, were genotyped with a single-nucleotide polymorphism array, and a consensus genetic map was produced. A major effect quantitative trait locus on C. sativa chromosome 1 (Chr01) and other smaller-effect quantitative trait loci (QTL) on four other chromosomes were identified. The most associated marker on Chr01 was located near CsMLO1, a candidate susceptibility gene. Genomic DNA and cDNA sequencing of CsMLO1 revealed a 6.8-kb insertion in FL 58, relative to TJ's CBD, of which 846 bp are typically spliced into the mRNA transcript encoding a premature stop codon. Molecular marker assays were developed using CsMLO1 sequences to distinguish PM-resistant and PM-susceptible genotypes. These data support the hypothesis that a mutated MLO susceptibility gene confers resistance to PM in C. sativa and provides new genetic resources to develop resistant cultivars. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- George M Stack
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456, U.S.A
| | - Ali R Cala
- Plant Pathology and Plant Microbe Biology Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456, U.S.A
| | - Michael A Quade
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456, U.S.A
| | - Jacob A Toth
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456, U.S.A
| | - Luis A Monserrate
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456, U.S.A
| | - Dustin G Wilkerson
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456, U.S.A
| | - Craig H Carlson
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456, U.S.A
| | - Allen Mamerto
- Plant Molecular and Cellular Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, U.S.A
| | - Todd P Michael
- Plant Molecular and Cellular Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, U.S.A
| | | | - Christine D Smart
- Plant Pathology and Plant Microbe Biology Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456, U.S.A
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456, U.S.A
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Rodriguez-Herrera KD, Ma X, Swingle B, Pethybridge SJ, Gonzalez-Giron JL, Hermann TQ, Damann KC, Smart CD. First Report of Cucurbit Yellow Vine Disease Caused by Serratia marcescens on Cucurbits in New York. Plant Dis 2023. [PMID: 37486276 DOI: 10.1094/pdis-06-23-1051-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Cucurbits are one of the most significant commodities in New York, with a value of $92.3 million in 2021 (NASS-USDA 2021). In August 2021, several acorn squash (Cucurbita pepo) cultivar Turbinate plants at Cornell AgriTech research farm in Geneva, NY, had chlorotic, wilting leaves, and older leaves appeared scorched. The phloem of stems, bisected at the crown, had a honey-brown discoloration. The incidence of symptomatic plants was 22% in a one-acre planting field. Most of the symptomatic plants rapidly declined and died. The following year, similar symptoms were observed on muskmelon (Cucumis melo), acorn squash, and winter squash (C. pepo) cultivar Bush Delicata at the same location. These symptoms were typical of Cucurbit Yellow Vine Disease (CYVD) caused by the Gram-negative bacterium Serratia marcescens (Bruton et al. 1998, 2003). Moreover, a high incidence of squash bugs (vector of CYVD) was observed. To identify the causal agent, 45 stems from the symptomatic Bush delicata plants were collected. Each stem was cut into small pieces (2 to 3 mm), surface sterilized with 70% ethanol for 60 sec, 10% bleach for 60 sec, and rinsed with sterile water. The tissue was macerated in sterile water, and the resultant suspension was streaked on King's B (KB) medium (King et al. 1954). Plates were incubated at 28°C for 24 h, and 11 developed white, round bacterial colonies that were smooth and creamy in appearance. Single colonies were transferred to new KB plates and incubated for 24 h. The genomic DNA of two isolates (22212 and 22213) was extracted with the Wizard® Genomic DNA Purification Kit Protocol (Promega, Madison, WI). PCR was carried out using YV1 and YV4 primers specific to the 16S rDNA region of S. marcescens and 79F/R primers specific for S. marcescens causing CYVD (Zhang et al. 2005). The DNA sequence of each PCR product was obtained using Sanger sequencing and submitted to GenBank. Accessions OQ584799 and OQ584800 for YV1/YV4 (isolates 22212 and 22213, respectively) exhibited 100% identity to S. marcescens (384/384 bp, nearest accession identity: CP083754). Accession numbers OQ693911 and OQ693912 for 79F/R showed 99% identity to S. marcescens isolates (309/313 bp, nearest accession identity: CP033623). To fulfill Koch's postulates, Bush Delicata squash plants were grown for two weeks in a greenhouse, and three plants per isolate were inoculated using S. marcescens 22212 and 22213, three plants with Escherichia coli DH5a as a non-pathogenic control, distilled water as a mock-inoculated control, and a noninoculated control. Inoculation was performed by taking a single bacterial colony with a small pin and puncturing the plant's lower stem four to five times (Bruton et al. 2003). Twenty-eight days after inoculation, three of the six plants inoculated with the two S. marcescens isolates (two from 22212 and one from 22213) developed CYVD symptoms as observed in the field. Isolations were made from the stems of symptomatic plants and the mock-inoculated controls. PCR was conducted using YV1/YV4 primers and 79F/R primers (Zhang et al. 2005). Only isolations from symptomatic plants amplified with these primers and PCR products were sequenced. These sequences were identical to the original isolates. To our knowledge, this is the first report of CYVD and phytopathogenic S. marcescens in New York. The impact of CYVD can be substantial, with losses up to 100% (Zhang et al. 2005). Therefore, more knowledge on S. marcescens is needed to determine its biology and prevalence in New York.
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Affiliation(s)
- Kensy D Rodriguez-Herrera
- Cornell AgriTech, 116317, Plant Pathology and Plant Micro Biology, 15 Castle Creek Dr, Geneva, New York, United States, 14456-1371;
| | - Xing Ma
- Cornell University, Plant Pathology and Plant-Microbe Biology, 304 Plant Science Building, Ithaca, New York, United States, 14853;
| | - Bryan Swingle
- Cornell University, 5922, Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Ithaca, New York, United States
- Robert W. Holley Center, United States Department of Agriculture-Agricultural Research Service, Emerging Pests and Pathogens Research Unit, Ithaca, New York, United States;
| | - Sarah Jane Pethybridge
- Cornell University, Plant Pathology and Plant-Microbe Biology, 630 West North Street, 211 Barton Laboratory, Geneva, New York, United States, 14456;
| | | | - Taylere Q Hermann
- Cornell University, School of Integrative Plant Science, 630 West W North St, Geneva, New York, United States, 14456;
| | - Kellie C Damann
- Cornell University, Plant Pathology and Plant Microbe Biology, 5850 Rossier Rd, Canandaigua, New York, United States, 14424;
| | - Christine D Smart
- Cornell University, Plant Pathology, 630 W. North St, Geneva, New York, United States, 14456;
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Nieto-Lopez EH, Cerritos-Garcia DG, Koch Bach RA, Petkar A, Smart CD, Hoepting C, Langston D, Rideout S, Dutta B, Everhart SE. Species Identification and Fungicide Sensitivity of Fungi Causing Alternaria Leaf Blight and Head Rot in Cole Crops in the Eastern United States. Plant Dis 2023:PDIS06221318SC. [PMID: 36324201 DOI: 10.1094/pdis-06-22-1318-sc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Alternaria leaf blight and head rot is an important disease of broccoli and other cole crops. With no resistant host varieties, fungicides are utilized to manage this disease. However, anecdotal evidence suggests that, in southeastern U.S. broccoli-producing states, there is a loss of disease control through the use of quinone outside inhibitor (QoI) fungicides. To understand why there is a reduced sensitivity to QoI fungicides in these states, we isolated Alternaria spp. from symptomatic lesions on cole crops from Georgia and Virginia (two states with observations of loss of fungicide sensitivity) as well as New York (a state with no observations of loss of fungicide sensitivity). Using multilocus sequencing and phylogenetic analysis, we identified two species, Alternaria brassicicola and A. japonica. Whereas A. brassicicola was isolated in all states, A. japonica was only isolated in Georgia. Next, we wanted to determine the sensitivity of these isolates to azoxystrobin-an active ingredient in some QoI fungicides-by estimating the effective concentration at which only 50% of spores germinate (EC50). The EC50 of A. brassicicola ranged from 0.01 to 0.17 ppm, whereas that of A. japonica was 8.1 to 28.1 ppm. None of the known target-site mutations that confer resistance to QoI fungicides were identified during screening of either species. A. japonica was first reported on the east coast of the United States in 2020 in South Carolina. The substantially higher EC50 value suggests that its emergence in the southeastern United States may play at least a part in the observed loss of disease control. However, further in planta and field studies are needed to thoroughly test this hypothesis.
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Affiliation(s)
- Edgar H Nieto-Lopez
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583
| | - Daniel G Cerritos-Garcia
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT 06269
| | - Rachel A Koch Bach
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT 06269
| | - Aparna Petkar
- Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton, GA 31793
| | - Christine D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456
| | - Christy Hoepting
- Cornell Vegetable Program, Cornell Cooperative Extension, Cornell University, Albion, NY 14411
| | - David Langston
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061
| | - Steven Rideout
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061
| | - Bhabesh Dutta
- Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton, GA 31793
| | - Sydney E Everhart
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT 06269
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Vogel G, Giles G, Robbins KR, Gore MA, Smart CD. Quantitative Genetic Analysis of Interactions in the Pepper- Phytophthora capsici Pathosystem. Mol Plant Microbe Interact 2022; 35:1018-1033. [PMID: 35914305 DOI: 10.1094/mpmi-12-21-0307-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The development of pepper cultivars with durable resistance to the oomycete Phytophthora capsici has been challenging due to differential interactions between the species that allow certain pathogen isolates to cause disease on otherwise resistant host genotypes. Currently, little is known about the pathogen genes involved in these interactions. To investigate the genetic basis of P. capsici virulence on individual pepper genotypes, we inoculated sixteen pepper accessions, representing commercial varieties, sources of resistance, and host differentials, with 117 isolates of P. capsici, for a total of 1,864 host-pathogen combinations. Analysis of disease outcomes revealed a significant effect of inter-species genotype-by-genotype interactions, although these interactions were quantitative rather than qualitative in scale. Isolates were classified into five pathogen subpopulations, as determined by their genotypes at over 60,000 single-nucleotide polymorphisms (SNPs). While absolute virulence levels on certain pepper accessions significantly differed between subpopulations, a multivariate phenotype reflecting relative virulence levels on certain pepper genotypes compared with others showed the strongest association with pathogen subpopulation. A genome-wide association study (GWAS) identified four pathogen loci significantly associated with virulence, two of which colocalized with putative RXLR effector genes and another with a polygalacturonase gene cluster. All four loci appeared to represent broad-spectrum virulence genes, as significant SNPs demonstrated consistent effects regardless of the host genotype tested. Host genotype-specific virulence variants in P. capsici may be difficult to map via GWAS with all but excessively large sample sizes, perhaps controlled by genes of small effect or by multiple allelic variants that have arisen independently. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Gregory Vogel
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, U.S.A
| | - Garrett Giles
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, U.S.A
| | - Kelly R Robbins
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
| | - Christine D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, U.S.A
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Giles G, Indermaur EJ, Gonzalez-Giron JL, Hermann TQ, Shelnutt S, Starr J, Myers K, Jensen S, Bergstrom GC, Crawford J, Hansen JL, Smart LB, Smart CD. First Report of Downy Mildew caused by Pseudoperonospora cannabina on Cannabis sativa in New York. Plant Dis 2022; 107:1638. [PMID: 36269588 DOI: 10.1094/pdis-08-22-1930-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Hemp (Cannabis sativa <0.3% tetrahydrocannabinol) is an emerging crop used for grain, fiber, and cannabinoid production (Fike et al. 2020). In New York, hemp is grown both in controlled environment facilities, including greenhouses, and as a field crop. In August 2020, downy mildew-like symptoms were observed on leaves and inflorescence of hemp plants in a field research trial in Ithaca, NY. Several cultivars, including 'Auto CBD', were affected. Disease was severe with some plants reaching 75% disease severity at the individual plant level. In the most severely affected plots, there was no marketable yield. The disease was characterized by chlorotic and necrotic lesions producing sporangiophores under high humidity. Pigmented sporangia were produced on branched sporangiophores. On artificially inoculated leaves incubated at 18°C, 80% humidity, 12h light for 5d, sporangiophores produced 8-19 pigmented, lemon-shaped sporangia with mean ± SD dimensions of 25.2 ± 3.0 (18.9 to 30.4) x 18.2 ± 2.1 (14.6 to 23.2) µm (n=50). Each sporangium produced 2-5 zoospores after less than 45 min in water at room temperature (22°C). Sporangia were collected from sporulating lesions and DNA was extracted as outlined in Crowell et al. (2020). Fragments of the ribosomal internal transcribed spacer (ITS) region (White et al. 1990), the beta-tubulin ras-associated ypt1 gene (Moorman et al. 2002), and the mitochondrial cytochrome B oxidase subunit 2 (cox2) gene (Hudspeth et al. 2000) were amplified by PCR and sequenced bidirectionally. Sequences were deposited in GenBank under accession numbers OK086084, OM867581, and OM867580, respectively. BLAST searches using the amplified ITS and cox2 sequences resulted in 100% identity to Pseudoperonospora cannabina (HM636051.1, HM636003.1) with ypt1 aligning at 97.95% identity (382/390 bp) with P. cannabina (KJ651402.1). The molecular characterization identified the causal agent as P. cannabina. A representative isolate was deposited in the Cornell Plant Pathology Herbarium as CUP-070922. Sporangia were rinsed from detached leaves and used to confirm pathogenicity on whole plants. Ten 4-week-old 'Anka' plants were spray-inoculated until run off with a suspension of 1x104 sporangia mL-1. Ten control plants were sprayed with water. After inoculation, plants were placed in a 19˚C growth chamber with a 12-h photoperiod and misted for 30 min twice daily to maintain humidity above 80%. Sporangia and previously described symptoms were observed 7 days post-inoculation, while control plants were asymptomatic. The pathogen was reisolated onto detached leaves of 'Anka' from inoculated leaves where both sporangia and oospores were observed. The reisolated pathogen was confirmed morphologically and molecularly, through PCR amplification and bidirectional sequencing of the ITS, cox2, and ypt1 genes, as P. cannabina. To our knowledge, this is the first report of P. cannabina causing hemp downy mildew in New York. Depending on the severity and timing of infections, this disease could pose a significant threat to hemp production in the state. Other members of the genus, P. cubensis and P. humuli cause downy mildew on cucurbits and hops, respectively. As these can cause devastating diseases on their hosts, P. cannabina must be monitored with vigilance as an emerging pathogen (Purayannur et al. 2021; Savory et al. 2011). Literature Cited: Crowell, C. R., et al.2020. Plant Dis. 104:2949. DOI 10.1094/PDIS-04-20-0718-RE Fike, J. H., et al. 2020. Page 89 In: Sustainable Agriculture Reviews, vol 42. Springer, Cham, Switzerland. DOI 10.1007/978-3-030-41384-2_3 Hudspeth, D. S. S., et al. 2000. Mycologia 92:674. DOI 10.2307/3761425 Moorman, G. W., et al. 2002. Plant Dis. 86:1227. DOI 10.1094/PDIS.2002.86.11.1227 Purayannur, S., et al. 2021. Mol. Plant Pathol. 22:755. DOI 10.1111/mpp.13063 Savory, E. A., et al. 2011. Mol. Plant Pathol. 12:217. DOI 10.1111/j.1364-3703.2010.00670.x White, T. J., et al. 1990. Page 315 In: PCR Protocols. A Guide to Methods and Applications. Academic Press, San Diego, CA. DOI 10.1016/B978-0-12-372180-8.50042-1.
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Affiliation(s)
- Garrett Giles
- Cornell University, School of Integrative Plant Science, Geneva, New York, United States;
| | - Elizabeth J Indermaur
- Cornell University, School of Integrative Plant Science, Geneva, New York, United States;
| | | | - Taylere Q Hermann
- Cornell University, School of Integrative Plant Science, Geneva, New York, United States;
| | - Savanna Shelnutt
- Cornell University, School of Integrative Plant Science, Geneva, New York, United States;
| | - Jennifer Starr
- Cornell University, 5922, School of Integrative Plant Science, Ithaca, New York, United States;
| | - Kevin Myers
- Cornell University, School of Integrative Plant Science, Ithaca, New York, United States;
| | - Sandra Jensen
- Cornell University, School of Integrative Plant Science, Ithaca, New York, United States;
| | - Gary C Bergstrom
- Cornell University, Plant Pathology and Plant-Microbe Biology, 334 Plant Science Building, Ithaca, New York, United States, 15853-5904;
| | - Jamie Crawford
- Cornell University, 5922, Plant Breeding and Genetics, School of Integrative Plant Science, Ithaca, New York, United States;
| | - Julie L Hansen
- Cornell University, 5922, Plant Breeding and Genetics Section, Ithaca, New York, United States;
| | - Lawrence B Smart
- Cornell University, 5922, Horticulture Section, School of Integrative Plant Science, 630 West North St, 102 Hedrick Hall, Geneva, New York, United States, 14456;
| | - Christine D Smart
- Cornell University, School of Integrative Plant Science, Geneva, New York, United States;
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Dubrow ZE, Carpenter SCD, Carter ME, Grinage A, Gris C, Lauber E, Butchachas J, Jacobs JM, Smart CD, Tancos MA, Noël LD, Bogdanove AJ. Cruciferous Weed Isolates of Xanthomonas campestris Yield Insight into Pathovar Genomic Relationships and Genetic Determinants of Host and Tissue Specificity. Mol Plant Microbe Interact 2022; 35:791-802. [PMID: 35536128 DOI: 10.1094/mpmi-01-22-0024-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Pathovars of Xanthomonas campestris cause distinct diseases on different brassicaceous hosts. The genomic relationships among pathovars as well as the genetic determinants of host range and tissue specificity remain poorly understood despite decades of research. Here, leveraging advances in multiplexed long-read technology, we fully sequenced the genomes of a collection of X. campestris strains isolated from cruciferous crops and weeds in New York and California as well as strains from global collections, to investigate pathovar relationships and candidate genes for host- and tissue-specificity. Pathogenicity assays and genomic comparisons across this collection and publicly available X. campestris genomes revealed a correlation between pathovar and genomic relatedness and provide support for X. campestris pv. barbareae, the validity of which had been questioned. Linking strain host range with type III effector repertoires identified AvrAC (also 'XopAC') as a candidate host-range determinant, preventing infection of Matthiola incana, and this was confirmed experimentally. Furthermore, the presence of a copy of the cellobiosidase gene cbsA with coding sequence for a signal peptide was found to correlate with the ability to infect vascular tissues, in agreement with a previous study of diverse Xanthomonas species; however, heterologous expression in strains lacking the gene gave mixed results, indicating that factors in addition to cbsA influence tissue specificity of X. campestris pathovars. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Zoë E Dubrow
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
| | - Sara C D Carpenter
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
| | - Morgan E Carter
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
- School of Plant Sciences, University of Arizona, Tucson, AZ, U.S.A
| | - Ayress Grinage
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
| | - Carine Gris
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul Sabatier, Castanet-Tolosan, France
| | - Emmanuelle Lauber
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul Sabatier, Castanet-Tolosan, France
| | - Jules Butchachas
- Department of Plant Pathology, The Ohio State University, Columbus, OH, U.S.A
| | - Jonathan M Jacobs
- Department of Plant Pathology, The Ohio State University, Columbus, OH, U.S.A
| | - Christine D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
| | - Matthew A Tancos
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture-Agricultural Research Service, Frederick, MD, U.S.A
| | - Laurent D Noël
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul Sabatier, Castanet-Tolosan, France
| | - Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
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Sudermann MA, McGilp L, Vogel G, Regnier M, Jaramillo AR, Smart CD. The Diversity of Passalora fulva Isolates Collected from Tomato Plants in U.S. High Tunnels. Phytopathology 2022; 112:1350-1360. [PMID: 35021861 DOI: 10.1094/phyto-06-21-0244-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
High tunnels extend the growing season of high value crops, including tomatoes, but the environmental conditions within high tunnels favor the spread of the tomato leaf mold pathogen, Passalora fulva (syn. Cladosporium fulvum). Tomato leaf mold results in defoliation, and if severe, losses in yield. Despite substantial research, little is known regarding the genetic structure and diversity of populations of P. fulva associated with high tunnel tomato production in the United States. From 2016 to 2019, a total of 50 P. fulva isolates were collected from tomato leaf samples in high tunnels in the Northeast and Minnesota. Other Cladosporium species were also isolated from the leaf surfaces. Koch's postulates were conducted to confirm that P. fulva was the cause of the disease symptoms observed. Race determination experiments revealed that the isolates belonged to either race 0 (six isolates) or race 2 (44 isolates). Polymorphisms were identified within four previously characterized effector genes: Avr2, Avr4, Avr4e, and Avr9. The largest number of polymorphisms were observed for Avr2. Both mating type genes, MAT1-1-1 and MAT1-2-1, were present in the isolate collection. For further insights into the pathogen diversity, the 50 isolates were genotyped at 7,514 single-nucleotide polymorphism loci using genotyping-by-sequencing. Differentiation by region but not by year was observed. Within the collection of 50 isolates, there were 18 distinct genotypes. Information regarding P. fulva population diversity will enable better management recommendations for growers, as high tunnel production of tomatoes expands.
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Affiliation(s)
- Martha A Sudermann
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, U.S.A
| | - Lillian McGilp
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Gregory Vogel
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, U.S.A
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
| | - Melissa Regnier
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, U.S.A
- Laboratory of Mycology and Phytopathology, Department of Biological Sciences, Universidad de los Andes, Bogotá 111711, Colombia
| | - Alejandra Rodríguez Jaramillo
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, U.S.A
| | - Christine D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, U.S.A
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Indermaur EJ, Day CTC, Smart CD. First Report of Didymella rhei causing leaf spot on rhubarb in New York. Plant Dis 2022; 107:222. [PMID: 35581909 DOI: 10.1094/pdis-03-22-0573-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
First Report of Didymella rhei causing leaf spot on rhubarb in New York E. J. Indermaur1, C. T. C. Day1, and C. D. Smart1† 1School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva NY 14456 †Corresponding author: C. D. Smart; Email: cds14@cornell.edu Rhubarb (Rheum spp.) is a perennial grown across the northern United States for petiole production (Foust & Marshall 1991). In August 2021, leaf spots were observed on rhubarb growing in a two-acre field in Erie Co., NY (Fig. S1). Approximately 30% of the plants in the field had leaf spot with disease severity of 5%. Initial symptoms on leaves were light brown, circular lesions with red margins that later coalesced into irregular spots. Lesion centers were dry with concentric rings, often perforating as they enlarged. Lesions on petioles were light brown, fusiform, and sunken with red margins. To identify the causal agent(s), symptomatic leaves and petioles from 50 plants (cultivar unknown) were collected with a W-shape sampling scheme. Lesion margins were surface sterilized with 70% ethanol for 60 s, 10% bleach for 60 s, rinsed in sterile water, plated on acidified potato dextrose agar (PDA), and incubated for two to four days at 20˚C. Hyphal tips from colony edges were transferred to new PDA plates. After 20 days, colonies (n=53) were olivaceous buff to grey olivaceous, producing white to grey, sparse aerial mycelium. Brown to black pycnidia were produced within five days in concentric rings around plate centers. Pycnidia were globose to subglobose, with one to two non-papillate or slightly papillate ostioles, and with mean diameter 75.8 (30.8 to 113.5) µm (n=20). Conidia were hyaline, ellipsoid or allantoid, and aseptate with mean ± SD dimensions of 6.2 ± 0.4 (4.9 to 8.1) x 2.2 ± 0.4 (1.3 to 3.3) µm (n=30) (Fig. S2). Based on these morphological characteristics, the isolates were initially identified as Didymella rhei [Ellis & Everh] (Qian Chen & L. Cai) (Boerema 2004). To confirm the identity, mycelia were scraped from PDA plates and homogenized using a TissueLyser II (Qiagen Inc.). Genomic DNA was extracted with a DNeasy Plant Mini Kit following manufacturer's instructions (Qiagen Inc.). PCR assays with primers ITS 4 and ITS 5 and fRPB2-7cR and RPB2-5F2 (Liu et al. 1999; Sung et al. 2007) were used to amplify the internal transcribed spacer (ITS) and the rpb2 gene regions of one representative isolate (strain RHU21204). Products were sequenced using Sanger chemistry. The sequences were deposited in GenBank with accession numbers OM903952 (ITS) and OM925897 (rpb2). The ITS and rpb2 sequences exhibited 99% (492/494 bp) and 100% (846/846 bp) identity with D. rhei accessions KF531831.1 and KP330428.1, respectively. Based on morphological and molecular characteristics, the pathogen was identified as D. rhei. To fulfill Koch's postulates, healthy leaves and petioles of four rhubarb seedlings (cultivars unknown) were spray-inoculated with a conidial suspension (1 × 107 conidia/ml) containing 0.2% Tween-20 from strain RHU21204. A tween suspension with no conidia was used as a control. Each treatment had three replicates. After inoculation, plants were placed in a 19˚C growth chamber with a 12-h photoperiod and misted for 30 min twice daily to maintain humidity above 80%. Initial symptoms were observed five days post inoculation (dpi), while control plants were asymptomatic. The pathogen was isolated 21 dpi from inoculated leaves and petioles with symptoms as described above (Fig. S1) and identified morphologically and molecularly as D. rhei. A representative isolate was deposited in the Cornell Plant Pathology Herbarium as CUP-070923. To our knowledge, this is the first report of D. rhei causing rhubarb leaf spot in New York and reducing the health and marketability of its host. Funding Source This project was funded by the College of Agriculture and Life Sciences, Cornell University. Literature Cited Boerema, G. H. et al. 2004. CABI Publishing. 288. Foust, C. M. and Marshall, D. E. 1991. HortScience 26:1360. DOI: 10.21273/HORTSCI.26.11.1360 Liu, Y. J. et al. 1999. Mol. Biol. Evol. 16:1799. Sung, G. H. et al. 2007. Mol. Phylogenet. Evol. 44:1204. DOI: 10.1016/j.ympev.2007.03.011.
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Affiliation(s)
- Elizabeth J Indermaur
- Cornell University, School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Geneva, New York, United States;
| | - Charles Thomas Colin Day
- Cornell University, School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Geneva, New York, United States;
| | - Christine D Smart
- Cornell University, School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Geneva, New York, United States;
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Crowell CR, Wilkerson DG, Beckauri M, Cala AR, McMullen PW, Mondo S, Andreopoulos W, Lipzen A, Lail K, Yan M, Ng V, Grigoriev IV, Smart LB, Smart CD. The Melampsora americana Population on Salix purpurea in the Great Lakes Region Is Highly Diverse with a Contributory Influence of Clonality. Phytopathology 2022; 112:907-916. [PMID: 34579556 DOI: 10.1094/phyto-05-21-0201-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Shrub willows (Salix spp.) are emerging as a viable lignocellulosic, second-generation bioenergy crop with many growth characteristics favorable for marginal lands in New York State and surrounding areas. Willow rust, caused by members of the genus Melampsora, is the most limiting disease of shrub willow in this region and remains extremely understudied. In this study, genetic diversity, genetic structure, and pathogen clonality were examined in Melampsora americana over two growing seasons via genotyping-by-sequencing to identify single-nucleotide polymorphism markers. In conjunction with this project, a reference genome of rust isolate R15-033-03 was generated to aid in variant discovery. Sampling between years allowed regional and site-specific investigation into population dynamics, in the context of both wild and cultivated hosts within high-density plantings. This work revealed that this pathogen is largely panmictic over the sampled areas, with few sites showing moderate genetic differentiation. These data support the hypothesis of sexual recombination between growing seasons because no genotype persisted across the two years of sampling. Additionally, clonality was determined as a driver of pathogen populations within cultivated fields and single shrubs; however, there is also evidence of high genetic diversity of rust isolates in all settings. This work provides a framework for M. americana population structure in the Great Lakes region, providing crucial information that can aid in future resistance breeding efforts.
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Affiliation(s)
- Chase R Crowell
- Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456
| | - Dustin G Wilkerson
- Horticulture Section, School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456
| | - Mariami Beckauri
- Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456
| | - Ali R Cala
- Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456
| | - Patrick W McMullen
- Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456
| | - Stephen Mondo
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598
| | | | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598
| | - Kathleen Lail
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598
| | - Mi Yan
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598
| | - Vivian Ng
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456
| | - Christine D Smart
- Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456
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Wilkerson DG, Crowell CR, Carlson CH, McMullen PW, Smart CD, Smart LB. Comparative transcriptomics and eQTL mapping of response to Melampsora americana in selected Salix purpurea F2 progeny. BMC Genomics 2022; 23:71. [PMID: 35065596 PMCID: PMC8783449 DOI: 10.1186/s12864-021-08254-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 12/10/2021] [Indexed: 11/20/2022] Open
Abstract
Background Melampsora spp. rusts are the greatest pathogen threat to shrub willow (Salix spp.) bioenergy crops. Genetic resistance is key to limit the effects of these foliar diseases on host response and biomass yield, however, the genetic basis of host resistance has not been characterized. The addition of new genomic resources for Salix provides greater power to investigate the interaction between S. purpurea and M. americana, species commonly found in the Northeast US. Here, we utilize 3′ RNA-seq to investigate host-pathogen interactions following controlled inoculations of M. americana on resistant and susceptible F2S. purpurea genotypes identified in a recent QTL mapping study. Differential gene expression, network analysis, and eQTL mapping were used to contrast the response to inoculation and to identify associated candidate genes. Results Controlled inoculation in a replicated greenhouse study identified 19 and 105 differentially expressed genes between resistant and susceptible genotypes at 42 and 66 HPI, respectively. Defense response gene networks were activated in both resistant and susceptible genotypes and enriched for many of the same defense response genes, yet the hub genes of these common response modules showed greater mean expression among the resistant plants. Further, eight and six eQTL hotspots were identified at 42 and 66 HPI, respectively. The combined results of three analyses highlight 124 candidate genes in the host for further analysis while analysis of pathogen RNA showed differential expression of 22 genes, two of which are candidate pathogen effectors. Conclusions We identified two differentially expressed M. americana transcripts and 124 S. purpurea genes that are good candidates for future studies to confirm their role in conferring resistance. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08254-1.
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Lange HW, Tancos MA, Smart CD. Cruciferous Weeds Do Not Act as Major Reservoirs of Inoculum for Black Rot Outbreaks in New York State. Plant Dis 2022; 106:174-181. [PMID: 34353128 DOI: 10.1094/pdis-05-21-0998-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cruciferous weeds have been shown to harbor diverse Xanthomonas campestris pathovars, including the agronomically damaging black rot of cabbage pathogen, X. campestris pv. campestris. However, the importance of weeds as inoculum sources for X. campestris pv. campestris outbreaks in New York remains unknown. To determine if cruciferous weeds act as primary reservoirs for X. campestris pv. campestris, fields that were rotating between cabbage or had severe black rot outbreaks were chosen for evaluation. Over a consecutive 3-year period, 148 cruciferous and noncruciferous weed samples were collected at 34 unique sites located across five New York counties. Of the 148 weed samples analyzed, 48 X. campestris isolates were identified, with a subset characterized using multilocus sequence analysis. All X. campestris isolates originated from weeds belonging to the Brassicaceae family, with predominant weed hosts being shepherd's purse (Capsella bursa-pastoris), wild mustard (Sinapis arvensis), yellow rocket (Barbarea vulgaris), and pennycress (Thlaspi arvense). Identifying pathogenic X. campestris weed isolates was rare, with only eight isolates causing brown necrotic leaf spots or typical V-shaped lesions on cabbage. There was no evidence of cabbage-infecting weed isolates persisting in an infected field by overwintering in weed hosts; however, similar cabbage and weed X. campestris haplotypes were identified in the same field during an active black rot outbreak. X. campestris weed isolates are genetically diverse both within and between fields, but our findings indicate that X. campestris weed isolates do not appear to act as primary sources of inoculum for B. oleracea fields in New York.
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Affiliation(s)
- Holly W Lange
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456
| | - Matthew A Tancos
- Foreign Disease-Weed Science Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Frederick, MD 21702
| | - Christine D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456
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13
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Carlson CH, Stack GM, Jiang Y, Taşkıran B, Cala AR, Toth JA, Philippe G, Rose JKC, Smart CD, Smart LB. Morphometric relationships and their contribution to biomass and cannabinoid yield in hybrids of hemp (Cannabis sativa). J Exp Bot 2021; 72:7694-7709. [PMID: 34286838 PMCID: PMC8643699 DOI: 10.1093/jxb/erab346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
The breeding of hybrid cultivars of hemp (Cannabis sativa L.) is not well described, especially the segregation and inheritance of traits that are important for yield. A total of 23 families were produced from genetically diverse parents to investigate the inheritance of morphological traits and their association with biomass accumulation and cannabinoid yield. In addition, a novel classification method for canopy architecture was developed. The strong linear relationship between wet and dry biomass provided an accurate estimate of final dry stripped floral biomass. Of all field and aerial measurements, basal stem diameter was determined to be the single best selection criterion for final dry stripped floral biomass yield. Along with stem diameter, canopy architecture and stem growth predictors described the majority of the explainable variation of biomass yield. Within-family variance for morphological and cannabinoid measurements reflected the heterozygosity of the parents. While selfed populations suffered from inbreeding depression, hybrid development in hemp will require at least one inbred parent to achieve uniform growth and biomass yield. Nevertheless, floral phenology remains a confounding factor in selection because of its underlying influence on biomass production, highlighting the need to understand the genetic basis for flowering time in the breeding of uniform cultivars.
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Affiliation(s)
- Craig H Carlson
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY, USA
| | - George M Stack
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY, USA
| | - Yu Jiang
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY, USA
| | - Bircan Taşkıran
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY, USA
| | - Ali R Cala
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY,USA
| | - Jacob A Toth
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY, USA
| | - Glenn Philippe
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Jocelyn K C Rose
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Christine D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY,USA
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY, USA
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Gouker FE, Carlson CH, Zou J, Evans L, Crowell CR, Smart CD, DiFazio SP, Smart LB. Sexual dimorphism in the dioecious willow Salix purpurea. Am J Bot 2021; 108:1374-1387. [PMID: 34406658 DOI: 10.1002/ajb2.1704] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 01/28/2021] [Indexed: 06/13/2023]
Abstract
PREMISE The evolution of sex chromosomes is driven by sexual dimorphism, yet it can be challenging to document sexually dimorphic traits in dioecious plant species. At the genetic level, sexual dimorphism can be identified through sequence variation between females and males associated with sexually antagonistic traits and different fitness optima. This study aims to examine sexual dimorphism for 26 traits in three populations of Salix purpurea (a diversity panel and F1 and F2 populations) and determine the effect of the traits on biomass yield, a key trait in Salix bioenergy crops across multiple years, locations, and under manipulated growth conditions. METHODS Sexual dimorphism was evaluated for morphological, phenological, physiological, and wood composition traits in a diversity panel of unrelated S. purpurea accessions and in full-sib F1 and F2 families produced through controlled cross pollinations and grown in replicated field trials. RESULTS We observed sexual dimorphism in the timing of development for several traits that were highly predictive of biomass yield across three populations of S. purpurea. Across all populations and years surveyed, males had significantly shallower branching angle. Male plants highly predictive of biomass yield across three populations of S. purpurea also accumulated more nitrogen under fertilizer amendment as measured by SPAD in the diversity panel and had greater susceptibility to the rust fungus Melampsora americana in the F2 family. Allometric modelling of biomass yield showed an effect of sex and of location on the interaction between yield and stem height. CONCLUSIONS These results provide evidence of sexual dimorphism for certain traits in S. purpurea that may be involved in sex chromosome evolution.
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Affiliation(s)
- Fred E Gouker
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, 14456, USA
| | - Craig H Carlson
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, 14456, USA
| | - Junzhu Zou
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, 14456, USA
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Luke Evans
- Department of Biology, West Virginia University, Morgantown, WV, 26506, USA
| | - Chase R Crowell
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, 14456, USA
| | - Christine D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, 14456, USA
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, 26506, USA
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, 14456, USA
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Abstract
The gram-positive actinobacterium Clavibacter michiganensis is the causal agent of bacterial canker of tomato, an economically impactful disease with a worldwide distribution. This seedborne pathogen systemically colonizes tomato xylem leading to unilateral leaflet wilt, marginal leaf necrosis, stem and petiole cankers, and plant death. Additionally, splash dispersal of the bacterium onto fruit exteriors causes bird's-eye lesions, which are characterized as necrotic centers surrounded by white halos. The pathogen can colonize developing seeds systemically through xylem and through penetration of fruit tissues from the exterior. There are currently no commercially available resistant cultivars, and bactericidal sprays have limited efficacy for managing the disease once the pathogen is in the vascular system. In this review, we summarize research on epidemiology, host colonization, the bacterial genetics underlying virulence, and management of bacterial canker. Finally, we highlight important areas of research into this pathosystem that have the potential to generate new strategies for prevention and mitigation of bacterial canker.
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Affiliation(s)
- F Christopher Peritore-Galve
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456
| | - Matthew A Tancos
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture-Agricultural Research Service, Frederick, MD 21702
| | - Christine D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456
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Vogel G, LaPlant KE, Mazourek M, Gore MA, Smart CD. A combined BSA-Seq and linkage mapping approach identifies genomic regions associated with Phytophthora root and crown rot resistance in squash. Theor Appl Genet 2021; 134:1015-1031. [PMID: 33388885 DOI: 10.1007/s00122-020-03747-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 12/05/2020] [Indexed: 06/12/2023]
Abstract
Two QTL mapping approaches were used to identify a total of six QTL associated with Phytophthora root and crown rot resistance in a biparental squash population. Phytophthora root and crown rot, caused by the soilborne oomycete pathogen Phytophthora capsici, leads to severe yield losses in squash (Cucurbita pepo). To identify quantitative trait loci (QTL) involved in resistance to this disease, we crossed a partially resistant squash breeding line with a susceptible zucchini cultivar and evaluated over 13,000 F2 seedlings in a greenhouse screen. Bulked segregant analysis with whole genome resequencing (BSA-Seq) resulted in the identification of five genomic regions-on chromosomes 4, 5, 8, 12, and 16-featuring significant allele frequency differentiation between susceptible and resistant bulks in each of two independent replicates. In addition, we conducted linkage mapping using a population of 176 F3 families derived from individually genotyped F2 individuals. Variation in disease severity among these families was best explained by a four-QTL model, comprising the same loci identified via BSA-Seq on chromosomes 4, 5, and 8 as well as an additional locus on chromosome 19, for a combined total of six QTL identified between both methods. Loci, whether those identified by BSA-Seq or linkage mapping, were of small-to-moderate effect, collectively accounting for 28-35% and individually for 2-10% of the phenotypic variance explained. However, a multiple linear regression model using one marker in each BSA-Seq QTL could predict F2:3 disease severity with only a slight drop in cross-validation accuracy compared to genomic prediction models using genome-wide markers. These results suggest that marker-assisted selection could be a suitable approach for improving Phytophthora crown and root rot resistance in squash.
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Affiliation(s)
- Gregory Vogel
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY, 14456, USA
| | - Kyle E LaPlant
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Michael Mazourek
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Christine D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY, 14456, USA.
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Vogel G, Gore MA, Smart CD. Genome-Wide Association Study in New York Phytophthora capsici Isolates Reveals Loci Involved in Mating Type and Mefenoxam Sensitivity. Phytopathology 2021; 111:204-216. [PMID: 32539639 DOI: 10.1094/phyto-04-20-0112-fi] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Phytophthora capsici is a soilborne oomycete plant pathogen that causes severe vegetable crop losses in New York (NY) state and worldwide. This pathogen is difficult to manage, in part due to its production of long-lasting sexual spores and its tendency to quickly evolve fungicide resistance. We single nucleotide polymorphism (SNP) genotyped 252 P. capsici isolates, predominantly from NY, in order to conduct a genome-wide association study for mating type and mefenoxam sensitivity. The population structure and extent of chromosomal copy number variation in this collection of isolates were also characterized. Population structure analyses showed isolates largely clustered by the field site where they were collected, with values of FST between pairs of fields ranging from 0.10 to 0.31. Thirty-three isolates were putative aneuploids, demonstrating evidence for having up to four linkage groups present in more than two copies, and an additional two isolates appeared to be genome-wide triploids. Mating type was mapped to a region on scaffold 4, consistent with previous findings, and mefenoxam sensitivity was associated with several SNP markers at a novel locus on scaffold 62. We identified several candidate genes for mefenoxam sensitivity, including a homolog of yeast ribosome synthesis factor Rrp5, but failed to locate near the scaffold 62 locus any subunits of RNA polymerase I, the hypothesized target site of phenylamide fungicides in oomycetes. This work expands our knowledge of the population biology of P. capsici and provides a foundation for functional validation of candidate genes associated with epidemiologically important phenotypes.
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Affiliation(s)
- Gregory Vogel
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Christine D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456
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Crowell CR, Bekauri MM, Cala AR, McMullen P, Smart LB, Smart CD. Differential Susceptibility of Diverse Salix spp. to Melampsora americana and Melampsora paradoxa. Plant Dis 2020; 104:2949-2957. [PMID: 32902356 DOI: 10.1094/pdis-04-20-0718-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Melampsora spp. willow rust is the most serious disease of shrub willow bioenergy production in the northeastern United States. Recent phylogenetic studies have identified several Melampsora spp. present on willow in the Northeast; however, in-depth understanding of Melampsora spp. host susceptibility remain unresolved. In this study, a panel of 82 rust isolates collected from the northeastern United States were genotyped via ribosomal DNA sequencing and a subset of these isolates were assayed for host susceptibility. This work revealed that Melampsora americana is the most prevalent species in the sampled geographic region and that there is potential for rust resistance breeding using the Salix spp. taxa assayed. Additionally, leaf morphology traits of these Salix spp. hosts were quantified for correlation analysis, revealing that trichome density and stomata density are possible contributors to resistance. This work provides foundational rust pathology information, which is crucial for M. americana resistance breeding.
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Affiliation(s)
- Chase R Crowell
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456
| | - Mariami M Bekauri
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456
| | - Ali R Cala
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456
| | - Patrick McMullen
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456
- Department of Biology, Lebanon Valley College, Annville, PA 17003
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456
| | - Christine D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456
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19
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Alexander MR, Schoeder CT, Brown JA, Smart CD, Moth C, Wikswo JP, Capra JA, Meiler J, Chen W, Madhur MS. Which animals are at risk? Predicting species susceptibility to Covid-19. bioRxiv 2020. [PMID: 32676592 DOI: 10.1101/2020.07.09.194563] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In only a few months, the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic, leaving physicians, scientists, and public health officials racing to understand, treat, and contain this zoonotic disease. SARS-CoV-2 has made the leap from animals to humans, but little is known about variations in species susceptibility that could identify potential reservoir species, animal models, and the risk to pets, wildlife, and livestock. While there is evidence that certain species, such as cats, are susceptible, the vast majority of animal species, including those in close contact with humans, have unknown susceptibility. Hence, methods to predict their infection risk are urgently needed. SARS-CoV-2 spike protein binding to angiotensin converting enzyme 2 (ACE2) is critical for viral cell entry and infection. Here we identified key ACE2 residues that distinguish susceptible from resistant species using in-depth sequence and structural analyses of ACE2 and its binding to SARS-CoV-2. Our findings have important implications for identification of ACE2 and SARS-CoV-2 residues for therapeutic targeting and identification of animal species with increased susceptibility for infection on which to focus research and protection measures for environmental and public health.
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20
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Peritore-Galve FC, Miller C, Smart CD. Characterizing Colonization Patterns of Clavibacter michiganensis During Infection of Tolerant Wild Solanum Species. Phytopathology 2020; 110:574-581. [PMID: 31725349 DOI: 10.1094/phyto-09-19-0329-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Clavibacter michiganensis is the Gram-positive causal agent of bacterial canker of tomato, an economically devastating disease with a worldwide distribution. C. michiganensis colonizes the xylem, leading to unilateral wilt, stem canker, and plant death. C. michiganensis can also infect developing tomato fruit through splash dispersal, forming exterior bird's eye lesions. There are no documented sources of qualitative resistance in Solanum spp.; however, quantitative trait loci conferring tolerance in Solanum arcanum and Solanum habrochaites have been identified. Mechanisms of tolerance and C. michiganensis colonization patterns in wild tomato species remain poorly understood. This study describes differences in symptom development and colonization patterns of the wild type (WT) and a hypervirulent bacterial expansin knockout (ΔCmEXLX2) in wild and cultivated tomato genotypes. Overall, WT and ΔCmEXLX2 cause less severe symptoms in wild tomato species and are impeded in spread and colonization of the vascular system. Laser scanning confocal microscopy and scanning electron microscopy were used to observe preferential colonization of protoxylem vessels and reduced intravascular spread in wild tomatoes. Differences in C. michiganensis in vitro growth and aggregation were determined in xylem sap, which may suggest that responses to pathogen colonization are occurring, leading to reduced colonization density in wild tomato species. Finally, wild tomato fruit was determined to be susceptible to C. michiganensis through in vivo inoculations and assessing lesion numbers and size. Fruit symptom severity was in some cases unrelated to severity of symptoms during vascular infection, suggesting different mechanisms for colonization of different tissues.
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Affiliation(s)
- F Christopher Peritore-Galve
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456
| | - Christine Miller
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27606
| | - Christine D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456
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21
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Carlson CH, Gouker FE, Crowell CR, Evans L, DiFazio SP, Smart CD, Smart LB. Joint linkage and association mapping of complex traits in shrub willow (Salix purpurea L.). Ann Bot 2019; 124:701-716. [PMID: 31008500 PMCID: PMC6821232 DOI: 10.1093/aob/mcz047] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 03/08/2019] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Increasing energy demands and the necessity to reduce greenhouse gas emissions are key motivating factors driving the development of lignocellulosic crops as an alternative to non-renewable energy sources. The effects of global climate change will require a better understanding of the genetic basis of complex adaptive traits to breed more resilient bioenergy feedstocks, like willow (Salix spp.). Shrub willow is a sustainable and dedicated bioenergy crop, bred to be fast-growing and high-yielding on marginal land without competing with food crops. In a rapidly changing climate, genomic advances will be vital for the sustained improvement of willow and other non-model bioenergy crops. Here, joint genetic mapping was used to exploit genetic variation garnered from both recent and historical recombination events in S. purpurea. METHODS A panel of North American naturalized S. purpurea accessions and full-sib F2S. purpurea population were genotyped and phenotyped for a suite of morphological, physiological, pest and disease resistance, and wood chemical composition traits, collected from multi-environment and multi-year replicated field trials. Controlling for population stratification and kinship in the association panel and spatial variation in the F2, a comprehensive mixed model analysis was used to dissect the complex genetic architecture and plasticity of these important traits. KEY RESULTS Individually, genome-wide association (GWAS) models differed in terms of power, but the combined approach, which corrects for yearly and environmental co-factors across datasets, improved the overall detection and resolution of associated loci. Although there were few significant GWAS hits located within support intervals of QTL for corresponding traits in the F2, many large-effect QTL were identified, as well as QTL hotspots. CONCLUSIONS This study provides the first comparison of linkage analysis and linkage disequilibrium mapping approaches in Salix, and highlights the complementarity and limits of these two methods for elucidating the genetic architecture of complex bioenergy-related traits of a woody perennial breeding programme.
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Affiliation(s)
- Craig H Carlson
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
| | - Fred E Gouker
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
| | - Chase R Crowell
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
| | - Luke Evans
- Institute for Behavioral Genetics and Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, USA
| | - Christine D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
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22
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Mazo-Molina C, Mainiero S, Hind SR, Kraus CM, Vachev M, Maviane-Macia F, Lindeberg M, Saha S, Strickler SR, Feder A, Giovannoni JJ, Smart CD, Peeters N, Martin GB. The Ptr1 Locus of Solanum lycopersicoides Confers Resistance to Race 1 Strains of Pseudomonas syringae pv. tomato and to Ralstonia pseudosolanacearum by Recognizing the Type III Effectors AvrRpt2 and RipBN. Mol Plant Microbe Interact 2019; 32:949-960. [PMID: 30785360 DOI: 10.1094/mpmi-01-19-0018-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Race 1 strains of Pseudomonas syringae pv. tomato, which cause bacterial speck disease of tomato, are becoming increasingly common and no simply inherited genetic resistance to such strains is known. We discovered that a locus in Solanum lycopersicoides, termed Pseudomonas tomato race 1 (Ptr1), confers resistance to race 1 P. syringae pv. tomato strains by detecting the activity of type III effector AvrRpt2. In Arabidopsis, AvrRpt2 degrades the RIN4 protein, thereby activating RPS2-mediated immunity. Using site-directed mutagenesis of AvrRpt2, we found that, like RPS2, activation of Ptr1 requires AvrRpt2 proteolytic activity. Ptr1 also detected the activity of AvrRpt2 homologs from diverse bacteria, including one in Ralstonia pseudosolanacearum. The genome sequence of S. lycopersicoides revealed no RPS2 homolog in the Ptr1 region. Ptr1 could play an important role in controlling bacterial speck disease and its future cloning may shed light on an example of convergent evolution for recognition of a widespread type III effector.
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Affiliation(s)
- Carolina Mazo-Molina
- 1Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, U.S.A
- 2Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
| | - Samantha Mainiero
- 1Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, U.S.A
| | - Sarah R Hind
- 1Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, U.S.A
| | - Christine M Kraus
- 1Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, U.S.A
| | - Mishi Vachev
- 1Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, U.S.A
| | | | - Magdalen Lindeberg
- 2Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
| | - Surya Saha
- 1Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, U.S.A
| | - Susan R Strickler
- 1Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, U.S.A
| | - Ari Feder
- 1Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, U.S.A
| | - James J Giovannoni
- 1Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, U.S.A
- 4Robert W. Holley Center for Agriculture and Health, USDA-ARS, Ithaca, NY 14853, U.S.A
| | - Christine D Smart
- 2Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
| | - Nemo Peeters
- 3LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Gregory B Martin
- 1Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, U.S.A
- 2Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
- 5Department of Horticultural Biotechnology, College of Life Sciences, Kyung Hee University, Yongin 17104, Republic of Korea
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23
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Goodwin SB, Legard DE, Smart CD, Levy M, Fry WE. Gene flow analysis of molecular markers confirms that Phytophthora mirabilis and P. infestans are separate species. Mycologia 2019. [DOI: 10.1080/00275514.1999.12061085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Stephen B. Goodwin
- USDA-ARS, Crop Production and Pest Control Research Unit, and Department of Botany and Plant Pathology, 1155 Lilly Hall, Purdue University, West Lafayette, Indiana 47907-1155
| | - Daniel E. Legard
- Department of Plant Pathology, University of Florida, Gulf Coast Research and Education Center, 13138 Lewis Gallagher Road, Dover, Florida 33527
| | - Christine D. Smart
- Department of Plant Pathology, 334 Plant Science Building, Cornell University, Ithaca, New York 14853
| | - Morris Levy
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
| | - William E. Fry
- Department of Plant Pathology, 334 Plant Science Building, Cornell University, Ithaca, New York 14853
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24
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Okiro LA, Tancos MA, Nyanjom SG, Smart CD, Parker ML. Comparative Evaluation of LAMP, qPCR, Conventional PCR, and ELISA to Detect Ralstonia solanacearum in Kenyan Potato Fields. Plant Dis 2019; 103:959-965. [PMID: 30895864 PMCID: PMC7779969 DOI: 10.1094/pdis-03-18-0489-re] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/04/2018] [Indexed: 05/25/2023]
Abstract
Bacterial wilt caused by Ralstonia solanacearum is considered among the most damaging diseases of potato in Sub-Saharan Africa and the most significant biotic constraint of potato production alongside late blight. Unlike late blight, which can be managed by chemical means, R. solanacearum can only be managed through cultural methods and clean seed. Laboratory testing to certify seed before planting is required to confirm the absence of the pathogen in Kenya. A loop-mediated isothermal amplification (LAMP) assay was developed using the UDP-(3-O-acyl)-N-acetylglucosamine deacetylase gene (IpxC) to screen seed potato for R. solanacearum strains. The assay was assessed using DNA extracted from R. solanacearum and other soil and potato pathogens to demonstrate specificity and sensitivity. The LAMP assay was validated using field samples from different potato growing regions of Kenya collected over two growing seasons and compared with established nucleic acid and protein-based assays. The IpxC LAMP assay was found to be specific and sensitive to R. solanacearum, detecting as low as 2.5 pg/µl of R. solanacearum DNA. Of the 47 potentially infected field samples collected, both IpxC LAMP and quantitative polymerase chain reaction (PCR) detected R. solanacearum DNA in 90% of the samples, followed by conventional PCR (86%) and ELISA (75%). This IpxC LAMP assay is a promising diagnostic tool to rapidly screen for R. solanacearum in seed potato with high sensitivity in Kenya. Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
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Affiliation(s)
- Lilian A. Okiro
- Department of Biochemistry and Molecular Biology, Egerton University, Njoro Campus, PO Box, 536 – 20115, Egerton, Kenya
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
- Biosciences Eastern and Central Africa–International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, 00100, Kenya
| | - Matthew A. Tancos
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY, U.S.A.; and
| | - Steven G. Nyanjom
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Christine D. Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY, U.S.A.; and
| | - Monica L. Parker
- CGIAR Research Program on Roots, Tubers and Bananas, International Potato Center, Nairobi, Kenya
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25
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Peritore-Galve FC, Schneider DJ, Yang Y, Thannhauser TW, Smart CD, Stodghill P. Proteome Profile and Genome Refinement of the Tomato-Pathogenic Bacterium Clavibacter michiganensis subsp. michiganensis. Proteomics 2019; 19:e1800224. [PMID: 30648817 DOI: 10.1002/pmic.201800224] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 11/29/2018] [Indexed: 11/07/2022]
Affiliation(s)
- F Christopher Peritore-Galve
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY, 14456, USA
| | - David J Schneider
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4J8, Canada
| | - Yong Yang
- United States Department of Agriculture (USDA), Agricultural Research Service, Robert W. Holley Center, Ithaca, NY, 14853, USA
| | - Theodore W Thannhauser
- United States Department of Agriculture (USDA), Agricultural Research Service, Robert W. Holley Center, Ithaca, NY, 14853, USA
| | - Christine D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY, 14456, USA
| | - Paul Stodghill
- United States Department of Agriculture (USDA), Agricultural Research Service, Robert W. Holley Center, Ithaca, NY, 14853, USA
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26
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Tancos MA, Lowe‐Power TM, Peritore‐Galve FC, Tran TM, Allen C, Smart CD. Plant-like bacterial expansins play contrasting roles in two tomato vascular pathogens. Mol Plant Pathol 2018; 19:1210-1221. [PMID: 28868644 PMCID: PMC5835177 DOI: 10.1111/mpp.12611] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/04/2017] [Accepted: 08/31/2017] [Indexed: 05/27/2023]
Abstract
Expansin proteins, which loosen plant cell walls, play critical roles in normal plant growth and development. The horizontal acquisition of functional plant-like expansin genes in numerous xylem-colonizing phytopathogenic bacteria suggests that bacterial expansins may also contribute to virulence. To investigate the role of bacterial expansins in plant diseases, we mutated the non-chimeric expansin genes (CmEXLX2 and RsEXLX) of two xylem-inhabiting bacterial pathogens, the Actinobacterium Clavibacter michiganensis ssp. michiganensis (Cmm) and the β-proteobacterium Ralstonia solanacearum (Rs), respectively. The Cmm ΔCmEXLX2 mutant caused increased symptom development on tomato, which was characterized by more rapid wilting, greater vascular necrosis and abundant atypical lesions on distant petioles. This increased disease severity correlated with larger in planta populations of the ΔCmEXLX2 mutant, even though the strains grew as well as the wild-type in vitro. Similarly, when inoculated onto tomato fruit, ΔCmEXLX2 caused significantly larger lesions with larger necrotic centres. In contrast, the Rs ΔRsEXLX mutant showed reduced virulence on tomato following root inoculation, but not following direct petiole inoculation, suggesting that the RsEXLX expansin contributes to early virulence at the root infection stage. Consistent with this finding, ΔRsEXLX attached to tomato seedling roots better than the wild-type Rs, which may prevent mutants from invading the plant's vasculature. These contrasting results demonstrate the diverse roles of non-chimeric bacterial expansins and highlight their importance in plant-bacterial interactions.
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Affiliation(s)
- Matthew A. Tancos
- Plant Pathology and Plant‐Microbe Biology Section, School of Integrative Plant SciencesCornell UniversityGenevaNY 14456USA
- Present address:
Foreign Disease‐Weed Science Research Unit, USDA‐ARSFort DetrickMD 21702USA
| | | | - F. Christopher Peritore‐Galve
- Plant Pathology and Plant‐Microbe Biology Section, School of Integrative Plant SciencesCornell UniversityGenevaNY 14456USA
| | - Tuan M. Tran
- Department of Plant PathologyUniversity of Wisconsin‐MadisonMadisonWI 53706USA
- Present address:
School of Biological SciencesNanyang Technological University639798Singapore
| | - Caitilyn Allen
- Department of Plant PathologyUniversity of Wisconsin‐MadisonMadisonWI 53706USA
| | - Christine D. Smart
- Plant Pathology and Plant‐Microbe Biology Section, School of Integrative Plant SciencesCornell UniversityGenevaNY 14456USA
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27
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Kraus CM, Mazo-Molina C, Smart CD, Martin GB. Pseudomonas syringae pv. tomato Strains from New York Exhibit Virulence Attributes Intermediate Between Typical Race 0 and Race 1 Strains. Plant Dis 2017; 101:1442-1448. [PMID: 30678591 DOI: 10.1094/pdis-03-17-0330-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Bacterial speck disease, caused by Pseudomonas syringae pv. tomato, is a persistent problem for fresh-market tomato growers in New York. Race 0 strains of this pathogen express either or both of the type III effectors AvrPto or AvrPtoB, which are recognized by tomato varieties expressing the Pto resistance gene. Pto encodes a protein kinase that activates the host immune system, thereby inhibiting bacterial multiplication and preventing disease development. Race 1 P. syringae pv. tomato strains do not express these effectors and are virulent on tomato whether or not the variety expresses Pto. Very few fresh-market tomato varieties have the Pto gene. We collected six P. syringae pv. tomato strains from naturally infected tomato plants across New York in 2015 and characterized them for their virulence and for the presence of specific effectors. In experiments conducted in the greenhouse, all strains reached population sizes in Pto-expressing tomato leaves that were intermediate between typical race 0 and race 1 strains. This phenotype has not been observed previously and suggests that the strains are recognized by Pto but such recognition is compromised by another P. syringae pv. tomato factor. The strains were found to encode avrPto, which is transcribed and translated. They also express avrPtoB although, as reported for other P. syringae pv. tomato strains, protein expression for this effector was not detectable. Deletion of avrPto from a representative New York strain allowed it to reach high populations in Pto-expressing tomato varieties, without compromising its virulence on susceptible tomato plants. Collectively, our data suggest that introgression of the Pto gene into fresh-market tomato varieties could enhance protection against extant P. syringae pv. tomato strains.
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Affiliation(s)
- Christine M Kraus
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, and Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Carolina Mazo-Molina
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, and Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Christine D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University
| | - Gregory B Martin
- Boyce Thompson Institute for Plant Research, and Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University
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28
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Carlson MO, Gazave E, Gore MA, Smart CD. Temporal Genetic Dynamics of an Experimental, Biparental Field Population of Phytophthora capsici. Front Genet 2017; 8:26. [PMID: 28348576 PMCID: PMC5347166 DOI: 10.3389/fgene.2017.00026] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 02/20/2017] [Indexed: 01/01/2023] Open
Abstract
Defining the contributions of dispersal, reproductive mode, and mating system to the population structure of a pathogenic organism is essential to estimating its evolutionary potential. After introduction of the devastating plant pathogen, Phytophthora capsici, into a grower's field, a lack of aerial spore dispersal restricts migration. Once established, coexistence of both mating types results in formation of overwintering recombinant oospores, engendering persistent pathogen populations. To mimic these conditions, in 2008, we inoculated a field with two P. capsici isolates of opposite mating type. We analyzed pathogenic isolates collected in 2009-2013 from this experimental population, using genome-wide single-nucleotide polymorphism markers. By tracking heterozygosity across years, we show that the population underwent a generational shift; transitioning from exclusively F1 in 2009-2010, to multi-generational in 2011, and ultimately all inbred in 2012-2013. Survival of F1 oospores, characterized by heterozygosity excess, coupled with a low rate of selfing, delayed declines in heterozygosity due to inbreeding and attainment of equilibrium genotypic frequencies. Large allele and haplotype frequency changes in specific genomic regions accompanied the generational shift, representing putative signatures of selection. Finally, we identified an approximately 1.6 Mb region associated with mating type determination, constituting the first detailed genomic analysis of a mating type region (MTR) in Phytophthora. Segregation patterns in the MTR exhibited tropes of sex-linkage, where maintenance of allele frequency differences between isolates of opposite mating type was associated with elevated heterozygosity despite inbreeding. Characterizing the trajectory of this experimental system provides key insights into the processes driving persistent, sexual pathogen populations.
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Affiliation(s)
- Maryn O. Carlson
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell UniversityGeneva, NY, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell UniversityIthaca, NY, USA
| | - Elodie Gazave
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell UniversityIthaca, NY, USA
| | - Michael A. Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell UniversityIthaca, NY, USA
| | - Christine D. Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell UniversityGeneva, NY, USA
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29
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Kreis RA, Dillard HR, Smart CD. Population Diversity and Sensitivity to Azoxystrobin of Alternaria brassicicola in New York State. Plant Dis 2016; 100:2422-2426. [PMID: 30686174 DOI: 10.1094/pdis-03-16-0414-re] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Alternaria brassicicola is the causal agent of Alternaria leaf spot, a common disease of brassica crops in New York State. New York isolates of A. brassicicola were collected from a variety of brassica crops and locations to evaluate the population diversity and screen for fungicide sensitivity. Isolates were genotyped for 10 microsatellite loci and assayed for sensitivity to azoxystrobin, a quinone outside inhibitor fungicide. The New York State population of A. brassicicola was found to have high levels of genotypic diversity and the population was found to be in linkage disequilibrium. Based on in vitro assays, the effective concentrations of azoxystrobin reducing spore germination by 50% ranged from 0.22 to 14.12 μg/ml. In order to confirm the sensitivity of 47 isolates to azoxystrobin, the cytb gene was characterized and sequenced to determine whether any of the mutations known to confer resistance to azoxystrobin were present. The mutations F129L, G137R, and G143A were not detected in the isolates studied.
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Affiliation(s)
- Rachel A Kreis
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456
| | - Helene R Dillard
- College of Agricultural and Environmental Sciences, University of California, Davis, CA 95616
| | - Christine D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456
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Hansen ZR, Everts KL, Fry WE, Gevens AJ, Grünwald NJ, Gugino BK, Johnson DA, Johnson SB, Judelson HS, Knaus BJ, McGrath MT, Myers KL, Ristaino JB, Roberts PD, Secor GA, Smart CD. Genetic Variation within Clonal Lineages of Phytophthora infestans Revealed through Genotyping-By-Sequencing, and Implications for Late Blight Epidemiology. PLoS One 2016; 11:e0165690. [PMID: 27812174 PMCID: PMC5094694 DOI: 10.1371/journal.pone.0165690] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 10/17/2016] [Indexed: 01/24/2023] Open
Abstract
Genotyping-by-sequencing (GBS) was performed on 257 Phytophthora infestans isolates belonging to four clonal lineages to study within-lineage diversity. The four lineages used in the study were US-8 (n = 28), US-11 (n = 27), US-23 (n = 166), and US-24 (n = 36), with isolates originating from 23 of the United States and Ontario, Canada. The majority of isolates were collected between 2010 and 2014 (94%), with the remaining isolates collected from 1994 to 2009, and 2015. Between 3,774 and 5,070 single-nucleotide polymorphisms (SNPs) were identified within each lineage and were used to investigate relationships among individuals. K-means hierarchical clustering revealed three clusters within lineage US-23, with US-23 isolates clustering more by collection year than by geographic origin. K-means hierarchical clustering did not reveal significant clustering within the smaller US-8, US-11, and US-24 data sets. Neighbor-joining (NJ) trees were also constructed for each lineage. All four NJ trees revealed evidence for pathogen dispersal and overwintering within regions, as well as long-distance pathogen transport across regions. In the US-23 NJ tree, grouping by year was more prominent than grouping by region, which indicates the importance of long-distance pathogen transport as a source of initial late blight inoculum. Our results support previous studies that found significant genetic diversity within clonal lineages of P. infestans and show that GBS offers sufficiently high resolution to detect sub-structuring within clonal populations.
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Affiliation(s)
- Zachariah R. Hansen
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY, United States of America
| | - Kathryne L. Everts
- Department of Plant Science and Landscape Architecture, University of Maryland, Salisbury, MD, United States of America
| | - William E. Fry
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY, United States of America
| | - Amanda J. Gevens
- Department of Plant Pathology, University of Wisconsin, Madison, WI, United States of America
| | - Niklaus J. Grünwald
- Horticultural Crops Research Laboratory, United States Department of Agriculture–Agricultural Research Service, Corvallis, OR, United States of America
| | - Beth K. Gugino
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, United States of America
| | - Dennis A. Johnson
- Department of Plant Pathology, Washington State University, Pullman, WA, United States of America
| | - Steven B. Johnson
- University of Maine Cooperative Extension, Presque Isle, ME, United States of America
| | - Howard S. Judelson
- Department of Plant Pathology and Microbiology, University of California Riverside, Riverside, CA, United States of America
| | - Brian J. Knaus
- Horticultural Crops Research Laboratory, United States Department of Agriculture–Agricultural Research Service, Corvallis, OR, United States of America
| | - Margaret T. McGrath
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Riverhead, NY, United States of America
| | - Kevin L. Myers
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY, United States of America
| | - Jean B. Ristaino
- Department of Plant Pathology, North Carolina State University, Raleigh, NC, United States of America
| | - Pamela D. Roberts
- Department of Plant Pathology, University of Florida, Immokalee, FL, United States of America
| | - Gary A. Secor
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States of America
| | - Christine D. Smart
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY, United States of America
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Tabima JF, Everhart SE, Larsen MM, Weisberg AJ, Kamvar ZN, Tancos MA, Smart CD, Chang JH, Grünwald NJ. Microbe-ID: an open source toolbox for microbial genotyping and species identification. PeerJ 2016; 4:e2279. [PMID: 27602267 PMCID: PMC4994078 DOI: 10.7717/peerj.2279] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 07/02/2016] [Indexed: 11/26/2022] Open
Abstract
Development of tools to identify species, genotypes, or novel strains of invasive organisms is critical for monitoring emergence and implementing rapid response measures. Molecular markers, although critical to identifying species or genotypes, require bioinformatic tools for analysis. However, user-friendly analytical tools for fast identification are not readily available. To address this need, we created a web-based set of applications called Microbe-ID that allow for customizing a toolbox for rapid species identification and strain genotyping using any genetic markers of choice. Two components of Microbe-ID, named Sequence-ID and Genotype-ID, implement species and genotype identification, respectively. Sequence-ID allows identification of species by using BLAST to query sequences for any locus of interest against a custom reference sequence database. Genotype-ID allows placement of an unknown multilocus marker in either a minimum spanning network or dendrogram with bootstrap support from a user-created reference database. Microbe-ID can be used for identification of any organism based on nucleotide sequences or any molecular marker type and several examples are provided. We created a public website for demonstration purposes called Microbe-ID (microbe-id.org) and provided a working implementation for the genus Phytophthora (phytophthora-id.org). In Phytophthora-ID, the Sequence-ID application allows identification based on ITS or cox spacer sequences. Genotype-ID groups individuals into clonal lineages based on simple sequence repeat (SSR) markers for the two invasive plant pathogen species P. infestans and P. ramorum. All code is open source and available on github and CRAN. Instructions for installation and use are provided at https://github.com/grunwaldlab/Microbe-ID.
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Affiliation(s)
- Javier F. Tabima
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Sydney E. Everhart
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
- Current affiliation: Department of Plant Pathology, University of Nebraska, Lincoln, NE, United States
| | - Meredith M. Larsen
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, OR, United States
| | - Alexandra J. Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Zhian N. Kamvar
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Matthew A. Tancos
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY, United States
| | - Christine D. Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY, United States
| | - Jeff H. Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
- Molecular and Cellular Biology Graduate Program and Center for Genome Biology and Biocomputing, Oregon State University, Corvallis, OR, United States
| | - Niklaus J. Grünwald
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, OR, United States
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY, United States
- Molecular and Cellular Biology Graduate Program and Center for Genome Biology and Biocomputing, Oregon State University, Corvallis, OR, United States
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Hansen ZR, Knaus BJ, Tabima JF, Press CM, Judelson HS, Grünwald NJ, Smart CD. SNP-Based Differentiation of Phytophthora infestans Clonal Lineages Using Locked Nucleic Acid Probes and High-Resolution Melt Analysis. Plant Dis 2016; 100:1297-1306. [PMID: 30686206 DOI: 10.1094/pdis-11-15-1247-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Phytophthora infestans, the cause of the devastating late blight disease of potato and tomato, exhibits a clonal reproductive lifestyle in North America. Phenotypes such as fungicide sensitivity and host preference are conserved among individuals within clonal lineages, while substantial phenotypic differences can exist between lineages. Whole P. infestans genomes were aligned and single nucleotide polymorphisms (SNPs) identified as targets for the development of clonal-lineage-specific molecular diagnostic tools. Informative SNPs were used to develop high-resolution melt (HRM) assays and locked nucleic acid (LNA) probes to differentiate lineage US-23, the predominant lineage in the Eastern United States for the past several years, from three other U.S. lineages. Three different primer pairs targeting one to three SNPs were capable of separating lineage US-23 from lineages US-8, US-11, and US-24 using HRM analysis. A fourth HRM primer pair targeted a highly variable genomic region containing nine polymorphisms within 63 bp. These primers separated US-23, US-11, and US-8 plus US-24 into three separate groups following HRM analysis but did not separate US-8 from US-24. Additionally, two LNA probes were designed to target a portion of the P. infestans genome containing two SNPs diagnostic for US-23. A single multiplex quantitative polymerase chain reaction assay containing both differentially labeled LNA probes differentiated individuals belonging to lineage US-23 from those belonging to US-8, US-11, and US-24.
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Affiliation(s)
- Zachariah R Hansen
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, NYSAES, Geneva, NY, 14456
| | - Brian J Knaus
- Horticultural Crops Research Laboratory, United States Department of Agriculture-Agricultural Research Service, (USDA-ARS) Corvallis, OR, 97331
| | - Javier F Tabima
- Botany and Plant Pathology, Oregon State University, Corvallis, 97331
| | | | - Howard S Judelson
- Department of Plant Pathology and Microbiology, University of California, Riverside, 92521
| | - Niklaus J Grünwald
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University; Horticultural Crops Research Laboratory, USDA-ARS; and Botany and Plant Pathology, Oregon State University
| | - Christine D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University
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Hansen ZR, Knaus BJ, Tabima JF, Press CM, Judelson HS, Grünwald NJ, Smart CD. Loop-mediated isothermal amplification for detection of the tomato and potato late blight pathogen, Phytophthora infestans. J Appl Microbiol 2016; 120:1010-20. [PMID: 26820117 DOI: 10.1111/jam.13079] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 01/20/2016] [Accepted: 01/21/2016] [Indexed: 12/01/2022]
Abstract
AIMS To design and validate a colorimetric loop-mediated isothermal amplification assay for rapid detection of Phytophthora infestans DNA. METHODS AND RESULTS Two sets of loop-mediated isothermal amplification (LAMP) primers were designed and evaluated for their sensitivity and specificity for P. infestans. ITSII primers targeted a portion of the internal transcribed spacer region of ribosomal DNA. These primers had a limit of detection of 2 pg P. infestans DNA and cross-reacted with the closely related species Phytophthora nicotianae. Rgn86_2 primers, designed to improve assay specificity, targeted a portion of a conserved hypothetical protein. These primers had a limit of detection of 200 pg P. infestans DNA and did not cross-react with P. nicotianae. The specificity of the Rgn86_2 assay was tested further using the closely related species P. andina, P. ipomoeae, P. mirabilis and P. phaseoli. Cross-reactions occurred with P. andina and P. mirabilis, but neither species occurs on tomato or potato. Both primer sets were able to detect P. infestans DNA extracted from tomato late blight leaf lesions. CONCLUSIONS Two colorimetric LAMP assays detected P. infestans DNA from pure cultures as well as infected leaf tissue. The ITSII primers had higher sensitivity, and the Rgn86_2 primers had higher specificity. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first report of a LAMP assay for the detection of P. infestans, the causal organism of potato and tomato late blight. These assays have potential for immediate utility in plant disease research and diagnostic laboratories.
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Affiliation(s)
- Z R Hansen
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY, USA
| | - B J Knaus
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, OR, USA
| | - J F Tabima
- Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - C M Press
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, OR, USA
| | - H S Judelson
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, USA
| | - N J Grünwald
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, OR, USA.,Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - C D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY, USA
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Lange HW, Tancos MA, Carlson MO, Smart CD. Diversity of Xanthomonas campestris Isolates from Symptomatic Crucifers in New York State. Phytopathology 2016; 106:113-122. [PMID: 26551450 DOI: 10.1094/phyto-06-15-0134-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
To assess the diversity of Xanthomonas campestris spp. infecting crucifers in New York, 154 isolates were collected over 10 years across the state. The goal was to determine if isolates of the pathogen were overwintering in New York and serving as primary inoculum in subsequent years, or if novel isolates were entering the state each year. Pure cultures of isolates were characterized using multilocus sequence analysis (MLSA), a greenhouse pathogenicity assay, repetitive element-polymerase chain reaction (Rep-PCR) using the BOX-A1R primer, and enzyme-linked immunosorbent assay. The MLSA scheme proved to be more efficient than Rep-PCR for a large sample population and for comparison with global isolates. X. campestris isolated from crucifers in New York comprised of X. campestris pv. campestris and X. campestris pv. raphani, with X. campestris pv. raphani being predominately isolated from transplants. Evidence for unique haplotypes persisting on the same farm for several years due to improper seedbed rotations was documented in addition to novel haplotypes being spread throughout states through infected transplants and seed. Rep-PCR confirmed the high diversity of X. campestris and was used to generate 15 unique fingerprint patterns from isolates collected in the first 5 years. A worldwide comparison of isolates suggests that the X. campestris pv. campestris population appears to be very homogenous with dominant haplotypes persisting for extended periods and being globally disseminated.
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Affiliation(s)
- H W Lange
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456
| | - M A Tancos
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456
| | - M O Carlson
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456
| | - C D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456
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35
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Summers CF, Gulliford CM, Carlson CH, Lillis JA, Carlson MO, Cadle-Davidson L, Gent DH, Smart CD. Identification of Genetic Variation between Obligate Plant Pathogens Pseudoperonospora cubensis and P. humuli Using RNA Sequencing and Genotyping-By-Sequencing. PLoS One 2015; 10:e0143665. [PMID: 26599440 PMCID: PMC4658093 DOI: 10.1371/journal.pone.0143665] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/06/2015] [Indexed: 12/29/2022] Open
Abstract
RNA sequencing (RNA-seq) and genotyping-by-sequencing (GBS) were used for single nucleotide polymorphism (SNP) identification from two economically important obligate plant pathogens, Pseudoperonospora cubensis and P. humuli. Twenty isolates of P. cubensis and 19 isolates of P. humuli were genotyped using RNA-seq and GBS. Principle components analysis (PCA) of each data set showed genetic separation between the two species. Additionally, results supported previous findings that P. cubensis isolates from squash are genetically distinct from cucumber and cantaloupe isolates. A PCA-based procedure was used to identify SNPs correlated with the separation of the two species, with 994 and 4,231 PCA-correlated SNPs found within the RNA-seq and GBS data, respectively. The corresponding unigenes (n = 800) containing these potential species-specific SNPs were then annotated and 135 putative pathogenicity genes, including 3 effectors, were identified. The characterization of genes containing SNPs differentiating these two closely related downy mildew species may contribute to the development of improved detection and diagnosis strategies and improve our understanding of host specificity pathways.
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Affiliation(s)
- Carly F. Summers
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, New York, United States of America
| | - Colwyn M. Gulliford
- Cornell Laboratory for Accelerator-based Sciences and Education, Cornell University, Ithaca, New York, United States of America
| | - Craig H. Carlson
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, New York, United States of America
| | - Jacquelyn A. Lillis
- United States Department of Agriculture Agricultural Research Service, Grape Genetics Research Unit, Geneva, New York, United States of America
| | - Maryn O. Carlson
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, New York, United States of America
| | - Lance Cadle-Davidson
- United States Department of Agriculture Agricultural Research Service, Grape Genetics Research Unit, Geneva, New York, United States of America
| | - David H. Gent
- United States Department of Agriculture Agricultural Research Service, Forage Seed and Cereal Research Unit and Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Christine D. Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, New York, United States of America
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Abstract
Using host resistance is an important strategy for managing pepper root and crown rot caused by Phytophthora capsici. An isolate of P. capsici constitutively expressing a gene for green fluorescent protein was used to investigate pathogen interactions with roots, crowns, and stems of Phytophthora-susceptible bell pepper 'Red Knight', Phytophthora-resistant bell pepper 'Paladin', and Phytophthora-resistant landrace Criollos de Morelos 334 (CM-334). In this study, the same number of zoospores attached to and germinated on roots of all cultivars 30 and 120 min postinoculation (pi), respectively. At 3 days pi, significantly more secondary roots had necrotic lesions on Red Knight than on Paladin and CM-334 plants. By 4 days pi, necrotic lesions had formed on the taproot of Red Knight but not Paladin or CM-334 plants. Although hyphae were visible in the crowns and stems of all Red Knight plants observed at 4 days pi, hyphae were observed in crowns of only a few Paladin and in no CM-334 plants, and never in stems of either resistant cultivar at 4 days pi. These results improve our understanding of how P. capsici infects plants and may contribute to the use of resistant pepper cultivars for disease management and the development of new cultivars.
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Affiliation(s)
- Amara R Dunn
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Sciences, Cornell University, Geneva, NY
| | - Christine D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Sciences, Cornell University, Geneva, NY
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37
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Fry WE, Birch PRJ, Judelson HS, Grünwald NJ, Danies G, Everts KL, Gevens AJ, Gugino BK, Johnson DA, Johnson SB, McGrath MT, Myers KL, Ristaino JB, Roberts PD, Secor G, Smart CD. Five Reasons to Consider Phytophthora infestans a Reemerging Pathogen. Phytopathology 2015; 105:966-81. [PMID: 25760519 DOI: 10.1094/phyto-01-15-0005-fi] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Phytophthora infestans has been a named pathogen for well over 150 years and yet it continues to "emerge", with thousands of articles published each year on it and the late blight disease that it causes. This review explores five attributes of this oomycete pathogen that maintain this constant attention. First, the historical tragedy associated with this disease (Irish potato famine) causes many people to be fascinated with the pathogen. Current technology now enables investigators to answer some questions of historical significance. Second, the devastation caused by the pathogen continues to appear in surprising new locations or with surprising new intensity. Third, populations of P. infestans worldwide are in flux, with changes that have major implications to disease management. Fourth, the genomics revolution has enabled investigators to make tremendous progress in terms of understanding the molecular biology (especially the pathogenicity) of P. infestans. Fifth, there remain many compelling unanswered questions.
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Affiliation(s)
- W E Fry
- First, fifth, and twelfth authors: Cornell University, Section of Plant Pathology and Plant-Microbe Biology, 334 Plant Science Bldg., Ithaca, NY 14850; second author: Division of Plant Sciences, University of Dundee at James Hutton Institute, Invergowrie, Dundee, DD2 4DA, UK; third author: Department of Plant Pathology and Microbiology, University of California, Riverside 92521; fourth author: Horticultural Crops Research Laboratory, United States Department of Agriculture-Agricultural Research Service, 3420 NW Orchard Ave., Corvallis, OR 97330; sixth author: Plant Pathology Department, University of Maryland, 27664 Nanticoke Rd., Salisbury 21801; seventh author: University of Wisconsin Department of Plant Pathology, 1630 Linden Dr., Madison 53706-1598; eighth author: Department of Plant Pathology and Environmental Microbiology, College of Agricultural Sciences, The Pennsylvania State University, 219 Buckhout Lab, University Park 16802; ninth author: Department of Plant Pathology, Washington State University, PO Box 646430, Pullman; tenth author: University of Maine Cooperative Extension, 57 Houlton Road, Presque Isle 04769; eleventh author: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Long Island Horticultural Research & Extension Center, Riverhead, NY 11901-1098; thirteenth author: Department of Plant Pathology, Room 2419 Gardner Hall, NC State University, Raleigh 27695; fourteenth author: Department of Plant Pathology, University of Florida, Southwest Florida Research and Education Center, 2685 SR 29 N, Immokalee 34142-9515; fifteenth author: Department of Plant Pathology, North Dakota State University, 328 Walster Hall, Dept. 7660, PO Box6050, Fargo 58108-6050; and sixteenth author: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Barton Lab, NYSAES, 630 West North Street, Geneva, NY 14456
| | - P R J Birch
- First, fifth, and twelfth authors: Cornell University, Section of Plant Pathology and Plant-Microbe Biology, 334 Plant Science Bldg., Ithaca, NY 14850; second author: Division of Plant Sciences, University of Dundee at James Hutton Institute, Invergowrie, Dundee, DD2 4DA, UK; third author: Department of Plant Pathology and Microbiology, University of California, Riverside 92521; fourth author: Horticultural Crops Research Laboratory, United States Department of Agriculture-Agricultural Research Service, 3420 NW Orchard Ave., Corvallis, OR 97330; sixth author: Plant Pathology Department, University of Maryland, 27664 Nanticoke Rd., Salisbury 21801; seventh author: University of Wisconsin Department of Plant Pathology, 1630 Linden Dr., Madison 53706-1598; eighth author: Department of Plant Pathology and Environmental Microbiology, College of Agricultural Sciences, The Pennsylvania State University, 219 Buckhout Lab, University Park 16802; ninth author: Department of Plant Pathology, Washington State University, PO Box 646430, Pullman; tenth author: University of Maine Cooperative Extension, 57 Houlton Road, Presque Isle 04769; eleventh author: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Long Island Horticultural Research & Extension Center, Riverhead, NY 11901-1098; thirteenth author: Department of Plant Pathology, Room 2419 Gardner Hall, NC State University, Raleigh 27695; fourteenth author: Department of Plant Pathology, University of Florida, Southwest Florida Research and Education Center, 2685 SR 29 N, Immokalee 34142-9515; fifteenth author: Department of Plant Pathology, North Dakota State University, 328 Walster Hall, Dept. 7660, PO Box6050, Fargo 58108-6050; and sixteenth author: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Barton Lab, NYSAES, 630 West North Street, Geneva, NY 14456
| | - H S Judelson
- First, fifth, and twelfth authors: Cornell University, Section of Plant Pathology and Plant-Microbe Biology, 334 Plant Science Bldg., Ithaca, NY 14850; second author: Division of Plant Sciences, University of Dundee at James Hutton Institute, Invergowrie, Dundee, DD2 4DA, UK; third author: Department of Plant Pathology and Microbiology, University of California, Riverside 92521; fourth author: Horticultural Crops Research Laboratory, United States Department of Agriculture-Agricultural Research Service, 3420 NW Orchard Ave., Corvallis, OR 97330; sixth author: Plant Pathology Department, University of Maryland, 27664 Nanticoke Rd., Salisbury 21801; seventh author: University of Wisconsin Department of Plant Pathology, 1630 Linden Dr., Madison 53706-1598; eighth author: Department of Plant Pathology and Environmental Microbiology, College of Agricultural Sciences, The Pennsylvania State University, 219 Buckhout Lab, University Park 16802; ninth author: Department of Plant Pathology, Washington State University, PO Box 646430, Pullman; tenth author: University of Maine Cooperative Extension, 57 Houlton Road, Presque Isle 04769; eleventh author: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Long Island Horticultural Research & Extension Center, Riverhead, NY 11901-1098; thirteenth author: Department of Plant Pathology, Room 2419 Gardner Hall, NC State University, Raleigh 27695; fourteenth author: Department of Plant Pathology, University of Florida, Southwest Florida Research and Education Center, 2685 SR 29 N, Immokalee 34142-9515; fifteenth author: Department of Plant Pathology, North Dakota State University, 328 Walster Hall, Dept. 7660, PO Box6050, Fargo 58108-6050; and sixteenth author: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Barton Lab, NYSAES, 630 West North Street, Geneva, NY 14456
| | - N J Grünwald
- First, fifth, and twelfth authors: Cornell University, Section of Plant Pathology and Plant-Microbe Biology, 334 Plant Science Bldg., Ithaca, NY 14850; second author: Division of Plant Sciences, University of Dundee at James Hutton Institute, Invergowrie, Dundee, DD2 4DA, UK; third author: Department of Plant Pathology and Microbiology, University of California, Riverside 92521; fourth author: Horticultural Crops Research Laboratory, United States Department of Agriculture-Agricultural Research Service, 3420 NW Orchard Ave., Corvallis, OR 97330; sixth author: Plant Pathology Department, University of Maryland, 27664 Nanticoke Rd., Salisbury 21801; seventh author: University of Wisconsin Department of Plant Pathology, 1630 Linden Dr., Madison 53706-1598; eighth author: Department of Plant Pathology and Environmental Microbiology, College of Agricultural Sciences, The Pennsylvania State University, 219 Buckhout Lab, University Park 16802; ninth author: Department of Plant Pathology, Washington State University, PO Box 646430, Pullman; tenth author: University of Maine Cooperative Extension, 57 Houlton Road, Presque Isle 04769; eleventh author: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Long Island Horticultural Research & Extension Center, Riverhead, NY 11901-1098; thirteenth author: Department of Plant Pathology, Room 2419 Gardner Hall, NC State University, Raleigh 27695; fourteenth author: Department of Plant Pathology, University of Florida, Southwest Florida Research and Education Center, 2685 SR 29 N, Immokalee 34142-9515; fifteenth author: Department of Plant Pathology, North Dakota State University, 328 Walster Hall, Dept. 7660, PO Box6050, Fargo 58108-6050; and sixteenth author: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Barton Lab, NYSAES, 630 West North Street, Geneva, NY 14456
| | - G Danies
- First, fifth, and twelfth authors: Cornell University, Section of Plant Pathology and Plant-Microbe Biology, 334 Plant Science Bldg., Ithaca, NY 14850; second author: Division of Plant Sciences, University of Dundee at James Hutton Institute, Invergowrie, Dundee, DD2 4DA, UK; third author: Department of Plant Pathology and Microbiology, University of California, Riverside 92521; fourth author: Horticultural Crops Research Laboratory, United States Department of Agriculture-Agricultural Research Service, 3420 NW Orchard Ave., Corvallis, OR 97330; sixth author: Plant Pathology Department, University of Maryland, 27664 Nanticoke Rd., Salisbury 21801; seventh author: University of Wisconsin Department of Plant Pathology, 1630 Linden Dr., Madison 53706-1598; eighth author: Department of Plant Pathology and Environmental Microbiology, College of Agricultural Sciences, The Pennsylvania State University, 219 Buckhout Lab, University Park 16802; ninth author: Department of Plant Pathology, Washington State University, PO Box 646430, Pullman; tenth author: University of Maine Cooperative Extension, 57 Houlton Road, Presque Isle 04769; eleventh author: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Long Island Horticultural Research & Extension Center, Riverhead, NY 11901-1098; thirteenth author: Department of Plant Pathology, Room 2419 Gardner Hall, NC State University, Raleigh 27695; fourteenth author: Department of Plant Pathology, University of Florida, Southwest Florida Research and Education Center, 2685 SR 29 N, Immokalee 34142-9515; fifteenth author: Department of Plant Pathology, North Dakota State University, 328 Walster Hall, Dept. 7660, PO Box6050, Fargo 58108-6050; and sixteenth author: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Barton Lab, NYSAES, 630 West North Street, Geneva, NY 14456
| | - K L Everts
- First, fifth, and twelfth authors: Cornell University, Section of Plant Pathology and Plant-Microbe Biology, 334 Plant Science Bldg., Ithaca, NY 14850; second author: Division of Plant Sciences, University of Dundee at James Hutton Institute, Invergowrie, Dundee, DD2 4DA, UK; third author: Department of Plant Pathology and Microbiology, University of California, Riverside 92521; fourth author: Horticultural Crops Research Laboratory, United States Department of Agriculture-Agricultural Research Service, 3420 NW Orchard Ave., Corvallis, OR 97330; sixth author: Plant Pathology Department, University of Maryland, 27664 Nanticoke Rd., Salisbury 21801; seventh author: University of Wisconsin Department of Plant Pathology, 1630 Linden Dr., Madison 53706-1598; eighth author: Department of Plant Pathology and Environmental Microbiology, College of Agricultural Sciences, The Pennsylvania State University, 219 Buckhout Lab, University Park 16802; ninth author: Department of Plant Pathology, Washington State University, PO Box 646430, Pullman; tenth author: University of Maine Cooperative Extension, 57 Houlton Road, Presque Isle 04769; eleventh author: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Long Island Horticultural Research & Extension Center, Riverhead, NY 11901-1098; thirteenth author: Department of Plant Pathology, Room 2419 Gardner Hall, NC State University, Raleigh 27695; fourteenth author: Department of Plant Pathology, University of Florida, Southwest Florida Research and Education Center, 2685 SR 29 N, Immokalee 34142-9515; fifteenth author: Department of Plant Pathology, North Dakota State University, 328 Walster Hall, Dept. 7660, PO Box6050, Fargo 58108-6050; and sixteenth author: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Barton Lab, NYSAES, 630 West North Street, Geneva, NY 14456
| | - A J Gevens
- First, fifth, and twelfth authors: Cornell University, Section of Plant Pathology and Plant-Microbe Biology, 334 Plant Science Bldg., Ithaca, NY 14850; second author: Division of Plant Sciences, University of Dundee at James Hutton Institute, Invergowrie, Dundee, DD2 4DA, UK; third author: Department of Plant Pathology and Microbiology, University of California, Riverside 92521; fourth author: Horticultural Crops Research Laboratory, United States Department of Agriculture-Agricultural Research Service, 3420 NW Orchard Ave., Corvallis, OR 97330; sixth author: Plant Pathology Department, University of Maryland, 27664 Nanticoke Rd., Salisbury 21801; seventh author: University of Wisconsin Department of Plant Pathology, 1630 Linden Dr., Madison 53706-1598; eighth author: Department of Plant Pathology and Environmental Microbiology, College of Agricultural Sciences, The Pennsylvania State University, 219 Buckhout Lab, University Park 16802; ninth author: Department of Plant Pathology, Washington State University, PO Box 646430, Pullman; tenth author: University of Maine Cooperative Extension, 57 Houlton Road, Presque Isle 04769; eleventh author: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Long Island Horticultural Research & Extension Center, Riverhead, NY 11901-1098; thirteenth author: Department of Plant Pathology, Room 2419 Gardner Hall, NC State University, Raleigh 27695; fourteenth author: Department of Plant Pathology, University of Florida, Southwest Florida Research and Education Center, 2685 SR 29 N, Immokalee 34142-9515; fifteenth author: Department of Plant Pathology, North Dakota State University, 328 Walster Hall, Dept. 7660, PO Box6050, Fargo 58108-6050; and sixteenth author: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Barton Lab, NYSAES, 630 West North Street, Geneva, NY 14456
| | - B K Gugino
- First, fifth, and twelfth authors: Cornell University, Section of Plant Pathology and Plant-Microbe Biology, 334 Plant Science Bldg., Ithaca, NY 14850; second author: Division of Plant Sciences, University of Dundee at James Hutton Institute, Invergowrie, Dundee, DD2 4DA, UK; third author: Department of Plant Pathology and Microbiology, University of California, Riverside 92521; fourth author: Horticultural Crops Research Laboratory, United States Department of Agriculture-Agricultural Research Service, 3420 NW Orchard Ave., Corvallis, OR 97330; sixth author: Plant Pathology Department, University of Maryland, 27664 Nanticoke Rd., Salisbury 21801; seventh author: University of Wisconsin Department of Plant Pathology, 1630 Linden Dr., Madison 53706-1598; eighth author: Department of Plant Pathology and Environmental Microbiology, College of Agricultural Sciences, The Pennsylvania State University, 219 Buckhout Lab, University Park 16802; ninth author: Department of Plant Pathology, Washington State University, PO Box 646430, Pullman; tenth author: University of Maine Cooperative Extension, 57 Houlton Road, Presque Isle 04769; eleventh author: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Long Island Horticultural Research & Extension Center, Riverhead, NY 11901-1098; thirteenth author: Department of Plant Pathology, Room 2419 Gardner Hall, NC State University, Raleigh 27695; fourteenth author: Department of Plant Pathology, University of Florida, Southwest Florida Research and Education Center, 2685 SR 29 N, Immokalee 34142-9515; fifteenth author: Department of Plant Pathology, North Dakota State University, 328 Walster Hall, Dept. 7660, PO Box6050, Fargo 58108-6050; and sixteenth author: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Barton Lab, NYSAES, 630 West North Street, Geneva, NY 14456
| | - D A Johnson
- First, fifth, and twelfth authors: Cornell University, Section of Plant Pathology and Plant-Microbe Biology, 334 Plant Science Bldg., Ithaca, NY 14850; second author: Division of Plant Sciences, University of Dundee at James Hutton Institute, Invergowrie, Dundee, DD2 4DA, UK; third author: Department of Plant Pathology and Microbiology, University of California, Riverside 92521; fourth author: Horticultural Crops Research Laboratory, United States Department of Agriculture-Agricultural Research Service, 3420 NW Orchard Ave., Corvallis, OR 97330; sixth author: Plant Pathology Department, University of Maryland, 27664 Nanticoke Rd., Salisbury 21801; seventh author: University of Wisconsin Department of Plant Pathology, 1630 Linden Dr., Madison 53706-1598; eighth author: Department of Plant Pathology and Environmental Microbiology, College of Agricultural Sciences, The Pennsylvania State University, 219 Buckhout Lab, University Park 16802; ninth author: Department of Plant Pathology, Washington State University, PO Box 646430, Pullman; tenth author: University of Maine Cooperative Extension, 57 Houlton Road, Presque Isle 04769; eleventh author: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Long Island Horticultural Research & Extension Center, Riverhead, NY 11901-1098; thirteenth author: Department of Plant Pathology, Room 2419 Gardner Hall, NC State University, Raleigh 27695; fourteenth author: Department of Plant Pathology, University of Florida, Southwest Florida Research and Education Center, 2685 SR 29 N, Immokalee 34142-9515; fifteenth author: Department of Plant Pathology, North Dakota State University, 328 Walster Hall, Dept. 7660, PO Box6050, Fargo 58108-6050; and sixteenth author: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Barton Lab, NYSAES, 630 West North Street, Geneva, NY 14456
| | - S B Johnson
- First, fifth, and twelfth authors: Cornell University, Section of Plant Pathology and Plant-Microbe Biology, 334 Plant Science Bldg., Ithaca, NY 14850; second author: Division of Plant Sciences, University of Dundee at James Hutton Institute, Invergowrie, Dundee, DD2 4DA, UK; third author: Department of Plant Pathology and Microbiology, University of California, Riverside 92521; fourth author: Horticultural Crops Research Laboratory, United States Department of Agriculture-Agricultural Research Service, 3420 NW Orchard Ave., Corvallis, OR 97330; sixth author: Plant Pathology Department, University of Maryland, 27664 Nanticoke Rd., Salisbury 21801; seventh author: University of Wisconsin Department of Plant Pathology, 1630 Linden Dr., Madison 53706-1598; eighth author: Department of Plant Pathology and Environmental Microbiology, College of Agricultural Sciences, The Pennsylvania State University, 219 Buckhout Lab, University Park 16802; ninth author: Department of Plant Pathology, Washington State University, PO Box 646430, Pullman; tenth author: University of Maine Cooperative Extension, 57 Houlton Road, Presque Isle 04769; eleventh author: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Long Island Horticultural Research & Extension Center, Riverhead, NY 11901-1098; thirteenth author: Department of Plant Pathology, Room 2419 Gardner Hall, NC State University, Raleigh 27695; fourteenth author: Department of Plant Pathology, University of Florida, Southwest Florida Research and Education Center, 2685 SR 29 N, Immokalee 34142-9515; fifteenth author: Department of Plant Pathology, North Dakota State University, 328 Walster Hall, Dept. 7660, PO Box6050, Fargo 58108-6050; and sixteenth author: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Barton Lab, NYSAES, 630 West North Street, Geneva, NY 14456
| | - M T McGrath
- First, fifth, and twelfth authors: Cornell University, Section of Plant Pathology and Plant-Microbe Biology, 334 Plant Science Bldg., Ithaca, NY 14850; second author: Division of Plant Sciences, University of Dundee at James Hutton Institute, Invergowrie, Dundee, DD2 4DA, UK; third author: Department of Plant Pathology and Microbiology, University of California, Riverside 92521; fourth author: Horticultural Crops Research Laboratory, United States Department of Agriculture-Agricultural Research Service, 3420 NW Orchard Ave., Corvallis, OR 97330; sixth author: Plant Pathology Department, University of Maryland, 27664 Nanticoke Rd., Salisbury 21801; seventh author: University of Wisconsin Department of Plant Pathology, 1630 Linden Dr., Madison 53706-1598; eighth author: Department of Plant Pathology and Environmental Microbiology, College of Agricultural Sciences, The Pennsylvania State University, 219 Buckhout Lab, University Park 16802; ninth author: Department of Plant Pathology, Washington State University, PO Box 646430, Pullman; tenth author: University of Maine Cooperative Extension, 57 Houlton Road, Presque Isle 04769; eleventh author: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Long Island Horticultural Research & Extension Center, Riverhead, NY 11901-1098; thirteenth author: Department of Plant Pathology, Room 2419 Gardner Hall, NC State University, Raleigh 27695; fourteenth author: Department of Plant Pathology, University of Florida, Southwest Florida Research and Education Center, 2685 SR 29 N, Immokalee 34142-9515; fifteenth author: Department of Plant Pathology, North Dakota State University, 328 Walster Hall, Dept. 7660, PO Box6050, Fargo 58108-6050; and sixteenth author: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Barton Lab, NYSAES, 630 West North Street, Geneva, NY 14456
| | - K L Myers
- First, fifth, and twelfth authors: Cornell University, Section of Plant Pathology and Plant-Microbe Biology, 334 Plant Science Bldg., Ithaca, NY 14850; second author: Division of Plant Sciences, University of Dundee at James Hutton Institute, Invergowrie, Dundee, DD2 4DA, UK; third author: Department of Plant Pathology and Microbiology, University of California, Riverside 92521; fourth author: Horticultural Crops Research Laboratory, United States Department of Agriculture-Agricultural Research Service, 3420 NW Orchard Ave., Corvallis, OR 97330; sixth author: Plant Pathology Department, University of Maryland, 27664 Nanticoke Rd., Salisbury 21801; seventh author: University of Wisconsin Department of Plant Pathology, 1630 Linden Dr., Madison 53706-1598; eighth author: Department of Plant Pathology and Environmental Microbiology, College of Agricultural Sciences, The Pennsylvania State University, 219 Buckhout Lab, University Park 16802; ninth author: Department of Plant Pathology, Washington State University, PO Box 646430, Pullman; tenth author: University of Maine Cooperative Extension, 57 Houlton Road, Presque Isle 04769; eleventh author: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Long Island Horticultural Research & Extension Center, Riverhead, NY 11901-1098; thirteenth author: Department of Plant Pathology, Room 2419 Gardner Hall, NC State University, Raleigh 27695; fourteenth author: Department of Plant Pathology, University of Florida, Southwest Florida Research and Education Center, 2685 SR 29 N, Immokalee 34142-9515; fifteenth author: Department of Plant Pathology, North Dakota State University, 328 Walster Hall, Dept. 7660, PO Box6050, Fargo 58108-6050; and sixteenth author: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Barton Lab, NYSAES, 630 West North Street, Geneva, NY 14456
| | - J B Ristaino
- First, fifth, and twelfth authors: Cornell University, Section of Plant Pathology and Plant-Microbe Biology, 334 Plant Science Bldg., Ithaca, NY 14850; second author: Division of Plant Sciences, University of Dundee at James Hutton Institute, Invergowrie, Dundee, DD2 4DA, UK; third author: Department of Plant Pathology and Microbiology, University of California, Riverside 92521; fourth author: Horticultural Crops Research Laboratory, United States Department of Agriculture-Agricultural Research Service, 3420 NW Orchard Ave., Corvallis, OR 97330; sixth author: Plant Pathology Department, University of Maryland, 27664 Nanticoke Rd., Salisbury 21801; seventh author: University of Wisconsin Department of Plant Pathology, 1630 Linden Dr., Madison 53706-1598; eighth author: Department of Plant Pathology and Environmental Microbiology, College of Agricultural Sciences, The Pennsylvania State University, 219 Buckhout Lab, University Park 16802; ninth author: Department of Plant Pathology, Washington State University, PO Box 646430, Pullman; tenth author: University of Maine Cooperative Extension, 57 Houlton Road, Presque Isle 04769; eleventh author: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Long Island Horticultural Research & Extension Center, Riverhead, NY 11901-1098; thirteenth author: Department of Plant Pathology, Room 2419 Gardner Hall, NC State University, Raleigh 27695; fourteenth author: Department of Plant Pathology, University of Florida, Southwest Florida Research and Education Center, 2685 SR 29 N, Immokalee 34142-9515; fifteenth author: Department of Plant Pathology, North Dakota State University, 328 Walster Hall, Dept. 7660, PO Box6050, Fargo 58108-6050; and sixteenth author: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Barton Lab, NYSAES, 630 West North Street, Geneva, NY 14456
| | - P D Roberts
- First, fifth, and twelfth authors: Cornell University, Section of Plant Pathology and Plant-Microbe Biology, 334 Plant Science Bldg., Ithaca, NY 14850; second author: Division of Plant Sciences, University of Dundee at James Hutton Institute, Invergowrie, Dundee, DD2 4DA, UK; third author: Department of Plant Pathology and Microbiology, University of California, Riverside 92521; fourth author: Horticultural Crops Research Laboratory, United States Department of Agriculture-Agricultural Research Service, 3420 NW Orchard Ave., Corvallis, OR 97330; sixth author: Plant Pathology Department, University of Maryland, 27664 Nanticoke Rd., Salisbury 21801; seventh author: University of Wisconsin Department of Plant Pathology, 1630 Linden Dr., Madison 53706-1598; eighth author: Department of Plant Pathology and Environmental Microbiology, College of Agricultural Sciences, The Pennsylvania State University, 219 Buckhout Lab, University Park 16802; ninth author: Department of Plant Pathology, Washington State University, PO Box 646430, Pullman; tenth author: University of Maine Cooperative Extension, 57 Houlton Road, Presque Isle 04769; eleventh author: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Long Island Horticultural Research & Extension Center, Riverhead, NY 11901-1098; thirteenth author: Department of Plant Pathology, Room 2419 Gardner Hall, NC State University, Raleigh 27695; fourteenth author: Department of Plant Pathology, University of Florida, Southwest Florida Research and Education Center, 2685 SR 29 N, Immokalee 34142-9515; fifteenth author: Department of Plant Pathology, North Dakota State University, 328 Walster Hall, Dept. 7660, PO Box6050, Fargo 58108-6050; and sixteenth author: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Barton Lab, NYSAES, 630 West North Street, Geneva, NY 14456
| | - G Secor
- First, fifth, and twelfth authors: Cornell University, Section of Plant Pathology and Plant-Microbe Biology, 334 Plant Science Bldg., Ithaca, NY 14850; second author: Division of Plant Sciences, University of Dundee at James Hutton Institute, Invergowrie, Dundee, DD2 4DA, UK; third author: Department of Plant Pathology and Microbiology, University of California, Riverside 92521; fourth author: Horticultural Crops Research Laboratory, United States Department of Agriculture-Agricultural Research Service, 3420 NW Orchard Ave., Corvallis, OR 97330; sixth author: Plant Pathology Department, University of Maryland, 27664 Nanticoke Rd., Salisbury 21801; seventh author: University of Wisconsin Department of Plant Pathology, 1630 Linden Dr., Madison 53706-1598; eighth author: Department of Plant Pathology and Environmental Microbiology, College of Agricultural Sciences, The Pennsylvania State University, 219 Buckhout Lab, University Park 16802; ninth author: Department of Plant Pathology, Washington State University, PO Box 646430, Pullman; tenth author: University of Maine Cooperative Extension, 57 Houlton Road, Presque Isle 04769; eleventh author: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Long Island Horticultural Research & Extension Center, Riverhead, NY 11901-1098; thirteenth author: Department of Plant Pathology, Room 2419 Gardner Hall, NC State University, Raleigh 27695; fourteenth author: Department of Plant Pathology, University of Florida, Southwest Florida Research and Education Center, 2685 SR 29 N, Immokalee 34142-9515; fifteenth author: Department of Plant Pathology, North Dakota State University, 328 Walster Hall, Dept. 7660, PO Box6050, Fargo 58108-6050; and sixteenth author: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Barton Lab, NYSAES, 630 West North Street, Geneva, NY 14456
| | - C D Smart
- First, fifth, and twelfth authors: Cornell University, Section of Plant Pathology and Plant-Microbe Biology, 334 Plant Science Bldg., Ithaca, NY 14850; second author: Division of Plant Sciences, University of Dundee at James Hutton Institute, Invergowrie, Dundee, DD2 4DA, UK; third author: Department of Plant Pathology and Microbiology, University of California, Riverside 92521; fourth author: Horticultural Crops Research Laboratory, United States Department of Agriculture-Agricultural Research Service, 3420 NW Orchard Ave., Corvallis, OR 97330; sixth author: Plant Pathology Department, University of Maryland, 27664 Nanticoke Rd., Salisbury 21801; seventh author: University of Wisconsin Department of Plant Pathology, 1630 Linden Dr., Madison 53706-1598; eighth author: Department of Plant Pathology and Environmental Microbiology, College of Agricultural Sciences, The Pennsylvania State University, 219 Buckhout Lab, University Park 16802; ninth author: Department of Plant Pathology, Washington State University, PO Box 646430, Pullman; tenth author: University of Maine Cooperative Extension, 57 Houlton Road, Presque Isle 04769; eleventh author: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Long Island Horticultural Research & Extension Center, Riverhead, NY 11901-1098; thirteenth author: Department of Plant Pathology, Room 2419 Gardner Hall, NC State University, Raleigh 27695; fourteenth author: Department of Plant Pathology, University of Florida, Southwest Florida Research and Education Center, 2685 SR 29 N, Immokalee 34142-9515; fifteenth author: Department of Plant Pathology, North Dakota State University, 328 Walster Hall, Dept. 7660, PO Box6050, Fargo 58108-6050; and sixteenth author: Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Barton Lab, NYSAES, 630 West North Street, Geneva, NY 14456
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Jones LA, Saha S, Collmer A, Smart CD, Lindeberg M. Genome-Assisted Development of a Diagnostic Protocol for Distinguishing High Virulence Pseudomonas syringae pv. tomato Strains. Plant Dis 2015; 99:527-534. [PMID: 30699553 DOI: 10.1094/pdis-08-14-0833-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A severe outbreak of bacterial speck of tomato, caused by Pseudomonas syringae pv. tomato, occurred in central New York in 2009. Isolate 09150, collected from this outbreak and subsequently named NYS-T1, was found to be highly virulent on tomato. To better understand the relationship of 09150 to other P. syringae strains and develop a diagnostic assay for aggressive strains of this pathogen, the 09150 genome was sequenced. Genome comparison revealed it to be highly similar to a previously sequenced isolate, T1. Genetic factors linked to host interaction including type III effectors, toxin biosynthetic genes, and elicitors of host innate immunity were identified. Type III effector repertoires were compared with other strains in the high virulence T1-like subgroup and lower virulence DC3000/P. syringae pv. maculicola subgroup within P. syringae phylogenetic Group I. Primers for conventional PCR were developed using sequences for avrA, hopW, conserved in the former subgroup and hopN, present in the latter. These were tested on isolates in the two subgroups, other pseudomonads, and other bacterial pathogens of tomato. Primers developed for avaA and hopW were diagnostic for more virulent strains of P. syringae pv. tomato while primers for hopN were diagnostic for P. syringae pv. tomato DC3000 and related P. syringe pv. maculicola strains. Primers designed against hopR distinguished both of these P. syringae subgroups from other P. syringae strains.
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Affiliation(s)
- Lisa A Jones
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456
| | - Surya Saha
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14850; and Boyce Thompson Institute for Plant Research, Ithaca, NY 14853
| | - Alan Collmer
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14850
| | - Christine D Smart
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456
| | - Magdalen Lindeberg
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14850
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Tancos MA, Lange HW, Smart CD. Characterizing the Genetic Diversity of the Clavibacter michiganensis subsp. michiganensis Population in New York. Phytopathology 2015; 105:169-179. [PMID: 25208240 DOI: 10.1094/phyto-06-14-0178-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
New York Clavibacter michiganensis subsp. michiganensis isolates, collected from disparate bacterial canker of tomato outbreaks over the past 11 years, were characterized with a multilocus sequence analysis (MLSA) scheme that differentiated the 51 isolates into 21 haplotypes with a discriminatory power of 0.944. The MLSA scheme consisted of five housekeeping genes (kdpA, sdhA, dnaA, ligA, and gyrB) and three putative pathogenicity genes (celA, tomA, and nagA). Repetitive polymerase chain reaction (PCR), with the BOX-A1R primer, confirmed the high diversity of C. michiganensis subsp. michiganensis isolates in New York by demonstrating that all six PCR patterns (A, B, 13C, 65C, 81C, and D) were present, with PCR patterns C and A being the most common. The MLSA scheme provided higher resolving power than the current repetitive-PCR approach. The plasmid profiles of New York isolates were diverse and differed from reference strain NCPPB382. PCR analysis indicated that the presence of putative pathogenicity genes varied between isolates and highlighted the ephemeral nature of pathogenicity genes in field populations of C. michiganensis subsp. michiganensis. Analysis of molecular variance between Serbian and New York C. michiganensis subsp. michiganensis isolates demonstrated that the two populations were not significantly different, with 98% genetic variation within each population and only 2% genetic variation between populations.
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Danies G, Myers K, Mideros MF, Restrepo S, Martin FN, Cooke DEL, Smart CD, Ristaino JB, Seaman AJ, Gugino BK, Grünwald NJ, Fry WE. An ephemeral sexual population of Phytophthora infestans in the Northeastern United States and Canada. PLoS One 2014; 9:e116354. [PMID: 25551215 PMCID: PMC4281225 DOI: 10.1371/journal.pone.0116354] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 12/08/2014] [Indexed: 12/02/2022] Open
Abstract
Phytophthora infestans, the causal agent of late blight disease, has been reported in North America since the mid-nineteenth century. In the United States the lack of or very limited sexual reproduction has resulted in largely clonal populations of P. infestans. In 2010 and 2011, but not in 2012 or 2013, 20 rare and diverse genotypes of P. infestans were detected in a region that centered around central New York State. The ratio of A1 to A2 mating types among these genotypes was close to the 50∶50 ratio expected for sexual recombination. These genotypes were diverse at the glucose-6-phosphate isomerase locus, differed in their microsatellite profiles, showed different banding patterns in a restriction fragment length polymorphism assay using a moderately repetitive and highly polymorphic probe (RG57), were polymorphic for four different nuclear genes and differed in their sensitivity to the systemic fungicide mefenoxam. The null hypothesis of linkage equilibrium was not rejected, which suggests the population could be sexual. These new genotypes were monomorphic in their mitochondrial haplotype that was the same as US-22. Through parentage exclusion testing using microsatellite data and sequences of four nuclear genes, recent dominant lineages US-8, US-11, US-23, and US-24 were excluded as possible parents for these genotypes. Further analyses indicated that US-22 could not be eliminated as a possible parent for 14 of the 20 genotypes. We conclude that US-22 could be a parent of some, but not all, of the new genotypes found in 2010 and 2011. There were at least two other parents for this population and the genotypic characteristics of the other parents were identified.
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Affiliation(s)
- Giovanna Danies
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, New York, United States of America
| | - Kevin Myers
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, New York, United States of America
| | - María F. Mideros
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Silvia Restrepo
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Frank N. Martin
- United States Department of Agriculture – Agriculture Research Services (USDA-ARS), Salinas, California, United States of America
| | | | - Christine D. Smart
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, New York, United States of America
| | - Jean B. Ristaino
- Department of Plant Pathology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Abby J. Seaman
- New York State Integrated Pest Management Program, Cornell Cooperative Extension, Geneva, New York, United States of America
| | - Beth K. Gugino
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Niklaus J. Grünwald
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, Oregon, United States of America
- Department of Botany & Pant pathology and Center for Genome Biology and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - William E. Fry
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, New York, United States of America
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Hansen ZR, Small IM, Mutschler M, Fry WE, Smart CD. Differential Susceptibility of 39 Tomato Varieties to Phytophthora infestans Clonal Lineage US-23. Plant Dis 2014; 98:1666-1670. [PMID: 30703875 DOI: 10.1094/pdis-03-14-0263-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
During the summers of 2012 and 2013, 39 tomato (Solanum lycopersicum) lines or varieties were evaluated for resistance to late blight in three separate field trials. In each trial, late blight was caused by field isolates of Phytophthora infestans clonal lineage US-23. Varieties with the late blight resistance genes Ph-1, Ph-2, Ph-3, and Ph-2 + Ph-3 were included, along with several heirloom varieties with grower-reported resistance and varieties with no known resistance. All six varieties with Ph-2 + Ph-3, along with NC25P, which is homozygous for Ph-3 only, showed a high level of resistance. Plum Regal F1, which is heterozygous for Ph-3 only, showed moderate resistance. Legend, the only variety with Ph-2 alone, also showed moderate resistance. Three heirloom varieties, Matt's Wild Cherry, Lemon Drop, and Mr. Stripey, showed a high level of resistance comparable with that of varieties with Ph-2 + Ph-3. New Yorker, possessing Ph-1 only, showed no resistance. Indeterminate varieties had significantly less disease than determinate varieties in two of the three trials. Overall, this study suggests that tomato varieties with both Ph-2 and Ph-3 can be used to effectively manage late blight caused by P. infestans clonal lineage US-23. Varieties possessing only Ph-2, or heterozygous for Ph-3, were better protected than those without any late blight resistance but might still require supplemental fungicide applications, while the variety that was homozygous for Ph-3 was highly resistant. Several heirloom varieties were also highly resistant, and the unknown mechanism of their resistance warrants further research. Finally, the plasticity observed in United States P. infestans populations over the past several decades necessitates continued monitoring for genetic changes within P. infestans that could lead to the breakdown of resistance reported here.
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Affiliation(s)
- Z R Hansen
- Department of Plant Pathology and Plant-Microbe Biology
| | - I M Small
- Department of Plant Pathology and Plant-Microbe Biology
| | | | - W E Fry
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853
| | - C D Smart
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853
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Dunn AR, Bruening SR, Grünwald NJ, Smart CD. Evolution of an Experimental Population of Phytophthora capsici in the Field. Phytopathology 2014; 104:1107-1117. [PMID: 24702666 DOI: 10.1094/phyto-12-13-0346-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Populations of the vegetable pathogen Phytophthora capsici are often highly diverse, with limited gene flow between fields. To investigate the structure of a newly established, experimental population, an uninfested research field was inoculated with two single-zoospore isolates of P. capsici in September 2008. From 2009 through 2012, ≈50 isolates of P. capsici were collected from the field each year and genotyped using five microsatellite loci. The same two isolates were also crossed in the lab. High levels of diversity were detected in the research field, with 26 to 37 unique multilocus genotypes detected each year. Through 2012, genotypic diversity did not decline and no evidence of genetic drift was observed. However, during the 2011 and 2012 growing seasons, four new alleles not present in either parental isolate were observed in the field. Selfing (but not apomixis) was observed at low frequency among in vitro progeny. In addition, evidence for loss of heterozygosity was observed in half of the in vitro progeny. These results suggest that recombination, mutation, and loss of heterozygosity can affect the genetic structure observed in P. capsici populations.
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Jones LA, Worobo RW, Smart CD. Plant-pathogenic oomycetes, Escherichia coli strains, and Salmonella spp. Frequently found in surface water used for irrigation of fruit and vegetable crops in New York State. Appl Environ Microbiol 2014; 80:4814-20. [PMID: 24878603 PMCID: PMC4135776 DOI: 10.1128/aem.01012-14] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 05/27/2014] [Indexed: 11/20/2022] Open
Abstract
In the United States, surface water is commonly used to irrigate a variety of produce crops and can harbor pathogens responsible for food-borne illnesses and plant diseases. Understanding when pathogens infest water sources is valuable information for produce growers to improve the food safety and production of these crops. In this study, prevalence data along with regression tree analyses were used to correlate water quality parameters (pH, temperature, turbidity), irrigation site properties (source, the presence of livestock or fowl nearby), and precipitation data to the presence and concentrations of Escherichia coli, Salmonella spp., and hymexazol-insensitive (HIS) oomycetes (Phytophthora and Pythium spp.) in New York State surface waters. A total of 123 samples from 18 sites across New York State were tested for E. coli and Salmonella spp., of which 33% and 43% were positive, respectively. Additionally, 210 samples from 38 sites were tested for HIS oomycetes, and 88% were found to be positive, with 10 species of Phytophthora and 11 species of Pythium being identified from the samples. Regression analysis found no strong correlations between water quality parameters, site factors, or precipitation to the presence or concentration of E. coli in irrigation sources. For Salmonella, precipitation (≤ 0.64 cm) 3 days before sampling was correlated to both presence and the highest counts. Analyses for oomycetes found creeks to have higher average counts than ponds, and higher turbidity levels were associated with higher oomycete counts. Overall, information gathered from this study can be used to better understand the food safety and plant pathogen risks of using surface water for irrigation.
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Affiliation(s)
- Lisa A Jones
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, New York, USA
| | - Randy W Worobo
- Department of Food Science, Cornell University, Geneva, New York, USA
| | - Christine D Smart
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, New York, USA
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Tancos MA, Chalupowicz L, Barash I, Manulis-Sasson S, Smart CD. Tomato fruit and seed colonization by Clavibacter michiganensis subsp. michiganensis through external and internal routes. Appl Environ Microbiol 2013; 79:6948-57. [PMID: 24014525 PMCID: PMC3811524 DOI: 10.1128/aem.02495-13] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 08/28/2013] [Indexed: 11/20/2022] Open
Abstract
The Gram-positive bacterium Clavibacter michiganensis subsp. michiganensis, causal agent of bacterial wilt and canker of tomato, is an economically devastating pathogen that inflicts considerable damage throughout all major tomato-producing regions. Annual outbreaks continue to occur in New York, where C. michiganensis subsp. michiganensis spreads via infected transplants, trellising stakes, tools, and/or soil. Globally, new outbreaks can be accompanied by the introduction of contaminated seed stock; however, the route of seed infection, especially the role of fruit lesions, remains undefined. In order to investigate the modes of seed infection, New York C. michiganensis subsp. michiganensis field strains were stably transformed with a gene encoding enhanced green fluorescent protein (eGFP). A constitutively eGFP-expressing virulent C. michiganensis subsp. michiganensis isolate, GCMM-22, was used to demonstrate that C. michiganensis subsp. michiganensis could not only access seeds systemically through the xylem but also externally through tomato fruit lesions, which harbored high intra- and intercellular populations. Active movement and expansion of bacteria into the fruit mesocarp and nearby xylem vessels followed, once the fruits began to ripen. These results highlight the ability of C. michiganensis subsp. michiganensis to invade tomato fruits and seeds through multiple entry routes.
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Affiliation(s)
- Matthew A. Tancos
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, New York, USA
| | - Laura Chalupowicz
- Department of Plant Pathology and Weed Research, ARO, The Volcani Center, Bet Dagan, Israel
| | - Isaac Barash
- Department of Molecular Biology and Ecology of Plants, Tel-Aviv University, Tel-Aviv, Israel
| | | | - Christine D. Smart
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, New York, USA
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Fry WE, McGrath MT, Seaman A, Zitter TA, McLeod A, Danies G, Small IM, Myers K, Everts K, Gevens AJ, Gugino BK, Johnson SB, Judelson H, Ristaino J, Roberts P, Secor G, Seebold K, Snover-Clift K, Wyenandt A, Grünwald NJ, Smart CD. The 2009 Late Blight Pandemic in the Eastern United States - Causes and Results. Plant Dis 2013; 97:296-306. [PMID: 30722376 DOI: 10.1094/pdis-08-12-0791-fe] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The tomato late blight pandemic of 2009 made late blight into a household term in much of the eastern United States. Many home gardeners and many organic producers lost most if not all of their tomato crop, and their experiences were reported in the mainstream press. Some CSAs (Community Supported Agriculture) could not provide tomatoes to their members. In response, many questions emerged: How did it happen? What was unusual about this event compared to previous late blight epidemics? What is the current situation in 2012 and what can be done? It's easiest to answer these questions, and to understand the recent epidemics of late blight, if one knows a bit of the history of the disease and the biology of the causal agent, Phytophthora infestans.
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Affiliation(s)
- W E Fry
- Cornell University, Ithaca, NY
| | | | | | | | - A McLeod
- University of Stellenbosch, Stellenbosch, South Africa
| | | | | | - K Myers
- Cornell University, Ithaca, NY
| | - K Everts
- University of Maryland, Salisbury
| | | | - B K Gugino
- The Pennsylvania State University, University Park
| | - S B Johnson
- University of Maine Cooperative Extension, Presque Isle
| | | | - J Ristaino
- North Carolina State University, Raleigh
| | | | - G Secor
- North Dakota State University, Fargo
| | | | | | - A Wyenandt
- Rutgers Agricultural Research and Extension Center, Bridgeton, NJ
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Abstract
A DNA macroarray was previously developed to detect major fungal and oomycete pathogens of solanaceous crops. To provide a convenient alternative for researchers with no access to X-ray film-developing facilities, specific CCD cameras or Chemidoc XRS systems, a chromogenic detection method with sensitivity comparable with chemiluminescent detection, has been developed. A fungal (Stemphylium solani) and an oomycete (Phytophthora capsici) pathogen were used to develop the protocol using digoxigenin (DIG)-labeled targets. The internal transcribed spacer (ITS) region of the nuclear ribosomal DNA (rDNA), including ITS1, 5.8S rDNA, and ITS2, was used as the target gene and polymerase chain reaction amplified as in the previous protocol. Various amounts of species-specific oligonucleotides on the array, quantities of DIG-labeled ITS amplicon, and hybridization temperatures were tested. The optimal conditions for hybridization were 55°C for 2 h using at least 10 pmol of each species-specific oligonucleotide and labeled target at 10 ng/ml of hybridization buffer. Incubation of the hybridized array with anti-DIG conjugated alkaline phosphatase substrates, NBT/BCIP, produced visible target signals between 1 and 3 h compared with 1 h in chemiluminescent detection. Samples from pure cultures, soil, and artificially inoculated plants were also used to compare the detection using chemiluminescent and chromogenic methods. Chromogenic detection was shown to yield similar results compared with chemiluminescent detection in regard to signal specificity, duration of hybridization between the array and targets, and cost, though it takes 1 to 2 h longer for the visualization process, thus providing a convenient alternative for researchers who lack darkroom facilities. To our knowledge, this is the first report of DNA macroarray detection of plant pathogens using a chromogenic method.
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Affiliation(s)
- Mui-Yun Wong
- Department of Plant Protection, Faculty of Agriculture, and Institute of Tropical Agriculture, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Christine D Smart
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456
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Balaji V, Smart CD. Over-expression of snakin-2 and extensin-like protein genes restricts pathogen invasiveness and enhances tolerance to Clavibacter michiganensis subsp. michiganensis in transgenic tomato (Solanum lycopersicum). Transgenic Res 2011; 21:23-37. [DOI: 10.1007/s11248-011-9506-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Accepted: 03/18/2011] [Indexed: 11/27/2022]
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Abstract
A DNA-based macroarray was designed to quickly and accurately identify certain Amanita mushroom specimens at the species level. The macroarray included probes for Amanita phalloides and Amanita ocreata, toxic species responsible for most mushroom poisonings, and Amanita lanei and Amanita velosa, edible species sometimes confused with toxic species, based on sequences of the highly variable internal transcribed spacer (ITS) region of rDNA. A cryptic species related to A. ocreata and one related to A. lanei, identifiable by ITS sequences, were also included. Specific multiple oligonucleotide probes were spotted onto nylon membranes and the optimal hybridization temperatures were determined. The Amanita DNA array was highly specific, sensitive (0.5 ng DNA/μL and higher were detected), and reproducible. In two case studies, the method proved useful when only small amounts of mushroom tissue remained after a suspected poisoning. An identification could be completed in 12 h.
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Affiliation(s)
- Kathryn A Harper
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
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Balaji V, Sessa G, Smart CD. Silencing of host basal defense response-related gene expression increases susceptibility of Nicotiana benthamiana to Clavibacter michiganensis subsp. michiganensis. Phytopathology 2011; 101:349-57. [PMID: 21062112 DOI: 10.1094/phyto-05-10-0132] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Clavibacter michiganensis subsp. michiganensis is an actinomycete, causing bacterial wilt and canker disease of tomato (Solanum lycopersicum). We used virus-induced gene silencing (VIGS) to identify genes playing a role in host basal defense response to C. michiganensis subsp. michiganensis infection using Nicotiana benthamiana as a model plant. A preliminary VIGS screen comprising 160 genes from tomato known to be involved in defense-related signaling identified a set of 14 genes whose suppression led to altered host-pathogen interactions. Expression of each of these genes and three additional targets was then suppressed in larger-scale VIGS experiments and the effect of silencing on development of wilt disease symptoms and bacterial growth during an N. benthamiana-C. michiganensis subsp. michiganensis compatible interaction was determined. Disease susceptibility and in planta bacterial population size were enhanced by silencing genes encoding N. benthamiana homologs of ubiquitin activating enzyme, snakin-2, extensin-like protein, divinyl ether synthase, 3-hydroxy-3-methylglutaryl-coenzyme A reductase 2, and Pto-like kinase. The identification of genes having a role in the host basal defense-response to C. michiganensis subsp. michiganensis advances our understanding of the plant responses activated by C. michiganensis subsp. michiganensis and raises possibilities for devising novel and effective molecular strategies to control bacterial canker and wilt in tomato.
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Affiliation(s)
- Vasudevan Balaji
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, NY, USA
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Dunn AR, Milgroom MG, Meitz JC, McLeod A, Fry WE, McGrath MT, Dillard HR, Smart CD. Population Structure and Resistance to Mefenoxam of Phytophthora capsici in New York State. Plant Dis 2010; 94:1461-1468. [PMID: 30743368 DOI: 10.1094/pdis-03-10-0221] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In 2006, 2007, and 2008, we sampled 257 isolates of Phytophthora capsici from vegetables at 22 sites in four regions of New York, to determine variation in mefenoxam resistance and population genetic structure. Isolates were assayed for mefenoxam resistance and genotyped for mating type and five microsatellite loci. We found mefenoxam-resistant isolates at a high frequency in the Capital District and Long Island, but none were found in western New York or central New York. Both A1 and A2 mating types were found at 12 of the 22 sites, and we detected 126 distinct multilocus genotypes, only nine of which were found at more than one site. Significant differentiation (FST) was found in more than 98% of the pairwise comparisons between sites; approximately 24 and 16% of the variation in the population was attributed to differences among regions and sites, respectively. These results indicate that P. capsici in New York is highly diverse, but gene flow among regions and fields is restricted. Therefore, each field needs to be considered an independent population, and efforts to prevent movement of inoculum among fields need to be further emphasized to prevent the spread of this pathogen.
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Affiliation(s)
- A R Dunn
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456
| | - M G Milgroom
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853
| | - J C Meitz
- Department of Plant Pathology, University of Stellenbosch, Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | - A McLeod
- Department of Plant Pathology, University of Stellenbosch, Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | - W E Fry
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853
| | - M T McGrath
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Riverhead, NY 11901
| | - H R Dillard
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456
| | - C D Smart
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456
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