1
|
Grünwald NJ, Bock CH, Chang JH, De Souza AA, Ponte EMD, du Toit LJ, Dorrance AE, Dung J, Gent D, Goss EM, Lowe-Power TM, Madden LV, Martin FN, McDowell J, Naegele RP, Potnis N, Quesada-Ocampo LM, Sundin GW, Thiessen L, Vinatzer BA, Zeng Q. Open Access and Reproducibility in Plant Pathology Research: Guidelines and Best Practices. Phytopathology 2024:PHYTO12230483IA. [PMID: 38330057 DOI: 10.1094/phyto-12-23-0483-ia] [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: 02/10/2024]
Abstract
The landscape of scientific publishing is experiencing a transformative shift toward open access, a paradigm that mandates the availability of research outputs such as data, code, materials, and publications. Open access provides increased reproducibility and allows for reuse of these resources. This article provides guidance for best publishing practices of scientific research, data, and associated resources, including code, in The American Phytopathological Society journals. Key areas such as diagnostic assays, experimental design, data sharing, and code deposition are explored in detail. This guidance aligns with that observed by other leading journals. We hope the information assembled in this paper will raise awareness of best practices and enable greater appraisal of the true effects of biological phenomena in plant pathology.
Collapse
Affiliation(s)
- Niklaus J Grünwald
- U.S. Department of Agriculture-Agricultural Research Service, Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR 97331, U.S.A
| | - Clive H Bock
- U.S. Department of Agriculture-Agricultural Research Service, Southeastern Fruit and Tree Nut Research Station, Byron, GA 31008, U.S.A
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, U.S.A
| | | | - Emerson M Del Ponte
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Lindsey J du Toit
- Department of Plant Pathology, Washington State University, Mount Vernon, WA 98273, U.S.A
| | - Anne E Dorrance
- Department of Plant Pathology, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, U.S.A
| | - Jeremiah Dung
- Department of Botany and Plant Pathology, Central Oregon Agricultural Research and Extension Center, Oregon State University, Madras, OR 97741, U.S.A
| | - David Gent
- U.S. Department of Agriculture-Agricultural Research Service, Forage Seed and Cereal Research Unit, Corvallis, OR 97331, U.S.A
| | - Erica M Goss
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, U.S.A
| | - Tiffany M Lowe-Power
- Department of Plant Pathology, University of California Davis, Davis, CA 95616, U.S.A
| | - Laurence V Madden
- Department of Plant Pathology, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, U.S.A
| | - Frank N Martin
- U.S. Department of Agriculture-Agricultural Research Service, Crop Protection and Improvement Research Center, Salinas, CA 93905, U.S.A
| | - John McDowell
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, U.S.A
| | - Rachel P Naegele
- U.S. Department of Agriculture-Agricultural Research Service, Sugarbeet and Bean Research Unit, East Lansing, MI 48824, U.S.A
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, U.S.A
| | - Lina M Quesada-Ocampo
- Department of Entomology and Plant Pathology and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC 27606, U.S.A
| | - George W Sundin
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Lindsey Thiessen
- Domestic and Emergency Scientific Support, U.S. Department of Agriculture-Animal & Plant Health Inspection Service-Plant Protection and Quarantine, Raleigh, NC 27606, U.S.A
| | - Boris A Vinatzer
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, U.S.A
| | - Quan Zeng
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT 06511, U.S.A
| |
Collapse
|
2
|
Dorrance AE, Vargas A, Navarro-Acevedo K, Wijeratne S, Myers J, Paredes JAA. Picarbutrazox effectiveness added to a seed treatment mixture for management of Oomycetes that impact soybean in Ohio. Plant Dis 2024. [PMID: 38190367 DOI: 10.1094/pdis-06-23-1223-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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
None of the current oomycota fungicides are effective towards all species of Phytophthora, Phytopythium, Globisporangium, and Pythium that affect soybean seed and seedlings in Ohio. Picarbutrazox is a new oomyceticide with a novel mode of action towards Oomycete pathogens. Our objectives were to evaluate picarbutrazox to determine i) baseline sensitivity (EC50) to 189 isolates of 29 species, ii) the efficacy with a base seed treatment with three cultivars with different levels of resistance in 14 field environments; and iii) if the rhizosphere microbiome was affected by the addition of the seed treatment on a moderately susceptible cultivar. The mycelial growth of all isolates was inhibited beginning at 0.001µg and the EC50 ranged from 0.0013 to 0.0483 µg a.i. ml-1. The effect of seed treatment was significantly different for plant population and yield in 8 of 14 and 6 of 12 environments, respectively. The addition of picarbutrazox at 1 and 2.5 g a.i. 100 kg seed-1 to the base seed treatment compared to the base alone was associated with higher plant populations and yield in 3 and 1 environment, respectively. There was limited impact of the seed treatment mefenoxam 7.5 g a.i. plus picarbutrazox 1 g a.i. per 100 kg seed-1 on the oomycetes detected in the rhizosphere of soybean seedlings collected at the V1 growth stage. Picarbutrazox has efficacy towards a wider range of oomycetes that cause disease on soybean and this will be another oomyceticide tool to combat early season damping-off in areas where environmental conditions highly favor disease development.
Collapse
Affiliation(s)
- Anne E Dorrance
- The Ohio State University, Plant Pathology, OARDC, 1680 Madison Ave., Wooster, Ohio, United States, 44691
- United States;
| | - Amilcar Vargas
- The Ohio State University, Plant Pathology, Wooster, Ohio, United States;
| | | | - Saranga Wijeratne
- Ohio State University College of Food Agricultural and Environmental Sciences, 155699, formerly with Molecular Cellular Imaging Center, Wooster, Ohio, United States;
| | - Jonell Myers
- Ohio State University College of Food Agricultural and Environmental Sciences, 155699, Dept. of Plant Pathology, Wooster, Ohio, United States;
| | - Juan Andres Andrés Paredes
- Instituto Nacional de Tecnología Agropecuaria IPAVE, Instituto de Patología Vegetal, Av. 11 de Septiempre 4755, Cordoba, Cordoba, Argentina, 5020;
| |
Collapse
|
3
|
Million CR, Wijeratne S, Karhoff S, Cassone BJ, McHale LK, Dorrance AE. Molecular mechanisms underpinning quantitative resistance to Phytophthora sojae in Glycine max using a systems genomics approach. Front Plant Sci 2023; 14:1277585. [PMID: 38023885 PMCID: PMC10662313 DOI: 10.3389/fpls.2023.1277585] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023]
Abstract
Expression of quantitative disease resistance in many host-pathogen systems is controlled by genes at multiple loci, each contributing a small effect to the overall response. We used a systems genomics approach to study the molecular underpinnings of quantitative disease resistance in the soybean-Phytophthora sojae pathosystem, incorporating expression quantitative trait loci (eQTL) mapping and gene co-expression network analysis to identify the genes putatively regulating transcriptional changes in response to inoculation. These findings were compared to previously mapped phenotypic (phQTL) to identify the molecular mechanisms contributing to the expression of this resistance. A subset of 93 recombinant inbred lines (RILs) from a Conrad × Sloan population were inoculated with P. sojae isolate 1.S.1.1 using the tray-test method; RNA was extracted, sequenced, and the normalized read counts were genetically mapped from tissue collected at the inoculation site 24 h after inoculation from both mock and inoculated samples. In total, more than 100,000 eQTLs were mapped. There was a switch from predominantly cis-eQTLs in the mock treatment to an almost entirely nonoverlapping set of predominantly trans-eQTLs in the inoculated treatment, where greater than 100-fold more eQTLs were mapped relative to mock, indicating vast transcriptional reprogramming due to P. sojae infection occurred. The eQTLs were organized into 36 hotspots, with the four largest hotspots from the inoculated treatment corresponding to more than 70% of the eQTLs, each enriched for genes within plant-pathogen interaction pathways. Genetic regulation of trans-eQTLs in response to the pathogen was predicted to occur through transcription factors and signaling molecules involved in plant-pathogen interactions, plant hormone signal transduction, and MAPK pathways. Network analysis identified three co-expression modules that were correlated with susceptibility to P. sojae and associated with three eQTL hotspots. Among the eQTLs co-localized with phQTLs, two cis-eQTLs with putative functions in the regulation of root architecture or jasmonic acid, as well as the putative master regulators of an eQTL hotspot nearby a phQTL, represent candidates potentially underpinning the molecular control of these phQTLs for resistance.
Collapse
Affiliation(s)
- Cassidy R. Million
- Department of Plant Pathology, The Ohio State University, Wooster, OH, United States
- Center for Soybean Research and Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, United States
| | - Saranga Wijeratne
- Molecular and Cellular Imaging Center, The Ohio State University, Wooster, OH, United States
| | - Stephanie Karhoff
- Center for Soybean Research and Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, United States
- Translational Plant Sciences Graduate Program, The Ohio State University, Columbus, OH, United States
| | - Bryan J. Cassone
- Center for Soybean Research and Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, United States
- Department of Biology, Brandon University, Brandon, Manitoba, MB, Canada
| | - Leah K. McHale
- Center for Soybean Research and Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, United States
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, United States
| | - Anne E. Dorrance
- Department of Plant Pathology, The Ohio State University, Wooster, OH, United States
- Center for Soybean Research and Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, United States
| |
Collapse
|
4
|
Lopez-Nicora HD, Ralston TI, Diers BW, Dorrance AE, Niblack TL. Interactions Among Heterodera glycines, Macrophomina phaseolina, and Soybean Genotype. Plant Dis 2023; 107:401-412. [PMID: 35787008 DOI: 10.1094/pdis-06-21-1169-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: 06/15/2023]
Abstract
Heterodera glycines, the soybean cyst nematode (SCN), and fungal pathogen Macrophomina phaseolina are economically important soybean pathogens that may coinfest fields. Resistance remains the most effective management tactic for SCN, and the rhg1-b resistance allele derived from plant introduction 88788 is most commonly deployed in the northern United States. The concomitant effects of SCN and M. phaseolina on soybean performance, as well as the effect of the rhg1-b allele in two different genetic backgrounds, were evaluated in three environments (during 2013 to 2015) and a greenhouse bioassay. Within two soybean populations, half of the lines had the rhg1-b allele, and the other half had the susceptible allele in the backgrounds of the cultivars IA3023 and LD00-3309. Significant interactions between soybean rhg1-b allele and M. phaseolina-infested plots were observed in 2014. In all experiments, initial SCN populations (Pi) and M. phaseolina in roots were associated with reduced soybean yield. SCN reproduction factor (RF = final population/Pi) was affected by SCN Pi, rhg1-b, and genetic background. A background-by-genotype interaction on yield was observed only in 2015, with a stronger rhg1-b effect in the LD00-3309 background, which suggested that the susceptible parent 'IA3023' is tolerant to SCN. SCN female index from greenhouse experiments was compared with field RF, and Lin's concordance and Pearson's correlation coefficients decreased with increasing field SCN Pi in soil. In this study, both SCN and M. phaseolina reduced soybean yield asymptomatically, and the impact of SCN rhg1-b resistance was dependent on SCN virulence but also population density.
Collapse
Affiliation(s)
- Horacio D Lopez-Nicora
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, U.S.A
- La Clínica Vegetal, Universidad San Carlos, Asunción 1884, Paraguay
| | - Timothy I Ralston
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Brian W Diers
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, U.S.A
| | - Anne E Dorrance
- Department of Plant Pathology, The Ohio State University, Wooster, OH 44691, U.S.A
| | - Terry L Niblack
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, U.S.A
| |
Collapse
|
5
|
Vargas A, Paul PA, Winger J, Balk CS, Eyre M, Clevinger B, Noggle S, Dorrance AE. Oxathiapiprolin Alone or Mixed with Metalaxyl Seed Treatment for Management of Soybean Seedling Diseases Caused by Species of Phytophthora, Phytopythium, and Pythium. Plant Dis 2022; 106:2127-2137. [PMID: 35133185 DOI: 10.1094/pdis-09-21-1952-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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
Species of Phytophthora, Phytopythium, and Pythium affect soybean seed and seedlings each year, primarily through reduced plant populations and yield. Oxathiapiprolin is effective at managing several foliar diseases caused by some oomycetes. The objectives of these studies were to evaluate oxathiapiprolin in a discriminatory dose assay in vitro; evaluate oxathiapiprolin as a soybean seed treatment on a moderately susceptible cultivar in 10 environments; compare the impact of seed treatment on plant populations and yields in environments with low and high precipitation; and compare a seed treatment mixture on cultivars with different levels of resistance in four environments. There was no reduction in growth in vitro among 13 species of Pythium at 0.1 µg ml-1. Soybean seed treated with the base fungicide plus oxathiapiprolin (12 and 24 µg a.i. seed-1) alone, oxathiapiprolin (12 µg a.i. seed-1) plus mefenoxam (6 µg a.i. seed-1), or oxathiapiprolin (24 µg a.i. seed-1) plus ethaboxam (12.1 µg a.i. seed-1) had greater yields in environments that received ≥50 mm of precipitation within 14 days after planting compared with those that received less. Early plant population and yield were significantly higher for seed treated with oxathiapiprolin (24 µg a.i. seed-1) + metalaxyl (13.2 µg a.i. seed-1) compared with nontreated for six of seven cultivars in at least one of four environments. Oxathiapiprolin combined with another Oomycota fungicide applied to seed has the potential to be used to protect soybean plant establishment and yield in regions prone to poor drainage after high levels of precipitation.
Collapse
Affiliation(s)
- Amilcar Vargas
- Former Graduate Research Associates, Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691
| | - Pierce A Paul
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691
| | - Jonell Winger
- Former Graduate Research Associates, Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691
| | - Christine Susan Balk
- Former Graduate Research Associates, Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691
| | - Meredith Eyre
- Former Graduate Research Associates, Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691
| | - Bruce Clevinger
- Department of Extension, The Ohio State University, Columbus, OH 43210
| | - Sarah Noggle
- Department of Extension, The Ohio State University, Columbus, OH 43210
| | - Anne E Dorrance
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691
| |
Collapse
|
6
|
Karhoff S, Vargas-Garcia C, Lee S, Mian MAR, Graham MA, Dorrance AE, McHale LK. Identification of Candidate Genes for a Major Quantitative Disease Resistance Locus From Soybean PI 427105B for Resistance to Phytophthora sojae. Front Plant Sci 2022; 13:893652. [PMID: 35774827 PMCID: PMC9237613 DOI: 10.3389/fpls.2022.893652] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/02/2022] [Indexed: 06/15/2023]
Abstract
Phytophthora root and stem rot is a yield-limiting soybean disease caused by the soil-borne oomycete Phytophthora sojae. Although multiple quantitative disease resistance loci (QDRL) have been identified, most explain <10% of the phenotypic variation (PV). The major QDRL explaining up to 45% of the PV were previously identified on chromosome 18 and represent a valuable source of resistance for soybean breeding programs. Resistance alleles from plant introductions 427105B and 427106 significantly increase yield in disease-prone fields and result in no significant yield difference in fields with less to no disease pressure. In this study, high-resolution mapping reduced the QDRL interval to 3.1 cm, and RNA-seq analysis of near-isogenic lines (NILs) varying at QDRL-18 pinpointed a single gene of interest which was downregulated in inoculated NILs carrying the resistant allele compared to inoculated NILs with the susceptible allele. This gene of interest putatively encodes a serine-threonine kinase (STK) related to the AtCR4 family and may be acting as a susceptibility factor, based on the specific increase of jasmonic acid concentration in inoculated NILs. This work facilitates further functional analyses and marker-assisted breeding efforts by prioritizing candidate genes and narrowing the targeted region for introgression.
Collapse
Affiliation(s)
- Stephanie Karhoff
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, United States
- Center for Soybean Research, The Ohio State University, Columbus, OH, United States
| | - Christian Vargas-Garcia
- Center for Soybean Research, The Ohio State University, Columbus, OH, United States
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, United States
| | - Sungwoo Lee
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, United States
| | - M. A. Rouf Mian
- United States Department of Agriculture-Agricultural Research Service, Soybean Research Unit, Raleigh, NC, United States
| | - Michelle A. Graham
- Department of Agronomy, Iowa State University, Ames, IA, United States
- United States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Resources Unit, Ames, IA, United States
| | - Anne E. Dorrance
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, United States
- Center for Soybean Research, The Ohio State University, Columbus, OH, United States
- Department of Plant Pathology, The Ohio State University, Wooster, OH, United States
| | - Leah K. McHale
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, United States
- Center for Soybean Research, The Ohio State University, Columbus, OH, United States
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, United States
| |
Collapse
|
7
|
Gluck-Thaler E, Ralston T, Konkel Z, Ocampos CG, Ganeshan VD, Dorrance AE, Niblack TL, Wood CW, Slot JC, Lopez-Nicora HD, Vogan AA. Giant Starship Elements Mobilize Accessory Genes in Fungal Genomes. Mol Biol Evol 2022; 39:msac109. [PMID: 35588244 PMCID: PMC9156397 DOI: 10.1093/molbev/msac109] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Accessory genes are variably present among members of a species and are a reservoir of adaptive functions. In bacteria, differences in gene distributions among individuals largely result from mobile elements that acquire and disperse accessory genes as cargo. In contrast, the impact of cargo-carrying elements on eukaryotic evolution remains largely unknown. Here, we show that variation in genome content within multiple fungal species is facilitated by Starships, a newly discovered group of massive mobile elements that are 110 kb long on average, share conserved components, and carry diverse arrays of accessory genes. We identified hundreds of Starship-like regions across every major class of filamentous Ascomycetes, including 28 distinct Starships that range from 27 to 393 kb and last shared a common ancestor ca. 400 Ma. Using new long-read assemblies of the plant pathogen Macrophomina phaseolina, we characterize four additional Starships whose activities contribute to standing variation in genome structure and content. One of these elements, Voyager, inserts into 5S rDNA and contains a candidate virulence factor whose increasing copy number has contrasting associations with pathogenic and saprophytic growth, suggesting Voyager's activity underlies an ecological trade-off. We propose that Starships are eukaryotic analogs of bacterial integrative and conjugative elements based on parallels between their conserved components and may therefore represent the first dedicated agents of active gene transfer in eukaryotes. Our results suggest that Starships have shaped the content and structure of fungal genomes for millions of years and reveal a new concerted route for evolution throughout an entire eukaryotic phylum.
Collapse
Affiliation(s)
- Emile Gluck-Thaler
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
- Department of Plant Pathology, The Ohio State University, Columbus, OH, USA
| | - Timothy Ralston
- Department of Plant Pathology, The Ohio State University, Columbus, OH, USA
| | - Zachary Konkel
- Department of Plant Pathology, The Ohio State University, Columbus, OH, USA
| | | | - Veena Devi Ganeshan
- Arabidopsis Biological Resource Center, The Ohio State University, Columbus, OH, USA
| | - Anne E. Dorrance
- Department of Plant Pathology, The Ohio State University, Wooster, OH, USA
| | - Terry L. Niblack
- Department of Plant Pathology, The Ohio State University, Columbus, OH, USA
| | - Corlett W. Wood
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Jason C. Slot
- Department of Plant Pathology, The Ohio State University, Columbus, OH, USA
| | - Horacio D. Lopez-Nicora
- Department of Plant Pathology, The Ohio State University, Columbus, OH, USA
- Departamento de Producción Agrícola, Universidad San Carlos, Asunción, Paraguay
| | - Aaron A. Vogan
- Systematic Biology, Department of Organismal Biology, University of Uppsala, Uppsala, Sweden
| |
Collapse
|
8
|
Hebb LM, Bradley CA, Mideros SX, Telenko DEP, Wise K, Dorrance AE. Pathotype Complexity and Genetic Characterization of Phytophthora sojae Populations in Illinois, Indiana, Kentucky, and Ohio. Phytopathology 2022; 112:663-681. [PMID: 34289716 DOI: 10.1094/phyto-12-20-0561-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: 06/13/2023]
Abstract
Phytophthora sojae, the causal agent of Phytophthora root and stem rot of soybean, has been managed with single Rps genes since the 1960s but has subsequently adapted to many of these resistance genes, rendering them ineffective. The objective of this study was to examine the pathotype and genetic diversity of P. sojae from soil samples across Illinois, Indiana, Kentucky, and Ohio by assessing which Rps genes were still effective and identifying possible population clusters. There were 218 pathotypes identified from 473 P. sojae isolates with an average of 6.7 out of 15 differential soybean lines exhibiting a susceptible response for each isolate. Genetic characterization of 103 P. sojae isolates from across Illinois, Indiana, Kentucky, and Ohio with 19 simple sequence repeat markers identified 92 multilocus genotypes. There was a moderate level of population differentiation between these four states, with pairwise FST values ranging from 0.026 to 0.246. There were also moderate to high levels of differentiation between fields, with pairwise FST values ranging from 0.071 to 0.537. Additionally, cluster analysis detected the presence of P. sojae population structure across neighboring states. The level of pathotype and genetic diversity, in addition to the identification of population clusters, supports the hypothesis of occasional outcrossing events that allow an increase in diversity and the potential to select for a loss in avirulence to specific resistance genes within regions. The trend of suspected gene flow among neighboring fields is expected to be an ongoing issue with current agricultural practices.
Collapse
Affiliation(s)
- Linda M Hebb
- Department of Plant Pathology, The Ohio State University, Ohio Agricultural Research and Development Center, Center for Soybean Research, Wooster, OH 44691
| | - Carl A Bradley
- Department of Plant Pathology, University of Kentucky Research and Education Center, Grain and Forage Center of Excellence, Princeton, KY 40546
| | | | - Darcy E P Telenko
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Kiersten Wise
- Department of Plant Pathology, University of Kentucky Research and Education Center, Grain and Forage Center of Excellence, Princeton, KY 40546
| | - Anne E Dorrance
- Department of Plant Pathology, The Ohio State University, Ohio Agricultural Research and Development Center, Center for Soybean Research, Wooster, OH 44691
| |
Collapse
|
9
|
Clevinger EM, Biyashev R, Lerch-Olson E, Yu H, Quigley C, Song Q, Dorrance AE, Robertson AE, Saghai Maroof MA. Identification of Quantitative Disease Resistance Loci Toward Four Pythium Species in Soybean. Front Plant Sci 2021; 12:644746. [PMID: 33859662 PMCID: PMC8042330 DOI: 10.3389/fpls.2021.644746] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/08/2021] [Indexed: 06/01/2023]
Abstract
In this study, four recombinant inbred line (RIL) soybean populations were screened for their response to infection by Pythium sylvaticum, Pythium irregulare, Pythium oopapillum, and Pythium torulosum. The parents, PI 424237A, PI 424237B, PI 408097, and PI 408029, had higher levels of resistance to these species in a preliminary screening and were crossed with "Williams," a susceptible cultivar. A modified seed rot assay was used to evaluate RIL populations for their response to specific Pythium species selected for a particular population based on preliminary screenings. Over 2500 single-nucleotide polymorphism (SNP) markers were used to construct chromosomal maps to identify regions associated with resistance to Pythium species. Several minor and large effect quantitative disease resistance loci (QDRL) were identified including one large effect QDRL on chromosome 8 in the population of PI 408097 × Williams. It was identified by two different disease reaction traits in P. sylvaticum, P. irregulare, and P. torulosum. Another large effect QDRL was identified on chromosome 6 in the population of PI 408029 × Williams, and conferred resistance to P. sylvaticum and P. irregulare. These large effect QDRL will contribute toward the development of improved soybean cultivars with higher levels of resistance to these common soil-borne pathogens.
Collapse
Affiliation(s)
- Elizabeth M. Clevinger
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Ruslan Biyashev
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Elizabeth Lerch-Olson
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States
| | - Haipeng Yu
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Charles Quigley
- Soybean Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Anne E. Dorrance
- Center for Applied Plant Sciences and Soybean Research, Department of Plant Pathology, Ohio State Sustainability Institute, The Ohio State University, Wooster, OH, United States
| | - Alison E. Robertson
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States
| | - M. A. Saghai Maroof
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| |
Collapse
|
10
|
Van K, Rolling W, Biyashev RM, Matthiesen RL, Abeysekara NS, Robertson AE, Veney DJ, Dorrance AE, McHale LK, Saghai Maroof MA. Mining germplasm panels and phenotypic datasets to identify loci for resistance to Phytophthora sojae in soybean. Plant Genome 2021; 14:e20063. [PMID: 33200586 DOI: 10.1002/tpg2.20063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/05/2020] [Indexed: 06/11/2023]
Abstract
Phytophthora sojae causes Phytophthora root and stem rot of soybean and has been primarily managed through deployment of qualitative Resistance to P. sojae genes (Rps genes). The effectiveness of each individual or combination of Rps gene(s) depends on the diversity and pathotypes of the P. sojae populations present. Due to the complex nature of P. sojae populations, identification of more novel Rps genes is needed. In this study, phenotypic data from previous studies of 16 panels of plant introductions (PIs) were analyzed. Panels 1 and 2 consisted of 448 Glycine max and 520 G. soja, which had been evaluated for Rps gene response with a combination of P. sojae isolates. Panels 3 and 4 consisted of 429 and 460 G. max PIs, respectively, which had been evaluated using individual P. sojae isolates with complex virulence pathotypes. Finally, Panels 5-16 (376 G. max PIs) consisted of data deposited in the USDA Soybean Germplasm Collection from evaluations with 12 races of P. sojae. Using these panels, genome-wide association (GWA) analyses were carried out by combining phenotypic and SoySNP50K genotypic data. GWA models identified two, two, six, and seven novel Rps loci with Panels 1, 2, 3, and 4, respectively. A total of 58 novel Rps loci were identified using Panels 5-16. Genetic and phenotypic dissection of these loci may lead to the characterization of novel Rps genes that can be effectively deployed in new soybean cultivars against diverse P. sojae populations.
Collapse
Affiliation(s)
- Kyujung Van
- Department of Horticulture and Crop Science, Ohio State University, Columbus, OH, 43210, USA
| | - William Rolling
- Center for Applied Plant Sciences, Ohio State University, Columbus, OH, 43210, USA
| | - Ruslan M Biyashev
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Rashelle L Matthiesen
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Nilwala S Abeysekara
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Alison E Robertson
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Deloris J Veney
- Department of Plant Pathology, Ohio State University, Wooster, OH, 44691, USA
| | - Anne E Dorrance
- Center for Applied Plant Sciences, Ohio State University, Columbus, OH, 43210, USA
- Department of Plant Pathology, Ohio State University, Wooster, OH, 44691, USA
- Center for Soybean Research, Ohio State University, Wooster, OH, 44691, USA
| | - Leah K McHale
- Department of Horticulture and Crop Science, Ohio State University, Columbus, OH, 43210, USA
- Center for Applied Plant Sciences, Ohio State University, Columbus, OH, 43210, USA
- Center for Soybean Research, Ohio State University, Wooster, OH, 44691, USA
| | - M A Saghai Maroof
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| |
Collapse
|
11
|
Rolling WR, Dorrance AE, McHale LK. Testing methods and statistical models of genomic prediction for quantitative disease resistance to Phytophthora sojae in soybean [Glycine max (L.) Merr] germplasm collections. Theor Appl Genet 2020; 133:3441-3454. [PMID: 32960288 DOI: 10.1007/s00122-020-03679-w] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 09/04/2020] [Indexed: 06/11/2023]
Abstract
KEY MESSAGE Genomic prediction of quantitative resistance toward Phytophthora sojae indicated that genomic selection may increase breeding efficiency. Statistical model and marker set had minimal effect on genomic prediction with > 1000 markers. Quantitative disease resistance (QDR) toward Phytophthora sojae in soybean is a complex trait controlled by many small-effect loci throughout the genome. Along with the technical and rate-limiting challenges of phenotyping resistance to a root pathogen, the trait complexity can limit breeding efficiency. However, the application of genomic prediction to traits with complex genetic architecture, such as QDR toward P. sojae, is likely to improve breeding efficiency. We provide a novel example of genomic prediction by measuring QDR to P. sojae in two diverse panels of more than 450 plant introductions (PIs) that had previously been genotyped with the SoySNP50K chip. This research was completed in a collection of diverse germplasm and contributes to both an initial assessment of genomic prediction performance and characterization of the soybean germplasm collection. We tested six statistical models used for genomic prediction including Bayesian Ridge Regression; Bayesian LASSO; Bayes A, B, C; and reproducing kernel Hilbert spaces. We also tested how the number and distribution of SNPs included in genomic prediction altered predictive ability by varying the number of markers from less than 50 to more than 34,000 SNPs, including SNPs based on sequential sampling, random sampling, or selections from association analyses. Predictive ability was relatively independent of statistical model and marker distribution, with a diminishing return when more than 1000 SNPs were included in genomic prediction. This work estimated relative efficiency per breeding cycle between 0.57 and 0.83, which may improve the genetic gain for P. sojae QDR in soybean breeding programs.
Collapse
Affiliation(s)
- William R Rolling
- Center for Applied Plant Science and Center for Soybean Research, The Ohio State University, Columbus, OH, 43210, US
- Vegetable Crop Research Unit, USDA-ARS, Madison, WI, 53706, US
| | - Anne E Dorrance
- Center for Applied Plant Science and Center for Soybean Research, The Ohio State University, Columbus, OH, 43210, US
- Department of Plant Pathology, The Ohio State University, Wooster, OH, 44691, US
| | - Leah K McHale
- Center for Applied Plant Science and Center for Soybean Research, The Ohio State University, Columbus, OH, 43210, US.
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, 43210, US.
| |
Collapse
|
12
|
Stasko AK, Batnini A, Bolanos-Carriel C, Lin JE, Lin Y, Blakeslee JJ, Dorrance AE. Auxin Profiling and GmPIN Expression in Phytophthora sojae-Soybean Root Interactions. Phytopathology 2020; 110:1988-2002. [PMID: 32602813 DOI: 10.1094/phyto-02-20-0046-r] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Auxin (indole-3-acetic acid, IAA) has been implicated as a susceptibility factor in both beneficial and pathogenic molecular plant-microbe interactions. Previous studies have identified a large number of auxin-related genes underlying quantitative disease resistance loci (QDRLs) for Phytophthora sojae. Thus, we hypothesized that auxin may be involved the P. sojae-soybean interaction. The levels of IAA and related metabolites were measured in mycelia and media supernatant as well as in mock and inoculated soybean roots in a time course assay. The expression of 11 soybean Pin-formed (GmPIN) auxin efflux transporter genes was also examined. Tryptophan, an auxin precursor, was detected in the P. sojae mycelia and media supernatant. During colonization of roots, levels of IAA and related metabolites were significantly higher in both moderately resistant Conrad and moderately susceptible Sloan inoculated roots compared with mock controls at 48 h postinoculation (hpi) in one experiment and at 72 hpi in a second, with Sloan accumulating higher levels of the auxin catabolite IAA-Ala than Conrad. Additionally, one GmPIN at 24 hpi, one at 48 hpi, and three at 72 hpi had higher expression in inoculated compared with the mock control roots in Conrad. The ability of resistant cultivars to cope with auxin accumulation may play an important role in quantitative disease resistance. Levels of jasmonic acid (JA), another plant hormone associated with defense responses, were also higher in inoculated roots at these same time points, suggesting that JA also plays a role during the later stages of infection.
Collapse
Affiliation(s)
- Anna K Stasko
- Department of Plant Pathology, The Ohio State University, Wooster, OH 44691
- Center for Soybean Research, The Ohio State University, Wooster, OH 44691
| | - Amine Batnini
- Department of Plant Pathology, The Ohio State University, Wooster, OH 44691
- Center for Soybean Research, The Ohio State University, Wooster, OH 44691
| | - Carlos Bolanos-Carriel
- Department of Plant Pathology, The Ohio State University, Wooster, OH 44691
- Center for Soybean Research, The Ohio State University, Wooster, OH 44691
| | - Jinshan Ella Lin
- Department of Horticulture and Crop Science and OARDC Metabolite Analysis Cluster, The Ohio State University, Wooster, OH 44691
| | - Yun Lin
- Department of Horticulture and Crop Science and OARDC Metabolite Analysis Cluster, The Ohio State University, Wooster, OH 44691
| | - Joshua J Blakeslee
- Department of Horticulture and Crop Science and OARDC Metabolite Analysis Cluster, The Ohio State University, Wooster, OH 44691
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH 43210
| | - Anne E Dorrance
- Department of Plant Pathology, The Ohio State University, Wooster, OH 44691
- Center for Soybean Research, The Ohio State University, Wooster, OH 44691
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH 43210
| |
Collapse
|
13
|
Abstract
Some Pythium spp. cause damping off and root rot in soybeans and other crop species. One of the most effective management tools to reduce disease is host resistance; however, little is known about resistance in soybean to Pythium spp. The soybean nested associated mapping (SoyNAM) parent lines are a set of germplasms that were crossed to a single hub parent to create recombinant inbred line populations for the purpose of mapping agronomic traits. The SoyNAM parents were screened for resistance to Pythium lutarium, Pythium oopapillum, Pythium sylvaticum, and Pythium torulosum in separate assays to evaluate seed and root rot severity. Of the 40 SoyNAM parents, only 'Maverick' was resistant to the four species tested; however, 13 were resistant to three species. Other lines were resistant to two, one, or none of the species tested. Correlations between seed and root rot severity for the lines assessed were weak or insignificant. Results indicate that mechanisms of resistance to seed and root rot caused by Pythium spp. may not necessarily be the same.
Collapse
Affiliation(s)
| | - Anne E Dorrance
- Department of Plant Pathology, Ohio State University, Wooster, OH 44691
| | - Alison E Robertson
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011
| |
Collapse
|
14
|
Fadel Sartori F, Floriano Pimpinato R, Tornisielo VL, Dieminger Engroff T, de Souza Jaccoud-Filho D, Menten JO, Dorrance AE, Dourado-Neto D. Soybean seed treatment: how do fungicides translocate in plants? Pest Manag Sci 2020; 76:2355-2359. [PMID: 32003142 DOI: 10.1002/ps.5771] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 01/20/2020] [Accepted: 01/30/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND Soybean seed treatment with fungicides is a well-established disease management strategy. However, the movement of these fungicides within seedlings is not always well characterized. Thus, the objectives of this study were to determine the pattern of translocation of three fungicides with different modes of action applied as a seed treatment, and the effect of soil type on translocation. RESULTS Most of the absorbed radioactivity was concentrated in the cotyledons and the maximum sum of the rates of absorption by roots, stems, and leaves of the plants was 15%. In most cases, absorption by roots, stems, and leaves were lower than 5% for 14 C-pyraclostrobin and 14 C-metalaxyl, and 1.6% for 14 C-carbendazim. Fungicides absorbed by the roots and the whole seedlings were higher when plants were grown in soil with lower organic matter content. Fungicides in the cotyledons are unlikely to be redistributed and are lost when cotyledons fall off the plants. CONCLUSION Cotyledons are the part of the plant where fungicides are most absorbed, regardless of the fungicide. Soil type affects the absorption of fungicides, and in this study it was most likely caused by soil organic matter. These data improve knowledge of the movement of seed treatment fungicides in soybean seedlings and may help the development of seed treatment chemistry to manage seed and soilborne pathogens.
Collapse
Affiliation(s)
- Felipe Fadel Sartori
- Department of Crop Sciences, Group of Applied Plant Physiology and Crop Production, Esalq/USP, São Paulo, Brazil
- Departament of Plant Health, Group of Applied Plant Pathology, UEPG, São Paulo, Brazil
- Department of Plant Pathology and Center for Soybean Research, The Ohio State University, Wooster, Ohio, USA
| | | | | | - Thaise Dieminger Engroff
- Department of Crop Sciences, Group of Applied Plant Physiology and Crop Production, Esalq/USP, São Paulo, Brazil
| | | | - José O Menten
- Departament of Plant Pathology, Esalq/USP, São Paulo, Brazil
| | - Anne E Dorrance
- Department of Plant Pathology and Center for Soybean Research, The Ohio State University, Wooster, Ohio, USA
| | - Durval Dourado-Neto
- Department of Crop Sciences, Group of Applied Plant Physiology and Crop Production, Esalq/USP, São Paulo, Brazil
| |
Collapse
|
15
|
Scott K, Eyre M, McDuffee D, Dorrance AE. The Efficacy of Ethaboxam as a Soybean Seed Treatment Toward Phytophthora, Phytopythium, and Pythium in Ohio. Plant Dis 2020; 104:1421-1432. [PMID: 32191161 DOI: 10.1094/pdis-09-19-1818-re] [Citation(s) in RCA: 8] [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] [Indexed: 06/10/2023]
Abstract
Phytophthora, Phytopythium, and Pythium species that cause early-season seed decay and pre-emergence and post-emergence damping off of soybean are most commonly managed with seed treatments. The phenylamide fungicides metalaxyl and mefenoxam, and ethaboxam are effective toward some but not all species. The primary objective of this study was to evaluate the efficacy of ethaboxam in fungicide mixtures and compare those with other fungicides as seed treatments to protect soybean against Pythium, Phytopythium, and Phytophthora species in both high-disease field environments and laboratory seed plate assays. The second objective was to evaluate these seed treatment mixtures on cultivars that have varying levels and combinations of resistance to these soilborne pathogens. Five of eight environments received adequate precipitation in the 14 days after planting for high levels of seedling disease development and treatment evaluations. Three environments had significantly greater stands, and three had significantly greater yield when ethaboxam was used in the seed treatment mixture compared with treatments containing metalaxyl or mefenoxam alone. Three fungicide formulations significantly reduced disease severity compared with nontreated in the seed plate assay for 17 species. However, the combination of ethaboxam plus metalaxyl in a mixture was more effective than either fungicide alone against some Pythium and Phytopythium species. Overall, our results indicate that the addition of ethaboxam to a fungicide seed treatment is effective in reducing seed rot caused by these pathogens commonly isolated from soybean in Ohio but that these effects can be masked when cultivars with resistance are planted.
Collapse
Affiliation(s)
- Kelsey Scott
- Department of Plant Pathology, The Ohio State University, Wooster, OH 44691
| | - Meredith Eyre
- Department of Plant Pathology, The Ohio State University, Wooster, OH 44691
| | | | - Anne E Dorrance
- Department of Plant Pathology, The Ohio State University, Wooster, OH 44691
| |
Collapse
|
16
|
Rolling W, Lake R, Dorrance AE, McHale LK. Genome-wide association analyses of quantitative disease resistance in diverse sets of soybean [Glycine max (L.) Merr.] plant introductions. PLoS One 2020; 15:e0227710. [PMID: 32196522 PMCID: PMC7083333 DOI: 10.1371/journal.pone.0227710] [Citation(s) in RCA: 13] [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: 08/29/2019] [Accepted: 12/25/2019] [Indexed: 12/17/2022] Open
Abstract
Phytophthora sojae is one of the costliest soybean pathogens in the US. Quantitative disease resistance (QDR) is a vital part of Phytophthora disease management. In this study, QDR was measured in 478 and 495 plant introductions (PIs) towards P. sojae isolates OH.121 and C2.S1, respectively, in genome-wide association (GWA) analyses to identify genetic markers linked to QDR loci (QDRL). Populations were generated by sampling PIs from the US, the Republic of Korea, and the full collection of PIs maintained by the USDA. Additionally, a meta-analysis of QDRL reported from bi-parental studies was done to compare past and present findings. Twenty-four significant marker-trait associations were identified from the 478 PIs phenotyped with OH.121, and an additional 24 marker-trait associations were identified from the 495 PIs phenotyped with C2.S1. In total, 48 significant markers were distributed across 16 chromosomes and based on linkage analysis, represent a total of 44 QDRL. The majority of QDRL were identified with only one of the two isolates, and only a region on chromosome 13 was consistently identified. Regions on chromosomes 3, 13, and 17 were identified in previous GWA-analyses and were re-identified in this study. Five QDRL co-localized with P. sojae meta-QDRL identified from QDRL reported in previous biparental mapping studies. The remaining regions represent novel QDRL, in the soybean-P. sojae pathosystem and were primarily identified in germplasm from the Republic of Korea. Overall, the number of loci identified in this study highlights the complexity of QDR to P. sojae.
Collapse
Affiliation(s)
- William Rolling
- Center for Applied Plant Science and Center for Soybean Research, The Ohio State University, Columbus, Ohio, United States of America
| | - Rhiannon Lake
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, Ohio, United States of America
| | - Anne E. Dorrance
- Center for Applied Plant Science and Center for Soybean Research, The Ohio State University, Columbus, Ohio, United States of America
- Department of Plant Pathology, The Ohio State University, Wooster, Ohio, United States of America
| | - Leah K. McHale
- Center for Applied Plant Science and Center for Soybean Research, The Ohio State University, Columbus, Ohio, United States of America
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, Ohio, United States of America
| |
Collapse
|
17
|
Lopez-Nicora HD, Carr JK, Paul PA, Dorrance AE, Ralston TI, Williams CA, Niblack TL. Evaluation of the Combined Effect of Heterodera glycines and Macrophomina phaseolina on Soybean Yield in Naturally Infested Fields with Spatial Regression Analysis and in Greenhouse Studies. Phytopathology 2020; 110:406-417. [PMID: 31535924 DOI: 10.1094/phyto-03-19-0087-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: 06/10/2023]
Abstract
Heterodera glycines, the soybean cyst nematode, and Macrophomina phaseolina, causal agent of charcoal rot, are economically important soybean pathogens. The impact and effect of these pathogens on soybean yield in coinfested fields in the Midwest production region is not known. Both pathogens are soilborne, with spatially aggregated distribution and effects. Spatial regression analysis, therefore, is an appropriate method to account for the spatial dependency in either the dependent variable or regression error term from data produced in fields naturally infested with H. glycines and M. phaseolina. The objectives of this study were twofold: to evaluate the combined effect of H. glycines and M. phaseolina on soybean yield in naturally infested commercial fields with ordinary least squares and spatial regression models; and to evaluate, under environmentally controlled conditions, the combined effect of H. glycines and M. phaseolina through nematode reproduction and plant tissue fungal colonization. Six trials were conducted in fields naturally infested with H. glycines and M. phaseolina in Ohio. Systematic-grid sampling was used to determine the population densities of H. glycines and M. phaseolina, and soybean yield estimates. Though not used in any statistical analysis, M. phaseolina colony forming units from plant tissue, charcoal rot severity, and H. glycines type were also recorded and summarized. In two greenhouse experiments, treatments consisted of H. glycines alone, M. phaseolina alone, and coinfestation of soybean with both pathogens. Moran's I test indicated that the yield from five fields was spatially correlated (P < 0.05) and aggregated. In these fields, to account for spatial dependence, spatial regression models were fitted to the data. Spatial regression analyses revealed a significant interaction effect between H. glycines and M. phaseolina on soybean yield for fields with high initial population densities of both pathogens. In the greenhouse experiments, H. glycines reproduction was significantly (P < 0.05) reduced in the presence of M. phaseolina; however, soybean tissue fungal colonization was not affected by the presence of H. glycines. The direct mechanisms by which H. glycines and M. phaseolina interact were not demonstrated in this study. Future studies must be conducted in the field and greenhouse to better understand this interaction effect.
Collapse
Affiliation(s)
- H D Lopez-Nicora
- Departamento de Producción Agrícola, Universidad San Carlos, Alfredo Seiferheld 4989, Asunción, C.P. 1884, Paraguay
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, U.S.A
| | - J K Carr
- Department of Geography, The Ohio State University, Columbus, OH 43210, U.S.A
| | - P A Paul
- Department of Plant Pathology, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, OH 44691, U.S.A
| | - A E Dorrance
- Department of Plant Pathology, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, OH 44691, U.S.A
| | - T I Ralston
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, U.S.A
| | - C A Williams
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, U.S.A
| | - T L Niblack
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, U.S.A
| |
Collapse
|
18
|
Ajayi-Oyetunde OO, Everhart SE, Brown PJ, Tenuta AU, Dorrance AE, Bradley CA. Genetic Structure of Rhizoctonia solani AG-2-2IIIB from Soybean in Illinois, Ohio, and Ontario. Phytopathology 2019; 109:2132-2141. [PMID: 31381483 DOI: 10.1094/phyto-01-19-0015-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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
Rhizoctonia solani AG-2-2IIIB is an important seedling pathogen of soybean in North America and other soybean-growing regions around the world. There is no information regarding the population genetics of field populations of R. solani associated with soybean seedling disease. More specifically, information regarding genetic diversity, the mode of reproduction, and the evolutionary factors that shape different R. solani populations separated in time and space are lacking. We exploited genotyping by sequencing as a tool to assess the genetic structure of R. solani AG-2-2IIIB populations from Illinois, Ohio, and Ontario and investigate the reproductive mode of this subgroup. Our results revealed differences in genotypic diversity among three populations, with the Ontario population having greatest diversity. An overrepresentation of multilocus genotypes (MLGs) and a rejection of the null hypothesis of random mating in all three populations suggested clonality within each population. However, phylogenetic analysis revealed long terminal multifurcating branches for most members of the Ontario population, suggesting a mixed reproductive mode for this population. Analysis of molecular variance revealed low levels of population differentiation, and sharing of similar MLGs among populations highlights the role of genotype flow as an evolutionary force shaping population structure of this subgroup.
Collapse
Affiliation(s)
| | - Sydney E Everhart
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583, U.S.A
| | - Patrick J Brown
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, U.S.A
| | - Albert U Tenuta
- Ontario Ministry of Agriculture, Food and Rural Affairs, Ridgetown, Ontario N0P2C0, Canada
| | - Anne E Dorrance
- Department of Plant Pathology, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691, OH, U.S.A
| | - Carl A Bradley
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, U.S.A
| |
Collapse
|
19
|
Million CR, Wijeratne S, Cassone BJ, Lee S, Rouf Mian MA, McHale LK, Dorrance AE. Hybrid Genome Assembly of a Major Quantitative Disease Resistance Locus in Soybean Toward Fusarium graminearum. Plant Genome 2019; 12. [PMID: 31290916 DOI: 10.3835/plantgenome2018.12.0102] [Citation(s) in RCA: 4] [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] [Received: 12/15/2018] [Accepted: 03/11/2019] [Indexed: 05/27/2023]
Abstract
Schwabe [teleomorph: Gibberella zeae (Schweintiz) Petch] has been identified as a pathogen of soybean [ (L.) Merr.] causing seed, seedling damping-off and root rot in North America. A major quantitative disease resistance locus (QDRL) that contributed 38.5% of the phenotypic variance toward in soybean was previously identified through mapping of a recombinant inbred line (RIL) population derived from a cross between 'Wyandot' and PI 567301B. This major QDRL mapped to chromosome 8 to a predicted 305 kb region harboring 36 genes. This locus maps near the locus for soybean cyst nematode (SCN) and the locus contributing to seed coat color. Long-read sequencing of the region was completed and variations in gene sequence and gene order compared with the 'Williams 82' reference were identified. Molecular markers were developed for genes within this region and mapped in the original population, slightly narrowing the region of interest. Analyses of the hybrid genome reassembly using three previously published bacterial artificial chromosome (BAC) sequences (BAC56G2, BAC104J7, and BAC77G7-a) combined with RNA-sequencing narrowed the region making candidate gene identification possible. The markers within this region may be used for marker-assisted selection (MAS). There were 10 differentially expressed genes between resistant and susceptible lines, with four of these candidates also located within the genomic interval defined by the flanking markers. These genes included an actin-related protein 2/3 complex subunit, an unknown protein, a hypothetical protein, and a chalcone synthase 3.
Collapse
|
20
|
Klepadlo M, Balk CS, Vuong TD, Dorrance AE, Nguyen HT. Molecular characterization of genomic regions for resistance to Pythium ultimum var. ultimum in the soybean cultivar Magellan. Theor Appl Genet 2019; 132:405-417. [PMID: 30443655 DOI: 10.1007/s00122-018-3228-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 11/02/2018] [Indexed: 06/09/2023]
Abstract
KEY MESSAGE Two novel QTL for resistance to Pythium ultimum var. ultimum were identified in soybean using an Illumina SNP Chip and whole genome re-sequencing. Pythium ultimum var. ultimum is one of numerous Pythium spp. that causes severe pre- and post-emergence damping-off of seedlings and root rot of soybean [Glycine max (L.) Merr.]. The objective of this research was to identify quantitative trait loci (QTL) for resistance to P. ultimum var. ultimum in a recombinant inbred line population derived from a cross of 'Magellan' (moderately resistant) and PI 438489B (susceptible). Two different mapping approaches were utilized: the universal soybean linkage panel (USLP 1.0) and the bin map constructed from whole genome re-sequencing (WGRS) technology. Two genomic regions associated with variation in three disease-related parameters were detected using both approaches, with the bin map providing higher resolution. Using WGRS, the first QTL were mapped within a 350-kbp region on Chr. 6 and explained 7.5-13.5% of the phenotypic variance. The second QTL were positioned in a 260-kbp confidence interval on Chr. 8 and explained 6.3-16.8% of the phenotypic variation. Candidate genes potentially associated with disease resistance were proposed. High-resolution genetic linkage maps with a number of significant SNP markers could benefit marker-assisted breeding and dissection of the molecular mechanisms underlying soybean resistance to Pythium damping-off in 'Magellan.' Additionally, the outputs of this study may encourage more screening of diverse soybean germplasm and utilization of genome-wide association studies to understand the genetic basis of quantitative disease resistance.
Collapse
Affiliation(s)
- Mariola Klepadlo
- Division of Plant Science, University of Missouri, Columbia, MO, 65211, USA
| | - Christine S Balk
- Department of Plant Pathology, The Ohio State University, Wooster, OH, 44691, USA
- Davey Tree, Kent, OH, USA
| | - Tri D Vuong
- Division of Plant Science, University of Missouri, Columbia, MO, 65211, USA
| | - Anne E Dorrance
- Department of Plant Pathology, The Ohio State University, Wooster, OH, 44691, USA
| | - Henry T Nguyen
- Division of Plant Science, University of Missouri, Columbia, MO, 65211, USA.
| |
Collapse
|
21
|
Huzar-Novakowiski J, Dorrance AE. Genetic Diversity and Population Structure of Pythium irregulare from Soybean and Corn Production Fields in Ohio. Plant Dis 2018; 102:1989-2000. [PMID: 30124360 DOI: 10.1094/pdis-11-17-1725-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
High levels of genetic diversity have been described within the Pythium irregulare complex from several host plants; however, little is known about the population structure in fields used for grain production. Therefore, the objective of this study was to evaluate the genetic diversity and population structure of 53 isolates baited from 28 soybean and corn production fields from 25 counties in Ohio. Genetic diversity was characterized based on sequence analysis of the internal transcribed spacer (ITS1-5.8S-ITS2) region and with 21 simple sequence repeat (SSR) markers. In addition, aggressiveness on soybean, optimum growth temperature, and sensitivity to metalaxyl fungicide were determined. ITS sequence analysis indicated that four isolates clustered with P. cryptoirregulare, whereas the remaining isolates clustered with P. irregulare that was subdivided into two groups (1 and 2). Cluster analysis of SSR data revealed a similar subdivision, which was also supported by structure analysis. The isolates from group 2 grew at a slower rate, but both groups of P. irregulare and P. cryptoirregulare recovered in this study had the same optimum growth at 27°C. Variability of aggressiveness and sensitivity toward metalaxyl fungicide was also observed among isolates within each group. The results from this study will help in the selection of isolates to be used in screening for resistance, assessment of fungicide efficacy, and disease management recommendations.
Collapse
Affiliation(s)
- J Huzar-Novakowiski
- Department of Plant Pathology, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, OH 44691
| | - A E Dorrance
- Department of Plant Pathology, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, OH 44691
| |
Collapse
|
22
|
Huzar-Novakowiski J, Dorrance AE. Ascospore Inoculum Density and Characterization of Components of Partial Resistance to Sclerotinia sclerotiorum in Soybean. Plant Dis 2018; 102:1326-1333. [PMID: 30673564 DOI: 10.1094/pdis-11-17-1786-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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Germplasm screening programs have primarily relied on inoculation with mycelia to determine the resistance reaction of soybean genotypes to Sclerotinia sclerotiorum. However, under field conditions, ascospores are the primary source of inoculum. Therefore, the objective of this study was to determine which components most accurately differentiate the resistance reaction of soybean genotypes inoculated with ascospores of S. sclerotiorum. Ascospores were produced in the laboratory and all of the experiments were carried out under controlled conditions with inoculations at flowering stage. Initially, inoculum densities of 1 × 104, 1 × 105 and 1 × 106 ascospores ml-1 were compared on six soybean genotypes with known resistance reactions. Disease symptoms developed on all genotypes and at all inoculum densities. The highest ascospore concentration increased infection efficiency but it was not correlated with an increase in lesion length. Components of resistance were then measured on a set of 17 cultivars with known resistance reactions at 1 × 105 ascospores ml-1. Resistance reactions could be differentiated based on the level of infection efficiency and lesion length on the main stem. Although inoculation with ascospores presents some limitations such as the time required for inoculum production as well as the time and space required for plant growth, it has the potential to be used to complement other methods for the characterization of resistance of soybean genotypes.
Collapse
Affiliation(s)
- Jaqueline Huzar-Novakowiski
- Department of Plant Pathology, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691
| | - Anne E Dorrance
- Department of Plant Pathology, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691
| |
Collapse
|
23
|
|
24
|
Huzar-Novakowiski J, Paul PA, Dorrance AE. Host Resistance and Chemical Control for Management of Sclerotinia Stem Rot of Soybean in Ohio. Phytopathology 2017; 107:937-949. [PMID: 28398874 DOI: 10.1094/phyto-01-17-0030-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Recent outbreaks of Sclerotinia stem rot (SSR) of soybean in Ohio, along with new fungicides and cultivars with resistance to this disease, have led to a renewed interest in studies to update disease management guidelines. The effect of host resistance (in moderately resistant [MR] and moderately susceptible [MS] cultivars) and chemical control on SSR and yield was evaluated in 12 environments from 2014 to 2016. The chemical treatments evaluated were an untreated check, four fungicides (boscalid, picoxystrobin, pyraclostrobin, and thiophanate-methyl), and one herbicide (lactofen) applied at soybean growth stage R1 (early flowering) alone or at R1 followed by a second application at R2 (full flowering). SSR developed in 6 of 12 environments, with mean disease incidence in the untreated check of 2.5 to 41%. The three environments with high levels of SSR (disease incidence in the untreated check >20%) were used for further statistical analysis. There were significant effects (P < 0.05) of soybean cultivar and chemical treatment on SSR levels. Significantly lower levels of SSR were observed in MR cultivars. Both boscalid and lactofen reduced SSR but did not increase yield. Pyraclostrobin increased SSR compared with the untreated check in the three environments with high levels of disease. In the six fields where SSR did not develop, chemical treatment did not increase yield, nor was the yield from the MR cultivar significantly different from the MS cultivar. For Ohio, MR cultivars alone were effective for management of SSR in soybean fields where this disease has historically occurred.
Collapse
Affiliation(s)
- Jaqueline Huzar-Novakowiski
- Department of Plant Pathology, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691
| | - Pierce A Paul
- Department of Plant Pathology, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691
| | - Anne E Dorrance
- Department of Plant Pathology, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691
| |
Collapse
|
25
|
Cheng P, Gedling CR, Patil G, Vuong TD, Shannon JG, Dorrance AE, Nguyen HT. Genetic mapping and haplotype analysis of a locus for quantitative resistance to Fusarium graminearum in soybean accession PI 567516C. Theor Appl Genet 2017; 130:999-1010. [PMID: 28275816 DOI: 10.1007/s00122-017-2866-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 01/24/2017] [Indexed: 05/16/2023]
Abstract
KEY MESSAGE A major novel quantitative disease resistance locus, qRfg_Gm06, for Fusarium graminearum was genetically mapped to chromosome 6. Genomic-assisted haplotype analysis within this region identified three putative candidate genes. Fusarium graminearum causes seed, root rot, and seedling damping-off in soybean which contributes to reduced stands and yield. A cultivar Magellan and PI 567516C were identified with low and high levels of partial resistance to F. graminearum, respectively. Quantitative disease resistance loci (QDRL) were mapped with 241 F7:8 recombinant inbred lines (RILs) derived from a cross of Magellan × PI 567516C. Phenotypic evaluation for resistance to F. graminearum used the rolled towel assay in a randomized incomplete block design. The genetic map was constructed from 927 polymorphic single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers. One major QDRL qRfg_Gm06 was detected and mapped to chromosome 6 with a LOD score of 20.3 explaining 40.2% of the total phenotypic variation. This QDRL was mapped to a ~400 kb genomic region of the Williams 82 reference genome. Genome mining of this region identified 14 putative candidate disease resistance genes. Haplotype analysis of this locus using whole genome re-sequencing (WGRS) of 106 diverse soybean lines narrowed the list to three genes. A SNP genotyping Kompetitive allele-specific PCR (KASP) assay was designed for one of the genes and was validated in a subset of the RILs and all 106 diverse lines.
Collapse
Affiliation(s)
- Peng Cheng
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA
| | - Cassidy R Gedling
- Department of Plant Pathology, The Ohio State University, 1680 Madison Avenue, Wooster, OH, 44691, USA
| | - Gunvant Patil
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA
| | - Tri D Vuong
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA
| | - J Grover Shannon
- Division of Plant Sciences, University of Missouri-Fisher Delta Research Center, Portageville, MO, 63873, USA
| | - Anne E Dorrance
- Department of Plant Pathology, The Ohio State University, 1680 Madison Avenue, Wooster, OH, 44691, USA.
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
| |
Collapse
|
26
|
Schneider R, Rolling W, Song Q, Cregan P, Dorrance AE, McHale LK. Genome-wide association mapping of partial resistance to Phytophthora sojae in soybean plant introductions from the Republic of Korea. BMC Genomics 2016; 17:607. [PMID: 27515508 PMCID: PMC4982113 DOI: 10.1186/s12864-016-2918-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 07/07/2016] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Phytophthora root and stem rot is one of the most yield-limiting diseases of soybean [Glycine max (L.) Merr], caused by the oomycete Phytophthora sojae. Partial resistance is controlled by several genes and, compared to single gene (Rps gene) resistance to P. sojae, places less selection pressure on P. sojae populations. Thus, partial resistance provides a more durable resistance against the pathogen. In previous work, plant introductions (PIs) originating from the Republic of Korea (S. Korea) have shown to be excellent sources for high levels of partial resistance against P. sojae. RESULTS Resistance to two highly virulent P. sojae isolates was assessed in 1395 PIs from S. Korea via a greenhouse layer test. Lines exhibiting possible Rps gene immunity or rot due to other pathogens were removed and the remaining 800 lines were used to identify regions of quantitative resistance using genome-wide association mapping. Sixteen SNP markers on chromosomes 3, 13 and 19 were significantly associated with partial resistance to P. sojae and were grouped into seven quantitative trait loci (QTL) by linkage disequilibrium blocks. Two QTL on chromosome 3 and three QTL on chromosome 19 represent possible novel loci for partial resistance to P. sojae. While candidate genes at QTL varied in their predicted functions, the coincidence of QTLs 3-2 and 13-1 on chromosomes 3 and 13, respectively, with Rps genes and resistance gene analogs provided support for the hypothesized mechanism of partial resistance involving weak R-genes. CONCLUSIONS QTL contributing to partial resistance towards P. sojae in soybean germplasm originating from S. Korea were identified. The QTL identified in this study coincide with previously reported QTL, Rps genes, as well as novel loci for partial resistance. Molecular markers associated with these QTL can be used in the marker-assisted introgression of these alleles into elite cultivars. Annotations of genes within QTL allow hypotheses on the possible mechanisms of partial resistance to P. sojae.
Collapse
Affiliation(s)
- Rhiannon Schneider
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, 43210, USA
- Present Address: Pioneer Hi-Bred International Inc., Napoleon, OH, 43545, USA
| | - William Rolling
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Qijian Song
- US Department of Agriculture, Soybean Genomics and Improvement Laboratory, Agricultural Research Service, Beltsville, MD, 20705, USA
| | - Perry Cregan
- US Department of Agriculture, Soybean Genomics and Improvement Laboratory, Agricultural Research Service, Beltsville, MD, 20705, USA
| | - Anne E Dorrance
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, 43210, USA
- Department of Plant Pathology, The Ohio State University, Wooster, OH, 44691, USA
| | - Leah K McHale
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, 43210, USA.
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, 43210, USA.
| |
Collapse
|
27
|
Dorrance AE, Kurle J, Robertson AE, Bradley CA, Giesler L, Wise K, Concibido VC. Pathotype Diversity of Phytophthora sojae in Eleven States in the United States. Plant Dis 2016; 100:1429-1437. [PMID: 30686193 DOI: 10.1094/pdis-08-15-0879-re] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [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
Pathotype diversity of Phytophthora sojae was assessed in 11 states in the United States during 2012 and 2013. Isolates of P. sojae were recovered from 202 fields, either from soil samples using a soybean seedling bioassay or by isolation from symptomatic plants. Each isolate was inoculated directly onto 12 soybean differentials; no Rps gene or Rps 1a, 1b, 1c, 1k, 3a, 3b, 3c, 4, 6, 7, or 8. There were 213 unique virulence pathotypes identified among the 873 isolates collected. None of the Rps genes were effective against all the isolates collected but Rps6 and Rps8 were effective against the majority of isolates collected in the northern regions of the sampled area. Virulence toward Rps1a, 1b, 1c, and 1k ranged from 36 to 100% of isolates collected in each state, while virulence to Rps6 and Rps8 was less than 36 and 10%, respectively. Depending on the state, the effectiveness of Rps3a ranged from totally effective to susceptible to more than 40% of the isolates. Pathotype complexity has increased in populations of P. sojae in the United States, emphasizing the increasing importance of stacked Rps genes in combination with high partial resistance as a means of limiting losses to P. sojae.
Collapse
Affiliation(s)
- A E Dorrance
- Department of Plant Pathology, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691
| | - J Kurle
- Department of Plant Pathology, University of Minnesota, St. Paul 55108
| | - A E Robertson
- Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011
| | - C A Bradley
- Department of Crop Sciences, University of Illinois, Urbana 61801
| | - L Giesler
- Department of Plant Pathology, University of Nebraska, Lincoln 68583
| | - K Wise
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47097
| | | |
Collapse
|
28
|
Stewart S, Robertson AE, Wickramasinghe D, Draper MA, Michel A, Dorrance AE. Population Structure Among and Within Iowa, Missouri, Ohio, and South Dakota Populations of Phytophthora sojae. Plant Dis 2016; 100:367-379. [PMID: 30694137 DOI: 10.1094/pdis-04-15-0437-re] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [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 root and stem rot, caused by Phytophthora sojae, is an economically important disease of soybean throughout the Midwestern United States. This disease has been successfully managed with resistance (Rps) genes; however, pathogen populations throughout the Midwest have developed virulence to many Rps genes, including those that have not been deployed. To gain a better understanding of the processes that influence P. sojae evolution, the population genetic structure was compared among populations using one isolate collected from 17, 33, and 20 fields in Iowa, Ohio, and South Dakota, respectively, as well as multiple isolates from individual fields in Iowa, Ohio, and Missouri. Genotypic diversity was measured using 21 polymorphic microsatellite (simple-sequence repeat) markers. and pathotype diversity using 15 soybean differentials. For all but three of the populations with low sample size, there was a high level of pathotype diversity and a low to moderate level of genotypic diversity among the populations for both comparisons between states and within-field variation. None of the Rps-gene differentials were resistant to all of the isolates. There were 103 unique multilocus genotypes identified in this study and only 2 were identified from the same field. Although no clones were identified in more than one field, pairwise FST indicated that some gene flow within neighboring fields does occur but not across the region, including fields from neighboring states. These results suggest that there is a strong probability that each state may have their own or several regional populations, as well as provide further evidence of high diversity within this homothallic pathogen which may be due, in part, to limited gene flow, mutation, or outcrossing, and this likely affects the success of deployment of resistance.
Collapse
Affiliation(s)
- S Stewart
- Department Plant Pathology and Microbiology, Iowa State University, Ames 50011
| | - A E Robertson
- Department Plant Pathology and Microbiology, Iowa State University, Ames 50011
| | - D Wickramasinghe
- Department of Plant Pathology, The Ohio State University, Ohio Agricultural Research and Development Center (OARDC), Wooster 44691
| | - M A Draper
- Plant Science Department, South Dakota State University, Brookings 57007-1090
| | | | - A E Dorrance
- Department of Plant Pathology, The Ohio State University, OARDC
| |
Collapse
|
29
|
Cassone BJ, Redinbaugh MG, Dorrance AE, Michel AP. Shifts in Buchnera aphidicola density in soybean aphids (Aphis glycines) feeding on virus-infected soybean. Insect Mol Biol 2015; 24:422-31. [PMID: 25845267 DOI: 10.1111/imb.12170] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [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: 09/15/2014] [Revised: 01/21/2015] [Accepted: 01/26/2015] [Indexed: 06/04/2023]
Abstract
Vertically transmitted bacterial symbionts are common in arthropods. Aphids undergo an obligate symbiosis with Buchnera aphidicola, which provides essential amino acids to its host and contributes directly to nymph growth and reproduction. We previously found that newly adult Aphis glycines feeding on soybean infected with the beetle-transmitted Bean pod mottle virus (BPMV) had significantly reduced fecundity. We hypothesized that the reduced fecundity was attributable to detrimental impacts of the virus on the aphid microbiome, namely Buchnera. To test this, mRNA sequencing and quantitative real-time PCR were used to assay Buchnera transcript abundance and titre in A. glycines feeding on Soybean mosaic virus-infected, BPMV-infected, and healthy soybean for up to 14 days. Our results indicated that Buchnera density was lower and ultimately suppressed in aphids feeding on virus-infected soybean. While the decreased Buchnera titre may be associated with reduced aphid fecundity, additional mechanisms are probably involved. The present report begins to describe how interactions among insects, plants, and plant pathogens influence endosymbiont population dynamics.
Collapse
Affiliation(s)
- Bryan J Cassone
- Center for Applied Plant Sciences, The Ohio State University, OARDC, Wooster, OH, 44691, USA
- Department of Plant Pathology, The Ohio State University, OARDC, Wooster, OH, 44691, USA
| | - Margaret G Redinbaugh
- Department of Plant Pathology, The Ohio State University, OARDC, Wooster, OH, 44691, USA
- USDA, ARS Corn, Soybean and Wheat Quality Research Unit, Wooster, OH, 44691, USA
| | - Anne E Dorrance
- Department of Plant Pathology, The Ohio State University, OARDC, Wooster, OH, 44691, USA
| | - Andrew P Michel
- Department of Entomology, the Ohio State University, OARDC, Wooster, OH, 44691, USA
| |
Collapse
|
30
|
Acharya B, Lee S, Rouf Mian MA, Jun TH, McHale LK, Michel AP, Dorrance AE. Identification and mapping of quantitative trait loci (QTL) conferring resistance to Fusarium graminearum from soybean PI 567301B. Theor Appl Genet 2015; 128:827-38. [PMID: 25690715 PMCID: PMC4544499 DOI: 10.1007/s00122-015-2473-5] [Citation(s) in RCA: 3] [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] [Received: 09/12/2014] [Accepted: 01/31/2015] [Indexed: 05/16/2023]
Abstract
KEY MESSAGE A major novel QTL was identified in a recombinant inbred line population derived from a cross of 'Wyandot' × PI 567301B for Fusarium graminearum, a seed and seedling pathogen of soybean. Fusarium graminearum is now recognized as a primary pathogen of soybean, causing root, seed rot and seedling damping-off in North America. In a preliminary screen, 'Wyandot' and PI 567301B were identified with medium and high levels of partial resistance to F. graminearum, respectively. The objective of this study was to characterise resistance towards F. graminearum using 184 recombinant inbred lines (RILs) derived from a cross of 'Wyandot' × PI 567301B. The parents and the RILs of the mapping population were evaluated for resistance towards F. graminearum using the rolled towel assay in a randomized incomplete block design. A genetic map was constructed from 2545 SNP markers and 2 SSR markers by composite interval mapping. One major and one minor QTL were identified on chromosomes 8 and 6, respectively, which explained 38.5 and 8.1 % of the phenotypic variance. The major QTL on chromosome 8 was mapped to a 300 kb size genomic region of the Williams 82 sequence. Annotation of this region indicates that there are 39 genes including the Rhg4 locus for soybean cyst nematode (SCN) resistance. Based on previous screens, PI 567301B is susceptible to SCN. Fine mapping of this locus will assist in cloning these candidate genes as well as identifying DNA markers flanking the QTL that can be used in marker-assisted breeding to develop cultivars with high levels of resistance to F. graminearum.
Collapse
Affiliation(s)
- Bhupendra Acharya
- Department of Plant Pathology, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691 USA
| | - Sungwoo Lee
- Department of Entomology, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691 USA
- Present Address: Department of Crop Science, North Carolina State University, 3127 Ligon Street, Raleigh, NC 27607 USA
| | - M. A. Rouf Mian
- USDA-ARS and Department of Horticulture and Crop Science, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691 USA
- Present Address: USDA-ARS, Soybean Nitrogen Fixation Unit, Raleigh, NC 27606 USA
| | - Tae-Hwan Jun
- Department of Entomology, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691 USA
- Present Address: Department of Plant Bioscience, Pusan National University, Busan, 609-735 South Korea
| | - Leah K. McHale
- Department of Horticulture and Crop Science, The Ohio State University, 2021 Coffey Road, Columbus, OH 43210 USA
| | - Andrew P. Michel
- Department of Entomology, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691 USA
| | - Anne E. Dorrance
- Department of Plant Pathology, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691 USA
| |
Collapse
|
31
|
Prince SJ, Song L, Qiu D, Maldonado Dos Santos JV, Chai C, Joshi T, Patil G, Valliyodan B, Vuong TD, Murphy M, Krampis K, Tucker DM, Biyashev R, Dorrance AE, Maroof MAS, Xu D, Shannon JG, Nguyen HT. Genetic variants in root architecture-related genes in a Glycine soja accession, a potential resource to improve cultivated soybean. BMC Genomics 2015; 16:132. [PMID: 25765991 PMCID: PMC4354765 DOI: 10.1186/s12864-015-1334-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 02/09/2015] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Root system architecture is important for water acquisition and nutrient acquisition for all crops. In soybean breeding programs, wild soybean alleles have been used successfully to enhance yield and seed composition traits, but have never been investigated to improve root system architecture. Therefore, in this study, high-density single-feature polymorphic markers and simple sequence repeats were used to map quantitative trait loci (QTLs) governing root system architecture in an inter-specific soybean mapping population developed from a cross between Glycine max and Glycine soja. RESULTS Wild and cultivated soybean both contributed alleles towards significant additive large effect QTLs on chromosome 6 and 7 for a longer total root length and root distribution, respectively. Epistatic effect QTLs were also identified for taproot length, average diameter, and root distribution. These root traits will influence the water and nutrient uptake in soybean. Two cell division-related genes (D type cyclin and auxin efflux carrier protein) with insertion/deletion variations might contribute to the shorter root phenotypes observed in G. soja compared with cultivated soybean. Based on the location of the QTLs and sequence information from a second G. soja accession, three genes (slow anion channel associated 1 like, Auxin responsive NEDD8-activating complex and peroxidase), each with a non-synonymous single nucleotide polymorphism mutation were identified, which may also contribute to changes in root architecture in the cultivated soybean. In addition, Apoptosis inhibitor 5-like on chromosome 7 and slow anion channel associated 1-like on chromosome 15 had epistatic interactions for taproot length QTLs in soybean. CONCLUSION Rare alleles from a G. soja accession are expected to enhance our understanding of the genetic components involved in root architecture traits, and could be combined to improve root system and drought adaptation in soybean.
Collapse
Affiliation(s)
- Silvas J Prince
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
| | - Li Song
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
| | - Dan Qiu
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
| | - Joao V Maldonado Dos Santos
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
| | - Chenglin Chai
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
| | - Trupti Joshi
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
- Department of Computer Science, University of Missouri, Columbia, MO, 65211, USA.
| | - Gunvant Patil
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
| | - Babu Valliyodan
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
| | - Tri D Vuong
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
| | - Mackensie Murphy
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
| | - Konstantinos Krampis
- Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA.
| | - Dominic M Tucker
- Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA.
| | - Ruslan Biyashev
- Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA.
| | - Anne E Dorrance
- Department of Plant Pathology, The Ohio State University, OARDC, Wooster, OH, 44691, USA.
| | - M A Saghai Maroof
- Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA.
| | - Dong Xu
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
- Department of Computer Science, University of Missouri, Columbia, MO, 65211, USA.
| | - J Grover Shannon
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
| | - Henry T Nguyen
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
| |
Collapse
|
32
|
Lin J, Guo J, Finer J, Dorrance AE, Redinbaugh MG, Qu F. The bean pod mottle virus RNA2-encoded 58-kilodalton protein P58 is required in cis for RNA2 accumulation. J Virol 2014; 88:3213-22. [PMID: 24390330 PMCID: PMC3957913 DOI: 10.1128/jvi.03301-13] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [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: 11/08/2013] [Accepted: 12/24/2013] [Indexed: 01/03/2023] Open
Abstract
UNLABELLED Bean pod mottle virus (BPMV) is a bipartite, positive-sense (+) RNA plant virus in the Secoviridae family. Its RNA1 encodes proteins required for genome replication, whereas RNA2 primarily encodes proteins needed for virion assembly and cell-to-cell movement. However, the function of a 58-kDa protein (P58) encoded by RNA2 has not been resolved. P58 and the movement protein (MP) of BPMV are two largely identical proteins differing only at their N termini, with P58 extending MP upstream by 102 amino acid residues. In this report, we unveil a unique role for P58. We show that BPMV RNA2 accumulation in infected cells was abolished when the start codon of P58 was eliminated. The role of P58 does not require the region shared by MP, as RNA2 accumulation in individual cells remained robust even when most of the MP coding sequence was removed. Importantly, the function of P58 required the P58 protein, rather than its coding RNA, as compensatory mutants could be isolated that restored RNA2 accumulation by acquiring new start codons upstream of the original one. Most strikingly, loss of P58 function could not be complemented by P58 provided in trans, suggesting that P58 functions in cis to selectively promote the accumulation of RNA2 copies that encode a functional P58 protein. Finally, we found that all RNA1-encoded proteins are cis-acting relative to RNA1. Together, our results suggest that P58 probably functions by recruiting the RNA1-encoded polyprotein to RNA2 to enable RNA2 reproduction. IMPORTANCE Bean pod mottle virus (BPMV) is one of the most important pathogens of the crop plant soybean, yet its replication mechanism is not well understood, hindering the development of knowledge-based control measures. The current study examined the replication strategy of BPMV RNA2, one of the two genomic RNA segments of this virus, and established an essential role for P58, one of the RNA2-encoded proteins, in the process of RNA2 replication. Our study demonstrates for the first time that P58 functions preferentially with the very RNA from which it is translated, thus greatly advancing our understanding of the replication mechanisms of this and related viruses. Furthermore, this study is important because it provides a potential target for BPMV-specific control, and hence could help to mitigate soybean production losses caused by this virus.
Collapse
Affiliation(s)
- Junyan Lin
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, USA
| | - Jiangbo Guo
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, USA
- School of Mathematics, Physics, and Biological Engineering, Inner Mongolia University of Science and Technology, Baotou, China
| | - John Finer
- Department of Horticulture and Crop Science, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, USA
| | - Anne E. Dorrance
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, USA
| | - Margaret G. Redinbaugh
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, USA
- USDA-ARS, Corn and Soybean Research Unit, Wooster, Ohio, USA
| | - Feng Qu
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, USA
| |
Collapse
|
33
|
Lee S, Mian MAR, Sneller CH, Wang H, Dorrance AE, McHale LK. Joint linkage QTL analyses for partial resistance to Phytophthora sojae in soybean using six nested inbred populations with heterogeneous conditions. Theor Appl Genet 2014; 127:429-44. [PMID: 24247235 DOI: 10.1007/s00122-013-2229-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Accepted: 10/31/2013] [Indexed: 05/10/2023]
Abstract
Partial resistance to Phytophthora sojae in soybean is controlled by multiple quantitative trait loci (QTL). With traditional QTL mapping approaches, power to detect such QTL, frequently of small effect, can be limited by population size. Joint linkage QTL analysis of nested recombinant inbred line (RIL) populations provides improved power to detect QTL through increased population size, recombination, and allelic diversity. However, uniform development and phenotyping of multiple RIL populations can prove difficult. In this study, the effectiveness of joint linkage QTL analysis was evaluated on combinations of two to six nested RIL populations differing in inbreeding generation, phenotypic assay method, and/or marker set used in genotyping. In comparison to linkage analysis in a single population, identification of QTL by joint linkage analysis was only minimally affected by different phenotypic methods used among populations once phenotypic data were standardized. In contrast, genotyping of populations with only partially overlapping sets of markers had a marked negative effect on QTL detection by joint linkage analysis. In total, 16 genetic regions with QTL for partial resistance against P. sojae were identified, including four novel QTL on chromosomes 4, 9, 12, and 16, as well as significant genotype-by-isolate interactions. Resistance alleles from PI 427106 or PI 427105B contributed to a major QTL on chromosome 18, explaining 10-45% of the phenotypic variance. This case study provides guidance on the application of joint linkage QTL analysis of data collected from populations with heterogeneous assay conditions and a genetic framework for partial resistance to P. sojae.
Collapse
Affiliation(s)
- Sungwoo Lee
- Department of Horticulture and Crop Science, The Ohio State University, 1680 Madison Avenue, Wooster, OH, 44691, USA,
| | | | | | | | | | | |
Collapse
|
34
|
Abstract
Soybean vein necrosis-associated virus (SVNaV), a newly discovered tospovirus that infects soybean, was first described as widespread in a number of southern and midwestern states, but so far has not been reported in Ohio (1). Here we describe its occurrence in six different soybean leaf samples collected from five Ohio counties: Champaign, Hardin, Sandusky, Seneca, and Wyandot. Specifically, SVNaV was initially identified through a comprehensive survey during the summer of 2011 that used high throughput sequencing to detect genome sequences of viruses present in a pool of 110 field samples collected from 24 Ohio counties. Three assembled contigs, with sizes of 7,551, 4,937, and 1,554 nucleotides (nt) respectively, share 99% nt identity with the three SVNaV genomic RNAs (L, M, and S), and thus constitute partial sequences of the SVNaV Ohio (OH) isolate. The distribution of this virus was further delineated using reverse transcription (RT)-PCR with primers SVNaV-1734F (5' CCATCTTTCTTTCCAGGCATTTCA 3') and SVNaV-S-2421R (5' GATTCAAGTTCAGCGAGTTCTACAA 3'). All plants from which the SVNaV-positive samples were collected showed typical virus symptoms, including systemic mosaic accompanied by leaf deformation, chlorosis, vein necrosis, and rusty spots on mature leaves. These symptoms are largely consistent with the previous report by Zhou and colleagues (1). Intriguingly, further analysis with RT-PCR revealed that five out of the six SVNaV-positive samples also contained a second virus, with Bean pod mottle virus found in four of the samples, and Tobacco ringspot virus in the fifth. Since it is not yet possible to initiate SVNaV infection mechanically, it is difficult to determine whether the co-infecting viruses contribute to the disease symptoms and yield losses. It should be noted that SVNaV may have been in Ohio for some time since symptoms similar to those reported by Zhou and colleagues (1) have been observed in soybean fields of this state since at least 2009. Furthermore, while in 2011 these symptoms were observed in only a few fields, as reflected by the detection of SVNaV in six of the 110 samples, the 2012 growing season has seen a big jump of symptomatic plants and fields. The current report confirms its presence with molecular evidence and lays the groundwork for further assessment of its impact on soybean production. Reference: (1) J. Zhou et al. Virus Genes 43:289, 2011.
Collapse
Affiliation(s)
- J Han
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, 44691
| | - L L Domier
- United States Department of Agriculture, Agricultural Research Service, Department of Crop Sciences, University of Illinois, Urbana, 61810
| | - A E Dorrance
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, 44691
| | - F Qu
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, 44691
| |
Collapse
|
35
|
Lee S, Mian MAR, McHale LK, Wang H, Wijeratne AJ, Sneller CH, Dorrance AE. Novel quantitative trait loci for partial resistance to Phytophthora sojae in soybean PI 398841. Theor Appl Genet 2013; 126:1121-32. [PMID: 23354974 PMCID: PMC3607739 DOI: 10.1007/s00122-013-2040-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 12/21/2012] [Indexed: 05/08/2023]
Abstract
Phytophthora root and stem rot caused by Phytophthora sojae Kaufmann and Gerdemann is one of the most severe soybean [Glycine max (L.) Merr] diseases in the USA. Partial resistance is as effective in managing this disease as single-gene (Rps gene)-mediated resistance and is more durable. The objective of this study was to identify quantitative trait loci (QTL) associated with partial resistance to P. sojae in PI 398841, which originated from South Korea. A population of 305 F7:8 recombinant inbred lines derived from a cross of OX20-8 × PI 398841 was used to evaluate partial resistance against P. sojae isolate C2S1 using a tray test. Composite interval mapping using a genome-wide logarithm of odd (LOD) threshold detected three QTL on chromosomes 1, 13, and 18, which individually explained 4-16 % of the phenotypic variance. Seven additional QTL, accounting for 2-3 % of phenotypic variance each, were identified using chromosome-wide LOD thresholds. Seven of the ten QTL for resistance to P. sojae were contributed by PI 398841. Seven QTL co-localized with known Rps genes and previously reported QTL for soil-borne root pathogens, isoflavone, and seed oil. Three QTL on chromosomes 3, 13, and 18 co-localized with known Rps genes, but PI 398841 did not exhibit an Rps gene-mediated resistance response following inoculation with 48 different isolates of P. sojae. PI 398841 is potentially a source of novel genes for improving soybean cultivars for partial resistance to P. sojae.
Collapse
Affiliation(s)
- Sungwoo Lee
- Department of Horticulture and Crop Science, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691 USA
| | - M. A. Rouf Mian
- USDA-ARS and Department of Horticulture and Crop Science, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691 USA
| | - Leah K. McHale
- Department of Horticulture and Crop Science, The Ohio State University, 2021 Coffey Road, Columbus, OH 43210 USA
| | - Hehe Wang
- Department of Plant Pathology, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691 USA
| | - Asela J. Wijeratne
- The Molecular and Cellular Imaging Center/Ohio Agricultural Research and Development Center, 1680 Madison Avenue, Wooster, OH 44691 USA
| | - Clay H. Sneller
- Department of Horticulture and Crop Science, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691 USA
| | - Anne E. Dorrance
- Department of Plant Pathology, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691 USA
| |
Collapse
|
36
|
Wang H, Wijeratne A, Wijeratne S, Lee S, Taylor CG, St Martin SK, McHale L, Dorrance AE. Dissection of two soybean QTL conferring partial resistance to Phytophthora sojae through sequence and gene expression analysis. BMC Genomics 2012; 13:428. [PMID: 22925529 PMCID: PMC3443417 DOI: 10.1186/1471-2164-13-428] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2012] [Accepted: 08/14/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Phytophthora sojae is the primary pathogen of soybeans that are grown on poorly drained soils. Race-specific resistance to P. sojae in soybean is gene-for-gene, although in many areas of the US and worldwide there are populations that have adapted to the most commonly deployed resistance to P. sojae ( Rps) genes. Hence, this system has received increased attention towards identifying mechanisms and molecular markers associated with partial resistance to this pathogen. Several quantitative trait loci (QTL) have been identified in the soybean cultivar 'Conrad' that contributes to the expression of partial resistance to multiple P. sojae isolates. RESULTS In this study, two of the Conrad QTL on chromosome 19 were dissected through sequence and expression analysis of genes in both resistant (Conrad) and susceptible ('Sloan') genotypes. There were 1025 single nucleotide polymorphisms (SNPs) in 87 of 153 genes sequenced from Conrad and Sloan. There were 304 SNPs in 54 genes sequenced from Conrad compared to those from both Sloan and Williams 82, of which 11 genes had SNPs unique to Conrad. Eleven of 19 genes in these regions analyzed with qRT-PCR had significant differences in fold change of transcript abundance in response to infection with P. sojae in lines with QTL haplotype from the resistant parent compared to those with the susceptible parent haplotype. From these, 8 of the 11 genes had SNPs in the upstream, untranslated region, exon, intron, and/or downstream region. These 11 candidate genes encode proteins potentially involved in signal transduction, hormone-mediated pathways, plant cell structural modification, ubiquitination, and basal resistance. CONCLUSIONS These findings may indicate a complex defense network with multiple mechanisms underlying these two soybean QTL conferring resistance to P. sojae. SNP markers derived from these candidate genes can contribute to fine mapping of QTL and marker assisted breeding for resistance to P. sojae.
Collapse
Affiliation(s)
- Hehe Wang
- The Department of Plant Pathology, The Ohio State University, Wooster, OH 44691, USA
| | - Asela Wijeratne
- Molecular and Cellular Imaging Center, OARDC, Wooster, OH 44691, USA
| | - Saranga Wijeratne
- Molecular and Cellular Imaging Center, OARDC, Wooster, OH 44691, USA
| | - Sungwoo Lee
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH 43210, USA
| | - Christopher G Taylor
- The Department of Plant Pathology, The Ohio State University, Wooster, OH 44691, USA
| | - Steven K St Martin
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH 43210, USA
| | - Leah McHale
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH 43210, USA
| | - Anne E Dorrance
- The Department of Plant Pathology, The Ohio State University, Wooster, OH 44691, USA
| |
Collapse
|
37
|
Luster DG, McMahon MB, Edwards HH, Boerma BL, Lewis Ivey ML, Miller SA, Dorrance AE. Novel Phakopsora pachyrhizi extracellular proteins are ideal targets for immunological diagnostic assays. Appl Environ Microbiol 2012; 78:3890-5. [PMID: 22447596 PMCID: PMC3346385 DOI: 10.1128/aem.07079-11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [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: 09/30/2011] [Accepted: 03/14/2012] [Indexed: 11/20/2022] Open
Abstract
Phakopsora pachyrhizi, the causal agent of Asian soybean rust (ASR), continues to spread across the southeast and midsouth regions of the United States, necessitating the use of fungicides by producers. Our objective in this research was to identify ASR proteins expressed early during infection for the development of immunodiagnostic assays. We have identified and partially characterized a small gene family encoding extracellular proteins in the P. pachyrhizi urediniospore wall, termed PHEPs (for Phakopsora extracellular protein). Two highly expressed protein family members, PHEP 107 and PHEP 369, were selected as ideal immunodiagnostic targets for antibody development, after we detected PHEPs in plants as early as 3 days postinfection (dpi). Monoclonal antibodies (MAbs; 2E8E5-1 and 3G6H7-3) generated against recombinant PHEP 369 were tested for sensitivity against the recombinant protein and extracts from ASR-infected plants and for specificity against a set of common soybean pathogens. These antibodies should prove applicable in immunodiagnostic assays to detect infected soybeans and to identify ASR spores from sentinel surveillance plots.
Collapse
Affiliation(s)
- Douglas G Luster
- USDA, Agricultural Research Service, Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD, USA
| | | | | | | | | | | | | |
Collapse
|
38
|
Ellis ML, Paul PA, Dorrance AE, Broders KD. Two new species of Pythium, P. schmitthenneri and P. selbyi pathogens of corn and soybean in Ohio. Mycologia 2012; 104:477-87. [PMID: 22123655 DOI: 10.3852/11-162] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Two new species of Pythium, pathogens of corn and soybean in Ohio, are described. Pythium schmitthenneri sp. nov. and Pythium selbyi sp. nov. both have morphological and sequence characteristics that place them in clade E1 of the genus Pythium. Morphology and sequence analysis of the ITS1-5.8S-ITS2 regions of these species were different from previously described species. The ITS region of Pythium schmitthenneri was 99.9% similar to P. acrogynum and 99.8% similar to P. hypogynum. All three species are characterized by globose to limoniform sporangia and plerotic oospores. Pythium schmitthenneri has mostly diclinous antheridia, compared to the strictly hypogynous antheridia of P. acrogynum and P. hypogynum. The temperature for growth of P. schmitthenneri is below 4 C to 32 C, and optimum growth is 18-25 C compared to 31-34 C for P. hypogynum. The ITS region of P. selbyi was 97.1% similar to P. longandrum and 97.5% similar to P. longisporangium. All three species are characterized by globose sporangia, mostly plerotic oospores, with one to two oospores per oogonium, and hypogynous or monoclinous antheridia. The temperature for growth of P. selbyi is below 4 to 32 C, with an optimum 18-25 C. These new species were widely dispersed throughout the soybean- and corn-producing regions in Ohio, making their characterization critical for managing the Pythium complex that causes seedling and root-rot disease in Ohio soybean and corn fields.
Collapse
Affiliation(s)
- Margaret L Ellis
- Department of Plant Pathology, Ohio State University, Wooster, OH, USA
| | | | | | | |
Collapse
|
39
|
Zhang X, Sato S, Ye X, Dorrance AE, Morris TJ, Clemente TE, Qu F. Robust RNAi-based resistance to mixed infection of three viruses in soybean plants expressing separate short hairpins from a single transgene. Phytopathology 2011; 101:1264-9. [PMID: 21999157 DOI: 10.1094/phyto-02-11-0056] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Transgenic plants expressing double-stranded RNA (dsRNA) of virus origin have been previously shown to confer resistance to virus infections through the highly conserved RNA-targeting process termed RNA silencing or RNA interference (RNAi). In this study we applied this strategy to soybean plants and achieved robust resistance to multiple viruses with a single dsRNA-expressing transgene. Unlike previous reports that relied on the expression of one long inverted repeat (IR) combining sequences of several viruses, our improved strategy utilized a transgene designed to express several shorter IRs. Each of these short IRs contains highly conserved sequences of one virus, forming dsRNA of less than 150 bp. These short dsRNA stems were interspersed with single-stranded sequences to prevent homologous recombination during the transgene assembly process. Three such short IRs with sequences of unrelated soybean-infecting viruses (Alfalfa mosaic virus, Bean pod mottle virus, and Soybean mosaic virus) were assembled into a single transgene under control of the 35S promoter and terminator of Cauliflower mosaic virus. Three independent transgenic lines were obtained and all of them exhibited strong systemic resistance to the simultaneous infection of the three viruses. These results demonstrate the effectiveness of this very straight forward strategy for engineering RNAi-based virus resistance in a major crop plant. More importantly, our strategy of construct assembly makes it easy to incorporate additional short IRs in the transgene, thus expanding the spectrum of virus resistance. Finally, this strategy could be easily adapted to control virus problems of other crop plants.
Collapse
Affiliation(s)
- Xiuchun Zhang
- Department of Plant Pathology, the Ohio State University, Wooster, OH, USA
| | | | | | | | | | | | | |
Collapse
|
40
|
Stewart S, Wickramasinghe D, Dorrance AE, Robertson AE. Comparison of three microsatellite analysis methods for detecting genetic diversity in Phytophthora sojae (Stramenopila: Oomycete). Biotechnol Lett 2011; 33:2217-23. [PMID: 21744147 PMCID: PMC3181407 DOI: 10.1007/s10529-011-0682-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 06/22/2011] [Indexed: 11/29/2022]
Abstract
Analysis of an organism's genetic diversity requires a method that gives reliable, reproducible results. Microsatellites are robust markers, however, detection of allele sizes can be difficult with some systems as well as consistency among laboratories. In this study, our two laboratories used 219 isolates of Phytophthora sojae to compare three microsatellite methods. Two capillary electrophoresis methods, the Applied Biosystems 3730 Genetic Analyzer and the CEQ 8000 Genetic Analysis system, detected an average of 2.4-fold more alleles compared to gel electrophoresis with a mean of 8.8 and 3.6 alleles per locus using capillary and gel methods, respectively. The two capillary methods were comparable, although allele sizes differed consistently by an average of 3.2 bp across isolates. Differences between capillary methods could be overcome if reference standard DNA genotypes are shared between collaborating laboratories.
Collapse
Affiliation(s)
- Silvina Stewart
- Department of Plant Pathology, Iowa State University, Ames, IA 50011, USA.
| | | | | | | |
Collapse
|
41
|
Ellis ML, Broders KD, Paul PA, Dorrance AE. Infection of Soybean Seed by Fusarium graminearum and Effect of Seed Treatments on Disease Under Controlled Conditions. Plant Dis 2011; 95:401-407. [PMID: 30743330 DOI: 10.1094/pdis-05-10-0317] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Fusarium graminearum causes seed decay and damping-off of soybean. This study evaluated the effect of inoculum density of F. graminearum, temperature, and fungicide seed treatments on disease development. To determine the optimum conditions for disease development, individual soybean seed was inoculated with 100 μl of a suspension of 2.5 × 102, 2.5 × 103, 2.5 × 104, or 2.5 × 105 macroconidia/ml in a rolled-towel assay at temperatures of 18, 22, and 25°C. Inoculum concentrations of 2.5 × 104 macroconidia/ml or higher were necessary for optimum disease development at all temperatures. The efficacy of captan, fludioxonil, mefenoxam + fludioxonil, azoxystrobin, trifloxystrobin, and pyraclostrobin as seed treatments was then evaluated with the same assay at 2.5 × 104 and 2.5 × 105 macroconidia/ml. Seed treated with captan at 61.9 g a.i. or fludioxonil at 2.5 or 5.0 g a.i. per 100 kg developed smaller lesions than other seed treatments and the nontreated control. Based on these results, there are limited choices in fungicide seed treatments for managing this seedling disease, and it is possible that shifts in seed treatment products may have played a role in the recent emergence of this soybean pathogen.
Collapse
Affiliation(s)
- M L Ellis
- Department of Plant Pathology, The Ohio State University, Wooster 44691
| | - K D Broders
- Department of Plant Pathology, The Ohio State University, Wooster 44691
| | - P A Paul
- Department of Plant Pathology, The Ohio State University, Wooster 44691
| | - A E Dorrance
- Department of Plant Pathology, The Ohio State University, Wooster 44691
| |
Collapse
|
42
|
Zelaya-Molina LX, Ortega MA, Dorrance AE. Easy and efficient protocol for oomycete DNA extraction suitable for population genetic analysis. Biotechnol Lett 2010; 33:715-20. [PMID: 21107649 PMCID: PMC3061009 DOI: 10.1007/s10529-010-0478-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2010] [Accepted: 11/12/2010] [Indexed: 11/30/2022]
Abstract
A simple and rapid DNA extraction protocol capable of obtaining high-quality and quantity DNA from a large number of individuals is essential for assaying population and phylogenetic studies of plant pathogens. Most DNA extraction protocols used with oomycetes are relatively lengthy and cumbersome for high throughput analysis. Commercial kits are widely used, but low quantities of DNA are usually obtained, and with large scale analysis multiple isolations are required. A protocol for DNA isolation from Phytophthora and Pythium suitable for the evaluation of a large set of molecular markers was modified from one previously developed for soybean seed. There was a one to three fold increase in the amount of DNA that was extracted using the modified protocol compared to a commercial kit. The DNA obtained using the modified protocol was suitable for the amplification of microsatellite markers as well as the ITS region. This protocol is inexpensive, easy, quick, and efficient in terms of the volume of reagents and the number of steps involved in the procedure. The method may be applicable to other oomycetes and effectively implemented in other laboratories.
Collapse
Affiliation(s)
- Lily X Zelaya-Molina
- Department of Plant Pathology, Ohio State University-OARDC, Wooster, OH 44691, USA.
| | | | | |
Collapse
|
43
|
Abstract
Brown spot, caused by Septoria glycines, is the most common foliar disease of soybean in Ohio, but its economic impact has not been assessed on modern cultivars. Therefore, the objectives of this study were to (i) evaluate the effect of S. glycines on soybean yield and (ii) evaluate the efficacy of strobilurin- and triazole-based fungicides on the control of brown spot. Yield loss associated with S. glycines was determined using weekly applications of chlorothalonil. The efficacy of azoxystrobin, pyraclostrobin, tebuconazole, and flutriafol alone and in combinations were also assessed using applications at the R3 and R5 growth stages at two locations over 3 years. Significantly different levels of brown spot developed following applications of chlorothalonil, with mean yield differences between treated and nontreated plots ranging from 196 to 293 kg/ha. Pyraclostrobin and azoxystrobin applied at the R3 growth stage significantly reduced final levels of brown spot; however, significant increases in yield occurred in only three of the six location-years. Triazoles, flutriafol and tebuconazole, applied at R3 or R5 did not significantly decrease levels of brown spot or impact yield. More data on the accurate timing of fungicides are still required to establish a long-term management program for this disease, and resistance to brown spot should be monitored in soybean cultivar development to prevent future yield losses.
Collapse
Affiliation(s)
- Christian D Cruz
- Department of Plant Pathology, The Ohio State University, Wooster 44691
| | - Dennis Mills
- Department of Plant Pathology, The Ohio State University, Wooster 44691
| | - Pierce A Paul
- Department of Plant Pathology, The Ohio State University, Wooster 44691
| | - Anne E Dorrance
- Department of Plant Pathology, The Ohio State University, Wooster 44691
| |
Collapse
|
44
|
Wang H, Waller L, Tripathy S, St. Martin SK, Zhou L, Krampis K, Tucker DM, Mao Y, Hoeschele I, Saghai Maroof M, Tyler BM, Dorrance AE. Analysis of Genes Underlying Soybean Quantitative Trait Loci Conferring Partial Resistance to
Phytophthora sojae. Plant Genome 2010. [PMID: 0 DOI: 10.3835/plantgenome2009.12.0029] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Affiliation(s)
- Hehe Wang
- Dep. of Plant PathologyThe Ohio State Univ.WoosterOH44691
| | - LaChelle Waller
- Virginia Bioinformatics Inst., Virginia Polytechnic Inst. and State Univ.BlacksburgVA24061
| | - Sucheta Tripathy
- Virginia Bioinformatics Inst., Virginia Polytechnic Inst. and State Univ.BlacksburgVA24061
| | | | - Lecong Zhou
- Virginia Bioinformatics Inst., Virginia Polytechnic Inst. and State Univ.BlacksburgVA24061
- Dep. of Crop and Soil Environmental SciencesVirginia Polytechnic Inst. and State Univ.BlacksburgVA24061
| | - Konstantinos Krampis
- Virginia Bioinformatics Inst., Virginia Polytechnic Inst. and State Univ.BlacksburgVA24061
- Dep. of Crop and Soil Environmental SciencesVirginia Polytechnic Inst. and State Univ.BlacksburgVA24061
| | - Dominic M. Tucker
- Dep. of Crop and Soil Environmental SciencesVirginia Polytechnic Inst. and State Univ.BlacksburgVA24061
| | - Yongcai Mao
- Virginia Bioinformatics Inst., Virginia Polytechnic Inst. and State Univ.BlacksburgVA24061
| | - Ina Hoeschele
- Virginia Bioinformatics Inst., Virginia Polytechnic Inst. and State Univ.BlacksburgVA24061
- Dep. of StatisticsVirginia Polytechnic Inst. and State Univ.BlacksburgVA24061
| | - M.A. Saghai Maroof
- Dep. of Crop and Soil Environmental SciencesVirginia Polytechnic Inst. and State Univ.BlacksburgVA24061
| | - Brett M. Tyler
- Virginia Bioinformatics Inst., Virginia Polytechnic Inst. and State Univ.BlacksburgVA24061
| | | |
Collapse
|
45
|
Redinbaugh MG, Molineros JE, Vacha J, Berry SA, Hammond RB, Madden LV, Dorrance AE. Bean pod mottle virus Spread in Insect-Feeding-Resistant Soybean. Plant Dis 2010; 94:265-270. [PMID: 30754260 DOI: 10.1094/pdis-94-2-0265] [Citation(s) in RCA: 11] [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
Bean pod mottle virus (BPMV) infection reduces yield and seed quality in soybean. To test the hypothesis that virus incidence and movement within plots would be reduced in soybean with resistance to feeding by the virus' bean leaf beetle (Cerotoma trifurcata) vector, BPMV spread was evaluated in five soybean genotypes at two inoculum levels over 2 years at two locations in Ohio. Soybean genotypes included two insect-feeding-susceptible genotypes (Williams 82 and Resnik), two insect-feeding-resistant, semidwarf genotypes (HC95-15 and HC95-24), and an insect-feeding-susceptible, semidwarf genotype (Troll). BPMV incidence was assessed in individual plants at growth stages R5/R6 and R7/R8 using enzyme-linked immunosorbent assay. Beetle feeding was visually assessed in 2004. Data for infection of individual plants were analyzed using a generalized linear mixed model, with a binomial distribution and logit-link. Within plots, BPMV incidence was highest in Resnik and Williams 82 and significantly lower in Troll. Incidence in HC95-15 was not significantly different than in Williams 82 and Resnik but incidence in HC95-24 was lower than in Resnik. BPMV incidence was also significantly (P < 0.05) affected by year, location, inoculum level and sampling date, with increasing incidence over time and higher incidence at the higher inoculum level. Beetle feeding damage was affected by the interaction of location-genotype. Significant spatial aggregation of infected plants was found for most plots but aggregation was independent of host genotype and inoculum level. Although the results indicate that BPMV infection varied by genotype, they do not support the hypothesis that insect-feeding resistance is sufficient to reduce the incidence and spread of BPMV.
Collapse
Affiliation(s)
- Margaret G Redinbaugh
- United States Department of Agriculture-Agricultural Research Service, Corn and Soybean Research, and Department of Plant Pathology, The Ohio State University-Ohio Agricultural Research and Development Center (OARDC), Wooster 44691
| | | | | | | | | | | | - Anne E Dorrance
- Department of Plant Pathology, The Ohio State University-OARDC
| |
Collapse
|
46
|
Zelaya-Molina LX, Ellis ML, Berry SA, Dorrance AE. First Report of Phytophthora sansomeana Causing Wilting and Stunting on Corn in Ohio. Plant Dis 2010; 94:125. [PMID: 30754406 DOI: 10.1094/pdis-94-1-0125c] [Citation(s) in RCA: 4] [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
During the spring of 2004, corn seedlings with symptoms of wilting and stunting were observed in corn fields with emergence problems in Madison and Brown counties, Ohio. Phytophthora isolates were recovered from sections of root tissue of diseased seedlings placed on dilute V8 media amended with pentachloronitrobenzene, iprodione, benlate, neomycin sulfate, and chloramphenicol. Colonies were rosaceous on potato dextrose agar, with a growth rate of 5 mm per day. Homothallic isolates with paragynous antheridia were observed on lima bean agar (LBA); oogonia were 35 to 50 μm in diameter. Sporangia were ovoid to obpyriform, nonpapillate, with an average size of 49 × 30 μm. Pathogenicity was tested on corn seeds using a petri dish assay with 3-day-old cultures on LBA and a sand-cornmeal cup test amended with inoculum from 7-day-old cultures on LBA (1). After 1 week in the petri dish assay, the seeds failed to germinate completely and were covered with white, fungal-like, aerial mycelia and the pathogen was recovered from brown discolored radicle roots. In the cup assay, 2-week-old seedlings developed the same symptoms observed in the field; the pathogen was also isolated from brown discolored roots. In both assays, no symptoms developed in the noninoculated controls. Both pathogenicity tests were repeated two times. Genomic DNA was extracted from mycelia of two isolates and the internal transcribed spacer (ITS) region was amplified and sequenced using ITS6/ITS4 primers (2). Both isolates had identical ITS sequences (GenBank Accession No. GQ853880). A BLAST search of the NCBI database showed 100% homology with the sequence of the haplotype isolate of Phytophthora sansomeana (Accession No. EU925375). P. sansomeana is a new species characterized principally by a large oogonial diameter (37 to 45 μm), rapid growth rate (7 to 10 mm/day), and an ITS sequence falling in Cooke's clade 8 (4). Pathogenicity tests, morphological characteristics, and the ITS sequence analysis indicate that P. samsomena is the causal agent of the symptoms observed on corn seedlings. P. sansomeana has been reported as a pathogen of soybean in Indiana, Douglas-fir in Oregon, and weeds in alfalfa fields in New York (4). To our knowledge, this is the first report of P. sansomeana infecting corn in Ohio, albeit other isolates have previously been recovered from soybean in the state. There are four previous reports of Phytophthora spp. affecting corn in the United States and Mexico (3). Crop rotation will have little effect in management of this pathogen since corn and soybean are produced in the same fields continuously throughout the state. References: (1) K. E. Broders et al. Plant. Dis. 91:727, 2007. (2) D. E. L. Cooke et al. Fungal Genet. Biol. 30:17, 2000. (3) D. F. Farr et al. Fungi on Plants and Plant Products in the United States. The American Phytopathological Society, St. Paul, MN. 1989. (4) E. M. Hansen et al. Mycologia 101:129, 2009.
Collapse
Affiliation(s)
- L X Zelaya-Molina
- Department of Plant Pathology, The Ohio State University-OARDC, Wooster 44691
| | - M L Ellis
- Department of Plant Pathology, The Ohio State University-OARDC, Wooster 44691
| | - S A Berry
- Department of Plant Pathology, The Ohio State University-OARDC, Wooster 44691
| | - A E Dorrance
- Department of Plant Pathology, The Ohio State University-OARDC, Wooster 44691
| |
Collapse
|
47
|
Dorrance AE, Robertson AE, Cianzo S, Giesler LJ, Grau CR, Draper MA, Tenuta AU, Anderson TR. Integrated Management Strategies for Phytophthora sojae Combining Host Resistance and Seed Treatments. Plant Dis 2009; 93:875-882. [PMID: 30754536 DOI: 10.1094/pdis-93-9-0875] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [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 sojae has re-emerged as a serious soybean pathogen in the past decade. This may be due in part to changes in resistance levels in current cultivars, adoption of P. sojae populations to deployed Rps genes, and highly favorable environments in the past decade. This multilocation study evaluated the effect of seed treatments on the incidence and severity of Phytophthora root and stem rot on soybeans with different combinations of Rps genes and levels of partial resistance. The efficacy of the seed treatments was highly variable across locations. Seed treatments (metalaxyl and mefenoxam) provided protection and increased yields across cultivars in locations where rain or irrigation occurred shortly after planting (Ohio, South Dakota, and Ontario). However, there were no significant differences in stand or yield consistently across cultivars in Iowa, Nebraska, Wisconsin, or Ohio, where heavy precipitation did not occur until later growth stages. The environment, levels of inoculum, and pathogen complex may have played a role in the different responses to the seed treatments and to the different combinations of Rps genes and levels of partial resistance to P. sojae in the cultivars. Fields that are poorly drained and have P. sojae populations with complex pathotypes may benefit the most from seed treatments. Individual fields where producers may see the greatest benefit to utilizing these integrated management strategies will need to be identified.
Collapse
Affiliation(s)
- A E Dorrance
- Department of Plant Pathology, The Ohio State University, OARDC, Wooster 44691
| | - A E Robertson
- Department of Plant Pathology, Iowa State University, Ames 50011-1020
| | - S Cianzo
- Department of Plant Pathology, Iowa State University, Ames 50011-1020
| | - L J Giesler
- Department of Plant Pathology, University of Nebraska, Lincoln 68583
| | - C R Grau
- Department of Plant Pathology, University of Wisconsin-Madison, Madison 53706-1598
| | - M A Draper
- formerly Plant Science Department, South Dakota State University, Brookings 57007-1090
| | - A U Tenuta
- Ontario Ministry of Agriculture, Food and Rural Affairs, Ridgetown, Ontario, Canada, N0L 2C0
| | - T R Anderson
- Agriculture and Agri-Food Canada, Harrow, Ontario, Canada, N0R 1G0
| |
Collapse
|
48
|
Broders KD, Wallhead MW, Austin GD, Lipps PE, Paul PA, Mullen RW, Dorrance AE. Association of soil chemical and physical properties with Pythium species diversity, community composition, and disease incidence. Phytopathology 2009; 99:957-67. [PMID: 19594315 DOI: 10.1094/phyto-99-8-0957] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A high-throughput baiting and identification process identified more than 7,000 isolates of Pythium from 88 locations in Ohio. Isolates were identified using direct-colony polymerase chain reaction followed by single-strand conformational polymorphism, and communities were assembled using the Jaccard similarity coefficient and cluster analysis. Both univariate and multivariate statistics were used to evaluate differences in soil properties between communities, and canonical discriminant analysis (CDA) was used to assess the strength of the association of soil variables within communities from 83 of the locations. In all, 21 species of Pythium were identified but only 6 were recovered from >40% of the locations. Five communities were formed using the cluster analysis, and significant differences were observed in disease incidence, as well as soil pH, calcium, magnesium, and cation exchange capacity between communities. Stepwise multiple discriminant analysis and CDA identified pH, calcium, magnesium, and field capacity as contributing the most to the separation of the five Pythium communities. There was a strong association between abiotic soil components and the structure of Pythium communities, as well as diversity of Pythium spp. collected from agronomic production fields in Ohio.
Collapse
Affiliation(s)
- K D Broders
- Department of Plant Pathology, School of Natural Resources, The Ohio State University, Wooster, OH 44691, USA
| | | | | | | | | | | | | |
Collapse
|
49
|
Abstract
A new species of Pythium isolated from soybean in Ohio is described. Pythium delawarii sp. nov. is characterized by globose internally proliferating sporangia, aplerotic oospores and diclinous antheridia that make broad lengthwise contact. Sporangia produce conspicuous papilla and germinate indirectly by producing zoospores via a vesicle and proliferate internally or the sporangia germinate directly with either one or more germ tubes. Pythium delawarii is pathogenic on soybean causing damping-off of seedlings. This oomycete can grow at 10-34 C with an optimum of 28 C. The sequence of the ITS1, 5.8S and ITS2 region of the rDNA did not match the sequence of any known Pythium species but was similar to P. citrinum, P. litorale and P. sterilum. P. delawarii can be distinguished from these three species based on the presence of aplerotic oospores and diclinous antheridia and the absence of hypogynous antheridia. Therefore biological, morphological and molecular data support the recognition of a new species.
Collapse
Affiliation(s)
- Kirk D Broders
- Department of Plant Pathology, Ohio State University, OARDC, Wooster, Ohio 44691, USA
| | | | | | | |
Collapse
|
50
|
Zhou L, Mideros SX, Bao L, Hanlon R, Arredondo FD, Tripathy S, Krampis K, Jerauld A, Evans C, St Martin SK, Maroof MAS, Hoeschele I, Dorrance AE, Tyler BM. Infection and genotype remodel the entire soybean transcriptome. BMC Genomics 2009; 10:49. [PMID: 19171053 PMCID: PMC2662884 DOI: 10.1186/1471-2164-10-49] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [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: 07/22/2008] [Accepted: 01/26/2009] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND High throughput methods, such as high density oligonucleotide microarray measurements of mRNA levels, are popular and critical to genome scale analysis and systems biology. However understanding the results of these analyses and in particular understanding the very wide range of levels of transcriptional changes observed is still a significant challenge. Many researchers still use an arbitrary cut off such as two-fold in order to identify changes that may be biologically significant. We have used a very large-scale microarray experiment involving 72 biological replicates to analyze the response of soybean plants to infection by the pathogen Phytophthora sojae and to analyze transcriptional modulation as a result of genotypic variation. RESULTS With the unprecedented level of statistical sensitivity provided by the high degree of replication, we show unambiguously that almost the entire plant genome (97 to 99% of all detectable genes) undergoes transcriptional modulation in response to infection and genetic variation. The majority of the transcriptional differences are less than two-fold in magnitude. We show that low amplitude modulation of gene expression (less than two-fold changes) is highly statistically significant and consistent across biological replicates, even for modulations of less than 20%. Our results are consistent through two different normalization methods and two different statistical analysis procedures. CONCLUSION Our findings demonstrate that the entire plant genome undergoes transcriptional modulation in response to infection and genetic variation. The pervasive low-magnitude remodeling of the transcriptome may be an integral component of physiological adaptation in soybean, and in all eukaryotes.
Collapse
Affiliation(s)
- Lecong Zhou
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
- Department of Crop and Soil Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Santiago X Mideros
- Department of Plant Pathology, The Ohio State University OARDC, Wooster, OH 44691, USA
| | - Lei Bao
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Regina Hanlon
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Felipe D Arredondo
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Sucheta Tripathy
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Konstantinos Krampis
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
- Department of Crop and Soil Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Adam Jerauld
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Clive Evans
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Steven K St Martin
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH 43210, USA
| | - MA Saghai Maroof
- Department of Crop and Soil Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Ina Hoeschele
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
- Department of Statistics, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Anne E Dorrance
- Department of Plant Pathology, The Ohio State University OARDC, Wooster, OH 44691, USA
| | - Brett M Tyler
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| |
Collapse
|