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Patel J, Allen TW, Buckley B, Chen P, Clubb M, Mozzoni LA, Orazaly M, Florez L, Moseley D, Rupe JC, Shrestha BK, Price PP, Ward BM, Koebernick J. Deciphering genetic factors contributing to enhanced resistance against Cercospora leaf blight in soybean ( Glycine max L.) using GWAS analysis. Front Genet 2024; 15:1377223. [PMID: 38798696 PMCID: PMC11116733 DOI: 10.3389/fgene.2024.1377223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 04/24/2024] [Indexed: 05/29/2024] Open
Abstract
Cercospora leaf blight (CLB), caused by Cercospora cf. flagellaris, C. kikuchii, and C. cf. sigesbeckiae, is a significant soybean [Glycine max (L.) Merr.] disease in regions with hot and humid conditions causing yield loss in the United States and Canada. There is limited information regarding resistant soybean cultivars, and there have been marginal efforts to identify the genomic regions underlying resistance to CLB. A Genome-Wide Association Study was conducted using a diverse panel of 460 soybean accessions from maturity groups III to VII to identify the genomic regions associated to the CLB disease. These accessions were evaluated for CLB in different regions of the southeastern United States over 3 years. In total, the study identified 99 Single Nucleotide Polymorphism (SNPs) associated with the disease severity and 85 SNPs associated with disease incidence. Across multiple environments, 47 disease severity SNPs and 23 incidence SNPs were common. Candidate genes within 10 kb of these SNPs were involved in biotic and abiotic stress pathways. This information will contribute to the development of resistant soybean germplasm. Further research is warranted to study the effect of pyramiding desirable genomic regions and investigate the role of identified genes in soybean CLB resistance.
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Affiliation(s)
- Jinesh Patel
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Tom W. Allen
- Delta Research and Extension Center, Mississippi State University, Stoneville, MS, United States
| | - Blair Buckley
- LSU AgCenter, Red River Research Station, Bossier City, LA, United States
| | - Pengyin Chen
- Fisher Delta Research Center, MO University of Missouri, Portageville, MO, United States
| | - Michael Clubb
- Fisher Delta Research Center, MO University of Missouri, Portageville, MO, United States
| | - Leandro A. Mozzoni
- Department of Crop, Soil, and Environmental Science, University of Arkansas, Fayetteville, AR, United States
| | - Moldir Orazaly
- Department of Crop, Soil, and Environmental Science, University of Arkansas, Fayetteville, AR, United States
| | - Liliana Florez
- Department of Crop, Soil, and Environmental Science, University of Arkansas, Fayetteville, AR, United States
| | - David Moseley
- Department of Crop, Soil, and Environmental Science, University of Arkansas, Fayetteville, AR, United States
| | - John C. Rupe
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR, United States
| | - Bishnu K. Shrestha
- LSU AgCenter, Macon Ridge Research Station, Winnsboro, LA, United States
| | - Paul P. Price
- LSU AgCenter, Macon Ridge Research Station, Winnsboro, LA, United States
| | - Brian M. Ward
- Department of Plant Pathology and Crop Physiology, LSU AgCenter, Baton Rouge, LA, United States
| | - Jenny Koebernick
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, United States
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Shrestha BK, Ward BM, Allen TW, da Silva ET, Zulli H, Dunford W, Doyle V, Bradley CA, Buckley B, Chen P, Clubb M, Kelly H, Koebernick J, Padgett B, Rupe JC, Sikora EJ, Spurlock TN, Thomas-Sharma S, Tolbert A, Zhou XG, Price PP. Characterization of QoI-Fungicide Resistance in Cercospora Isolates Associated with Cercospora Leaf Blight of Soybean from the Southern United States. PLANT DISEASE 2024; 108:149-161. [PMID: 37578368 DOI: 10.1094/pdis-03-23-0588-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Cercospora leaf blight (CLB) of soybean, caused by Cercospora cf. flagellaris, C. kikuchii, and C. cf. sigesbeckiae, is an economically important disease in the southern United States. Cultivar resistance to CLB is inconsistent; therefore, fungicides in the quinone outside inhibitor (QoI) class have been relied on to manage the disease. Approximately 620 isolates from plants exhibiting CLB were collected between 2018 and 2021 from 19 locations in eight southern states. A novel polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay based on two genes, calmodulin and histone h3, was developed to differentiate between the dominant species of Cercospora, C. cf. flagellaris, and C. cf. sigesbeckiae. A multilocus phylogenetic analysis of actin, calmodulin, histone h3, ITS rDNA, and transcription elongation factor 1-α was used to confirm PCR-RFLP results and identify remaining isolates. Approximately 80% of the isolates collected were identified as C. cf. flagellaris, while 15% classified as C. cf. sigesbeckiae, 2% as C. kikuchii, and 3% as previously unreported Cercospora species associated with CLB in the United States. PCR-RFLP of cytochrome b (cytb) identified QoI-resistance conferred by the G143A substitution. Approximately 64 to 83% of isolates were determined to be QoI-resistant, and all contained the G143A substitution. Results of discriminatory dose assays using azoxystrobin (1 ppm) were 100% consistent with PCR-RFLP results. To our knowledge, this constitutes the first report of QoI resistance in CLB pathogen populations from Alabama, Arkansas, Kentucky, Mississippi, Missouri, Tennessee, and Texas. In areas where high frequencies of resistance have been identified, QoI fungicides should be avoided, and fungicide products with alternative modes-of-action should be utilized in the absence of CLB-resistant soybean cultivars.
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Affiliation(s)
| | - Brian M Ward
- Department of Plant Pathology and Crop Physiology, LSU AgCenter, Baton Rouge, LA
| | - Tom W Allen
- Delta Research and Extension Center, Mississippi State University, Stoneville, MS
| | - Ernesto T da Silva
- Department of Plant Pathology and Crop Physiology, LSU AgCenter, Baton Rouge, LA
| | - Hannah Zulli
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA
| | - Will Dunford
- Department of Plant Pathology and Crop Physiology, LSU AgCenter, Baton Rouge, LA
| | - Vinson Doyle
- Department of Plant Pathology and Crop Physiology, LSU AgCenter, Baton Rouge, LA
| | - Carl A Bradley
- Department of Plant Pathology, University of Kentucky, Princeton, KY
| | - Blair Buckley
- Red River Research Station, LSU AgCenter, Bossier, LA
| | - Pengyin Chen
- Fisher Delta Research Center, University of Missouri, Portageville, MO
| | - Michael Clubb
- Fisher Delta Research Center, University of Missouri, Portageville, MO
| | - Heather Kelly
- West Tennessee Research and Education Center, University of Tennessee, Jackson, TN
| | - Jenny Koebernick
- Department of Crop, Soil, and Environmental Science, Auburn University, Auburn, AL
| | - Boyd Padgett
- Dean Lee Research and Extension Center, LSU AgCenter, Alexandria, LA
| | - John C Rupe
- Department of Crop, Soil, and Environmental Science, University of Arkansas, Fayetteville, AR
| | - Ed J Sikora
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL
| | - Terry N Spurlock
- Department of Crop, Soil, and Environmental Science, University of Arkansas, Fayetteville, AR
| | - Sara Thomas-Sharma
- Department of Plant Pathology and Crop Physiology, LSU AgCenter, Baton Rouge, LA
| | - Amanda Tolbert
- Department of Crop, Soil, and Environmental Science, University of Arkansas, Fayetteville, AR
| | - Xin-Gen Zhou
- Research and Extension Center, Texas A&M University, Beaumont, TX
| | - Paul P Price
- Macon Ridge Research Station, LSU AgCenter, Winnsboro, LA
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Lin F, Chhapekar SS, Vieira CC, Da Silva MP, Rojas A, Lee D, Liu N, Pardo EM, Lee YC, Dong Z, Pinheiro JB, Ploper LD, Rupe J, Chen P, Wang D, Nguyen HT. Breeding for disease resistance in soybean: a global perspective. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3773-3872. [PMID: 35790543 PMCID: PMC9729162 DOI: 10.1007/s00122-022-04101-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 04/11/2022] [Indexed: 05/29/2023]
Abstract
KEY MESSAGE This review provides a comprehensive atlas of QTLs, genes, and alleles conferring resistance to 28 important diseases in all major soybean production regions in the world. Breeding disease-resistant soybean [Glycine max (L.) Merr.] varieties is a common goal for soybean breeding programs to ensure the sustainability and growth of soybean production worldwide. However, due to global climate change, soybean breeders are facing strong challenges to defeat diseases. Marker-assisted selection and genomic selection have been demonstrated to be successful methods in quickly integrating vertical resistance or horizontal resistance into improved soybean varieties, where vertical resistance refers to R genes and major effect QTLs, and horizontal resistance is a combination of major and minor effect genes or QTLs. This review summarized more than 800 resistant loci/alleles and their tightly linked markers for 28 soybean diseases worldwide, caused by nematodes, oomycetes, fungi, bacteria, and viruses. The major breakthroughs in the discovery of disease resistance gene atlas of soybean were also emphasized which include: (1) identification and characterization of vertical resistance genes reside rhg1 and Rhg4 for soybean cyst nematode, and exploration of the underlying regulation mechanisms through copy number variation and (2) map-based cloning and characterization of Rps11 conferring resistance to 80% isolates of Phytophthora sojae across the USA. In this review, we also highlight the validated QTLs in overlapping genomic regions from at least two studies and applied a consistent naming nomenclature for these QTLs. Our review provides a comprehensive summary of important resistant genes/QTLs and can be used as a toolbox for soybean improvement. Finally, the summarized genetic knowledge sheds light on future directions of accelerated soybean breeding and translational genomics studies.
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Affiliation(s)
- Feng Lin
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824 USA
| | - Sushil Satish Chhapekar
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211 USA
| | - Caio Canella Vieira
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211 USA
- Fisher Delta Research Center, University of Missouri, Portageville, MO 63873 USA
| | - Marcos Paulo Da Silva
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR 72701 USA
| | - Alejandro Rojas
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR 72701 USA
| | - Dongho Lee
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211 USA
- Fisher Delta Research Center, University of Missouri, Portageville, MO 63873 USA
| | - Nianxi Liu
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun,, 130033 Jilin China
| | - Esteban Mariano Pardo
- Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA) [Estación Experimental Agroindustrial Obispo Colombres (EEAOC) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)], Av. William Cross 3150, C.P. T4101XAC, Las Talitas, Tucumán, Argentina
| | - Yi-Chen Lee
- Fisher Delta Research Center, University of Missouri, Portageville, MO 63873 USA
| | - Zhimin Dong
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun,, 130033 Jilin China
| | - Jose Baldin Pinheiro
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz” (ESALQ/USP), PO Box 9, Piracicaba, SP 13418-900 Brazil
| | - Leonardo Daniel Ploper
- Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA) [Estación Experimental Agroindustrial Obispo Colombres (EEAOC) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)], Av. William Cross 3150, C.P. T4101XAC, Las Talitas, Tucumán, Argentina
| | - John Rupe
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR 72701 USA
| | - Pengyin Chen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211 USA
- Fisher Delta Research Center, University of Missouri, Portageville, MO 63873 USA
| | - Dechun Wang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824 USA
| | - Henry T. Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211 USA
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Jayawardena RS, Hyde KD, Chen YJ, Papp V, Palla B, Papp D, Bhunjun CS, Hurdeal VG, Senwanna C, Manawasinghe IS, Harischandra DL, Gautam AK, Avasthi S, Chuankid B, Goonasekara ID, Hongsanan S, Zeng X, Liyanage KK, Liu N, Karunarathna A, Hapuarachchi KK, Luangharn T, Raspé O, Brahmanage R, Doilom M, Lee HB, Mei L, Jeewon R, Huanraluek N, Chaiwan N, Stadler M, Wang Y. One stop shop IV: taxonomic update with molecular phylogeny for important phytopathogenic genera: 76–100 (2020). FUNGAL DIVERS 2020. [DOI: 10.1007/s13225-020-00460-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
AbstractThis is a continuation of a series focused on providing a stable platform for the taxonomy of phytopathogenic fungi and fungus-like organisms. This paper focuses on one family: Erysiphaceae and 24 phytopathogenic genera: Armillaria, Barriopsis, Cercospora, Cladosporium, Clinoconidium, Colletotrichum, Cylindrocladiella, Dothidotthia,, Fomitopsis, Ganoderma, Golovinomyces, Heterobasidium, Meliola, Mucor, Neoerysiphe, Nothophoma, Phellinus, Phytophthora, Pseudoseptoria, Pythium, Rhizopus, Stemphylium, Thyrostroma and Wojnowiciella. Each genus is provided with a taxonomic background, distribution, hosts, disease symptoms, and updated backbone trees. Species confirmed with pathogenicity studies are denoted when data are available. Six of the genera are updated from previous entries as many new species have been described.
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Santos Rezende J, Zivanovic M, Costa de Novaes MI, Chen Z. The AVR4 effector is involved in cercosporin biosynthesis and likely affects the virulence of Cercospora cf. flagellaris on soybean. MOLECULAR PLANT PATHOLOGY 2020; 21:53-65. [PMID: 31642594 PMCID: PMC6913201 DOI: 10.1111/mpp.12879] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
One of the most devastating fungal diseases of soybean in the southern USA is Cercospora leaf blight (CLB), which is caused mainly by Cercospora cf. flagellaris. Recent studies found that the fungal effector AVR4, originally identified in Cladosporium fulvum as a chitin-binding protein, is highly conserved among other Cercospora species. We wanted to determine whether it is present in C. cf. flagellaris and, if so, whether it plays a role in the pathogen infection of soybean. We cloned the Avr4 gene and created C. cf. flagellaris ∆avr4 mutants, which produced little cercosporin and significantly reduced expression of cercosporin biosynthesis genes. The ∆avr4 mutants were also more sensitive to chitinase and showed reduced virulence on soybean compared to the wild-type. The observed reduced virulence of C. cf. flagellaris ∆avr4 mutants on detached soybean leaves is likely due to reduced cercosporin biosynthesis. The phenotypes of reduced cercosporin production and cercosporin pathway gene expression, similar to those of the ∆avr4 mutants, were reproduced when wild-type C. cf. flagellaris was treated with double-stranded RNA targeting Avr4 in vitro. These two independent approaches demonstrated for the first time the direct involvement of AVR4 in the biosynthesis of cercosporin.
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Affiliation(s)
- Josielle Santos Rezende
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLA70803USA
| | - Marija Zivanovic
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLA70803USA
| | - Maria Izabel Costa de Novaes
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLA70803USA
| | - Zhi‐Yuan Chen
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLA70803USA
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6
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Li S, Sciumbato G, Boykin D, Shannon G, Chen P. Evaluation of soybean genotypes for reaction to natural field infection by Cercospora species causing purple seed stain. PLoS One 2019; 14:e0222673. [PMID: 31600229 PMCID: PMC6786595 DOI: 10.1371/journal.pone.0222673] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 09/03/2019] [Indexed: 11/19/2022] Open
Abstract
Purple seed stain (PSS) of soybean (Glycine max (L.) Merr.) is a prevalent seed disease. It results in poor seed quality and reduced seed lot market grade, and thus undermines value of soybean worldwide. The objectives of this research were to evaluate the reaction of selected soybean genotypes collected from 15 countries representing maturity groups (MGs) III, IV, and V to PSS, and to identify new sources of resistance to PSS based on three years of evaluation of natural field infection by Cercospora spp. in the Mississippi Delta of the U. S. In this study, 42 soybean genotypes were evaluated in 2010, 2011, and 2012. Seventeen lines including six MG III (PI 88490, PI 504488, PI 417361, PI 548298, PI 437482, and PI 578486), seven MG IV (PI 404173, PI 346308, PI 355070, PI 416779, PI 80479, PI 346307, and PI 264555), and four MG V (PI 417567, PI 417420, PI 381659, and PI 407749) genotypes had significantly lower percent seed infection by Cercospora spp. than the susceptible checks and other genotypes evaluated (P ≤ 0.05). These genotypes of soybean can be used in developing soybean cultivars or germplasm lines with resistance to PSS and for genetic mapping of PSS resistance genes. In addition, among these 17 lines with different levels of resistance to PSS, nine soybean genotypes (PI 417361, PI 504488, PI 88490, PI 346308, PI 416779, PI 417567, PI 381659, PI 417567, and PI 407749) were previously reported as resistant to Phomopsis seed decay. Therefore, they could be useful in breeding programs to develop soybean cultivars with improved resistance to both seed diseases.
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Affiliation(s)
- Shuxian Li
- United States Department of Agriculture, Agricultural Research Service (USDA, ARS), Crop Genetics Research Unit, Stoneville, Mississippi, United States of America
| | - Gabe Sciumbato
- Mississippi State University, Delta Research and Extension Center, Stoneville, Mississippi, United States of America
| | - Debbie Boykin
- USDA, ARS, Stoneville, Mississippi, United States of America
| | - Grover Shannon
- Division of Plant Sciences, University of Missouri, Portageville, Missouri, United States of America
| | - Pengyin Chen
- Division of Plant Sciences, University of Missouri, Portageville, Missouri, United States of America
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Silva EC, Abhayawardhana PL, Lygin AV, Robertson CL, Liu M, Liu Z, Schneider RW. Coumestrol Confers Partial Resistance in Soybean Plants Against Cercospora Leaf Blight. PHYTOPATHOLOGY 2018; 108:935-947. [PMID: 29451417 DOI: 10.1094/phyto-05-17-0189-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Although previous research showed that the purple symptom of Cercospora leaf blight (CLB) is associated with lower biomass of Cercospora cf. flagellaris and lower concentrations of cercosporin, a reactive oxygen species producer, as compared with blighted leaves, the hypothesis that the purple symptom is a plant reaction to the pathogen has never been tested. In this study, we demonstrated that high levels of coumestrol (COU) were associated with purple symptoms of CLB and that COU has strong antioxidant activity. Additionally, we found that COU is restricted to the pigmented areas of purple leaves, and the pigmentation is restricted to the adaxial surfaces, suggesting that COU may be acting as a sunscreen. Even though COU is associated with the purple leaf symptom, this coumestan is not the direct cause of discoloration in that COU is colorless. Quantification of chlorophyll a and b and total carotenoids suggested that blighted but not purple or asymptomatic leaves were undergoing photooxidative stress. Because the purple symptom is associated with high COU concentrations, lower biomass of C. cf. flagellaris, and lower cercosporin concentrations, we conclude that the purple symptom is a disease resistance reaction, mediated in part by COU, which provides a high level of antioxidant activity and, hence, partial resistance.
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Affiliation(s)
- E C Silva
- First, second, fourth, and seventh authors, Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge 70803; third author, Department of Crop Sciences, University of Illinois, Urbana 61801; and fifth and sixth authors, Medicinal Plant Lab, School of Renewable Natural Resources, Louisiana State University Agricultural Center
| | - P L Abhayawardhana
- First, second, fourth, and seventh authors, Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge 70803; third author, Department of Crop Sciences, University of Illinois, Urbana 61801; and fifth and sixth authors, Medicinal Plant Lab, School of Renewable Natural Resources, Louisiana State University Agricultural Center
| | - A V Lygin
- First, second, fourth, and seventh authors, Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge 70803; third author, Department of Crop Sciences, University of Illinois, Urbana 61801; and fifth and sixth authors, Medicinal Plant Lab, School of Renewable Natural Resources, Louisiana State University Agricultural Center
| | - C L Robertson
- First, second, fourth, and seventh authors, Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge 70803; third author, Department of Crop Sciences, University of Illinois, Urbana 61801; and fifth and sixth authors, Medicinal Plant Lab, School of Renewable Natural Resources, Louisiana State University Agricultural Center
| | - M Liu
- First, second, fourth, and seventh authors, Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge 70803; third author, Department of Crop Sciences, University of Illinois, Urbana 61801; and fifth and sixth authors, Medicinal Plant Lab, School of Renewable Natural Resources, Louisiana State University Agricultural Center
| | - Z Liu
- First, second, fourth, and seventh authors, Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge 70803; third author, Department of Crop Sciences, University of Illinois, Urbana 61801; and fifth and sixth authors, Medicinal Plant Lab, School of Renewable Natural Resources, Louisiana State University Agricultural Center
| | - R W Schneider
- First, second, fourth, and seventh authors, Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge 70803; third author, Department of Crop Sciences, University of Illinois, Urbana 61801; and fifth and sixth authors, Medicinal Plant Lab, School of Renewable Natural Resources, Louisiana State University Agricultural Center
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8
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Albu S, Sharma S, Bluhm BH, Price PP, Schneider RW, Doyle VP. Draft Genome Sequence of Cercospora cf. sigesbeckiae, a Causal Agent of Cercospora Leaf Blight on Soybean. GENOME ANNOUNCEMENTS 2017; 5:e00708-17. [PMID: 28883128 PMCID: PMC5589522 DOI: 10.1128/genomea.00708-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 07/19/2017] [Indexed: 11/23/2022]
Abstract
Cercospora cf. sigesbeckiae is an ascomycete fungal pathogen that infects various plants, including important agricultural commodities, such as soybean. Here, we report the first draft genome sequence and assembly of this pathogen.
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Affiliation(s)
- Sebastian Albu
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Sandeep Sharma
- Department of Plant Pathology, University of Arkansas, Division of Agriculture, Fayetteville, Arkansas, USA
| | - Burton H Bluhm
- Department of Plant Pathology, University of Arkansas, Division of Agriculture, Fayetteville, Arkansas, USA
| | - Paul P Price
- Louisiana State University Agricultural Center, Macon Ridge Research Station, Winnsboro, Louisiana, USA
| | - Raymond W Schneider
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Vinson P Doyle
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
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9
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Albu S, Schneider RW, Price PP, Doyle VP. Cercospora cf. flagellaris and Cercospora cf. sigesbeckiae Are Associated with Cercospora Leaf Blight and Purple Seed Stain on Soybean in North America. PHYTOPATHOLOGY 2016; 106:1376-1385. [PMID: 27183302 DOI: 10.1094/phyto-12-15-0332-r] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Cercospora kikuchii has long been considered the causal agent of Cercospora leaf blight (CLB) and purple seed stain (PSS) on soybean, but a recent study found C. cf. flagellaris associated with CLB and PSS in Arkansas (United States) and Argentina. Here, we provide a broader perspective on the distribution of C. cf. flagellaris on soybean and alternate hosts within the United States (Arkansas, Louisiana, Mississippi, Missouri, and Kansas). We used a multilocus phylogenetic approach with data from actin, calmodulin, translation elongation factor 1-α, histone 3, the internal transcribed spacer region of rDNA and the mating-type locus to determine that two species, C. cf. flagellaris (200 of 205 isolates) and C. cf. sigesbeckiae (five of 205 isolates), are associated with CLB and PSS in the United States. In our phylogenetic analyses, species-level lineages were generally well-supported, though deeper-level evolutionary relationships remained unresolved, indicating that these genes do not possess sufficient phylogenetic signal to resolve the evolutionary history of Cercospora. We also investigated the potential for sexual reproduction in C. cf. flagellaris in Louisiana by determining the frequency of MAT1-1/MAT1-2 mating-type idiomorphs within the Louisiana population of C. cf. flagellaris. Though the MAT 1-2 idiomorph was significantly more common in our collection, the presence of both mating types suggests the potential for sexual reproduction exists.
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Affiliation(s)
- S Albu
- First, second, and fourth authors: Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge
- and third author: Louisiana State University Agricultural Center, Macon Ridge Research Station, Winnsboro
| | - R W Schneider
- First, second, and fourth authors: Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge
- and third author: Louisiana State University Agricultural Center, Macon Ridge Research Station, Winnsboro
| | - P P Price
- First, second, and fourth authors: Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge
- and third author: Louisiana State University Agricultural Center, Macon Ridge Research Station, Winnsboro
| | - V P Doyle
- First, second, and fourth authors: Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge
- and third author: Louisiana State University Agricultural Center, Macon Ridge Research Station, Winnsboro
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10
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Soares APG, Guillin EA, Borges LL, da Silva ACT, de Almeida ÁMR, Grijalba PE, Gottlieb AM, Bluhm BH, de Oliveira LO. More Cercospora Species Infect Soybeans across the Americas than Meets the Eye. PLoS One 2015; 10:e0133495. [PMID: 26252018 PMCID: PMC4529236 DOI: 10.1371/journal.pone.0133495] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 06/29/2015] [Indexed: 11/18/2022] Open
Abstract
Diseases of soybean caused by Cercospora spp. are endemic throughout the world's soybean production regions. Species diversity in the genus Cercospora has been underestimated due to overdependence on morphological characteristics, symptoms, and host associations. Currently, only two species (Cercospora kikuchii and C. sojina) are recognized to infect soybean; C. kikuchii causes Cercospora leaf blight (CLB) and purple seed stain (PSS), whereas C. sojina causes frogeye leaf spot. To assess cryptic speciation among pathogens causing CLB and PSS, phylogenetic and phylogeographic analyses were performed with isolates from the top three soybean producing countries (USA, Brazil, and Argentina; collectively accounting for ~80% of global production). Eight nuclear genes and one mitochondrial gene were partially sequenced and analyzed. Additionally, amino acid substitutions conferring fungicide resistance were surveyed, and the production of cercosporin (a polyketide toxin produced by many Cercospora spp.) was assessed. From these analyses, the long-held assumption of C. kikuchii as the single causal agent of CLB and PSS was rejected experimentally. Four cercosporin-producing lineages were uncovered with origins (about 1 Mya) predicted to predate agriculture. Some of the Cercospora spp. newly associated with CLB and PSS appear to represent undescribed species; others were not previously reported to infect soybeans. Lineage 1, which contained the ex-type strain of C. kikuchii, was monophyletic and occurred in Argentina and Brazil. In contrast, lineages 2 and 3 were polyphyletic and contained wide-host range species complexes. Lineage 4 was monophyletic, thrived in Argentina and the USA, and included the generalist Cercospora cf. flagellaris. Interlineage recombination was detected, along with a high frequency of mutations linked to fungicide resistance in lineages 2 and 3. These findings point to cryptic Cercospora species as underappreciated global considerations for soybean production and phytosanitary vigilance, and urge a reassessment of host-specificity as a diagnostic tool for Cercospora.
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Affiliation(s)
- Ana Paula Gomes Soares
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa (MG), Brazil
| | - Eduardo A. Guillin
- Instituto de Genética Ewald A. Favret, CNIA, INTA Castelar, Buenos Aires, Argentina
| | - Leandro Luiz Borges
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa (MG), Brazil
| | - Amanda C. T. da Silva
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa (MG), Brazil
| | | | - Pablo E. Grijalba
- Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Alexandra M. Gottlieb
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Burton H. Bluhm
- University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Luiz Orlando de Oliveira
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa (MG), Brazil
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Chanda AK, Ward NA, Robertson CL, Chen ZY, Schneider RW. Development of a Quantitative Polymerase Chain Reaction Detection Protocol for Cercospora kikuchii in Soybean Leaves and Its Use for Documenting Latent Infection as Affected by Fungicide Applications. PHYTOPATHOLOGY 2014; 104:1118-24. [PMID: 24805074 DOI: 10.1094/phyto-07-13-0200-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Cercospora leaf blight (CLB) of soybean, caused by Cercospora kikuchii, is a serious disease in the southern United States. A sensitive TaqMan probe-based real-time quantitative polymerase chain reaction (qPCR) assay was developed to specifically detect and quantify C. kikuchii in naturally infected soybean plants. The sensitivity was 1 pg of genomic DNA, which was equivalent to about 34 copies of genome of C. kikuchii. Using this qPCR assay, we documented a very long latent infection period for C. kikuchii in soybean leaves beginning at the V3 growth stage (as early as 22 days after planting). The levels of biomass of C. kikuchii remained low until R1, and a rapid increase was detected from the R2/R3 to R4/R5 growth stages shortly before the appearance of symptoms at R6. The efficacy of various fungicide regimens under field conditions also was evaluated over a 3-year period using this qPCR method. Our results showed that multiple fungicide applications beginning at R1 until late reproductive stages suppressed the development of C. kikuchii in leaves and delayed symptom expression. Different fungicide chemistries also had differential effects on the amount of latent infection and symptom expression during late reproductive growth stages.
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