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Barro JP, Del Ponte EM, Allen TW, Bond JP, Faske TR, Hollier CA, Kandel YR, Mueller DS, Kelly HM, Kleczewski NM, Ames KA, Price PP, Sikora EJ, Bradley CA. Efficacy and Profitability of Fungicides for Managing Frogeye Leaf Spot on Soybean in the United States: A 10-Year Quantitative Summary. PLANT DISEASE 2023; 107:3487-3496. [PMID: 37157104 DOI: 10.1094/pdis-02-23-0291-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: 05/10/2023]
Abstract
Frogeye leaf spot (FLS), caused by Cercospora sojina, is an economically important disease of soybean in the United States. Data from 66 uniform fungicide trials (UFTs) conducted from 2012 to 2021 across eight states (Alabama, Arkansas, Illinois, Iowa, Kentucky, Louisiana, Mississippi, and Tennessee) were gathered and analyzed to determine the efficacy and profitability of the following fungicides applied at the beginning pod developmental stage (R3): azoxystrobin + difenoconazole (AZOX + DIFE), difenoconazole + pydiflumetofen (DIFE + PYDI), pyraclostrobin (PYRA), pyraclostrobin + fluxapyroxad + propiconazole (PYRA + FLUX + PROP), tetraconazole (TTRA), thiophanate-methyl (TMET), thiophanate-methyl + tebuconazole (TMET + TEBU), and trifloxystrobin + prothioconazole (TFLX + PROT). A network meta-analytic model was fitted to the log of the means of FLS severity data and to the nontransformed mean yield for each treatment, including the nontreated. The percent reduction in disease severity (%) and the yield response (kg/ha) relative to the nontreated was the lowest for PYRA (11%; 136 kg/ha) and the greatest for DIFE + PYDI (57%; 441 kg/ha). A significant decline in efficacy over time was detected for PYRA (18 percentage points [p.p.]), TTRA (27 p.p.), AZOX + DIFE (18 p.p.), and TMET + TEBU (19 p.p.) by using year as a continuous covariate in the model. Finally, probabilities of breaking even were the greatest (>65%) for the most effective fungicide DIFE + PYDI and the lowest (<55%) for PYRA. Results of this meta-analysis may be useful to support decisions when planning fungicide programs.
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Affiliation(s)
- Jhonatan P Barro
- Department of Plant Pathology, University of Kentucky, Princeton, KY 42445, U.S.A
- Departamento de Fitopatologia, Universidade Federal de Viçosa, 36570-000 Viçosa, Brazil
| | - Emerson M Del Ponte
- Departamento de Fitopatologia, Universidade Federal de Viçosa, 36570-000 Viçosa, Brazil
| | - Tom W Allen
- Delta Research and Extension Center, Mississippi State University, Stoneville, MS 38776, U.S.A
| | - Jason P Bond
- Department of Plant, Soil Science, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, U.S.A
| | - Travis R Faske
- Department of Entomology and Plant Pathology, Division of Agriculture, Lonoke Extension Center, University of Arkansas, Lonoke, AR 72086, U.S.A
| | - Clayton A Hollier
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, U.S.A
| | - Yuba R Kandel
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Daren S Mueller
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Heather M Kelly
- Department of Entomology and Plant Pathology, University of Tennessee, Jackson, TN 38301, U.S.A
| | - Nathan M Kleczewski
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, U.S.A
| | - Keith A Ames
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, U.S.A
| | - Paul P Price
- Macon Ridge Research Station, LSU AgCenter, Winnsboro, LA 71295, U.S.A
| | - Edward J Sikora
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, U.S.A
| | - Carl A Bradley
- Department of Plant Pathology, University of Kentucky, Princeton, KY 42445, U.S.A
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Dai Y, Gan L, Lan C, Liu X, Liu W, Yang X. Population structure and mixed reproductive strategies in Bipolaris maydis from single and multiple corn cultivars in Fujian Province, China. FRONTIERS IN PLANT SCIENCE 2023; 14:1232414. [PMID: 37860250 PMCID: PMC10583543 DOI: 10.3389/fpls.2023.1232414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/12/2023] [Indexed: 10/21/2023]
Abstract
Bipolaris maydis is the pathogenic microorganism of southern corn leaf blight, a persistent biotic constraint responsible for substantial yield losses of corn worldwide. In the present study, 96 isolates from six representative fields growing single and multiple sweet corn cultivars in Pingnan, Fuqing, and Jian'ou in Fujian Province, which are characterized by different geographical characteristics and cropping patterns, were genetically analyzed using inter-simple sequence repeat (ISSR) markers to assess the impact of geographical origins and corn cultivars on B. maydis population differentiation. B. maydis isolates originated from diverse regions possessed higher genetic variety than those from single and multiple sweet corn cultivars. Phylogenetic analysis showed that the isolates from single and multiple sweet corn cultivars were randomly grouped into different clusters, with those from the same location tending to form clusters. A greater genetic differentiation among different geographical populations than between those from single and multiple sweet corn cultivars was observed by pairwise comparison. Hierarchical analysis indicated that among-population variation was higher when comparatively analyzed B. maydis populations from different locations than in those from single and multiple sweet corn cultivars. In conclusion, these results suggest that geographical origin acts a more considerable role in genetic differentiation of B. maydis than corn cultivar. Two divided genetic clusters were detected in the B. maydis populations from single and multiple sweet corn cultivars at the three locations in Fujian Province, with major genetic variation being derived within populations. The high haplotypic diversity and expected mating type ratio of 1:1 in combination with significant linkage disequilibrium suggested that a mixed reproductive strategy occurs in the B. maydis population in Fujian Province. This study will enrich the information on the role that geographical origins and corn cultivars play in the population structure of the pathogen as well as the reproductive strategies in B. maydis population in Fujian Province.
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Affiliation(s)
- Yuli Dai
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Lin Gan
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Chengzhong Lan
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Xiaofei Liu
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiujuan Yang
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
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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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Sun M, Na C, Jing Y, Cui Z, Li N, Zhan Y, Teng W, Li Y, Li W, Zhao X, Han Y. Genome-Wide Association Analysis and Gene Mining of Resistance to China Race 1 of Frogeye Leaf Spot in Soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:867713. [PMID: 35812941 PMCID: PMC9257224 DOI: 10.3389/fpls.2022.867713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Soybean frogeye leaf spot (FLS) is a worldwide fungal disease. Its higher occurrence frequency and wider distribution range always led to severe yield losses of soybean, therefore, breeding new cultivars with FLS resistance has been an important breeding goal for soybean breeders. In this study, an association panel of 183 representative soybean accessions was used to evaluate their resistance to FLS race 1, and to identify quantitative trait nucleotides (QTNs) and candidate genes based on genome-wide association study (GWAS) and high-throughput single-nucleotide polymorphisms (SNPs). A total of 23,156 high-quality SNPs were developed using the specific locus-amplified fragment sequencing (SLAF-seq) approach. Finally, 13 novel association signals associated with FLS race 1 resistance were identified by the compressed mixed linear model (CMLM). In addition, 119 candidate genes were found within the 200-kb flanking genomic region of these 13 peak SNPs. Based on the gene-based association analysis, haplotype analysis, expression pattern analysis, and virus-induced gene silencing (VIGS) systems, four genes (Glyma.05G121100, Glyma.17G228300, Glyma.19G006900, and Glyma.19G008700) were preliminarily proved to play an important role in the soybean resistance to FLS race 1.
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Affiliation(s)
- Maolin Sun
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, China
| | - Chen Na
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, China
| | - Yan Jing
- College of Tropical Crops, Hainan University, Haikou, China
| | - Zhihui Cui
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, China
| | - Na Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, China
| | - Yuhang Zhan
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, China
| | - Weili Teng
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, China
| | - Yongguang Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, China
| | - Wenbin Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, China
| | - Xue Zhao
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, China
| | - Yingpeng Han
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, China
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Gu X, Huang S, Zhu Z, Ma Y, Yang X, Yao L, Gao X, Zhang M, Liu W, Qiu L, Zhao H, Wang Q, Li Z, Li Z, Meng Q, Yang S, Wang C, Hu X, Ding J. Genome-wide association of single nucleotide polymorphism loci and candidate genes for frogeye leaf spot (Cercospora sojina) resistance in soybean. BMC PLANT BIOLOGY 2021; 21:588. [PMID: 34895144 PMCID: PMC8665500 DOI: 10.1186/s12870-021-03366-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 11/25/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Frogeye leaf spot (FLS) is a destructive fungal disease that affects soybean production. The most economical and effective strategy to control FLS is the use of resistant cultivars. However, the use of a limited number of resistant loci in FLS management will be countered by the emergence of new high-virulence Cercospora sojina races. Therefore, we identified quantitative trait loci (QTL) that control resistance to FLS and identified novel resistant genes using a genome-wide association study (GWAS) on 234 Chinese soybean cultivars. RESULTS A total of 30,890 single nucleotide polymorphism (SNP) markers were used to estimate linkage disequilibrium (LD) and population structure. The GWAS results showed four loci (p < 0.0001) distributed over chromosomes (Chr.) 5 and 20, that are significantly associated with FLS resistance. No previous studies have reported resistance loci in these regions. Subsequently, 45 genes in the two resistance-related haplotype blocks were annotated. Among them, Glyma20g31630 encoding pyruvate dehydrogenase (PDH), Glyma05g28980, which encodes mitogen-activated protein kinase 7 (MPK7), and Glyma20g31510, Glyma20g31520 encoding calcium-dependent protein kinase 4 (CDPK4) in the haplotype blocks deserves special attention. CONCLUSIONS This study showed that GWAS can be employed as an effective strategy for identifying disease resistance traits in soybean and narrowing SNPs and candidate genes. The prediction of candidate genes in the haplotype blocks identified by disease resistance loci can provide a useful reference to study systemic disease resistance.
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Affiliation(s)
- Xin Gu
- Wuhu Institute of Technology, Wuhu, 241003, China
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture Harmful Biology of Crop Scientific Monitoring Station Jiamusi Experiment Station, China Agriculture Research System of MOF and MARA, Jiamusi, 154007, China
| | - Shanshan Huang
- Key Laboratory of Crop Biotechnology Breeding of the Ministry of Agriculture, Beidahuang Kenfeng Seed Co., Ltd., Harbin, 150030, China
| | - Zhiguo Zhu
- Wuhu Institute of Technology, Wuhu, 241003, China
| | - Yansong Ma
- Key Laboratory of Crop Biotechnology Breeding of the Ministry of Agriculture, Beidahuang Kenfeng Seed Co., Ltd., Harbin, 150030, China
| | - Xiaohe Yang
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture Harmful Biology of Crop Scientific Monitoring Station Jiamusi Experiment Station, China Agriculture Research System of MOF and MARA, Jiamusi, 154007, China
| | - Liangliang Yao
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture Harmful Biology of Crop Scientific Monitoring Station Jiamusi Experiment Station, China Agriculture Research System of MOF and MARA, Jiamusi, 154007, China
| | - Xuedong Gao
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture Harmful Biology of Crop Scientific Monitoring Station Jiamusi Experiment Station, China Agriculture Research System of MOF and MARA, Jiamusi, 154007, China
| | - Maoming Zhang
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture Harmful Biology of Crop Scientific Monitoring Station Jiamusi Experiment Station, China Agriculture Research System of MOF and MARA, Jiamusi, 154007, China
| | - Wei Liu
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture Harmful Biology of Crop Scientific Monitoring Station Jiamusi Experiment Station, China Agriculture Research System of MOF and MARA, Jiamusi, 154007, China
| | - Lei Qiu
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture Harmful Biology of Crop Scientific Monitoring Station Jiamusi Experiment Station, China Agriculture Research System of MOF and MARA, Jiamusi, 154007, China
| | - Haihong Zhao
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture Harmful Biology of Crop Scientific Monitoring Station Jiamusi Experiment Station, China Agriculture Research System of MOF and MARA, Jiamusi, 154007, China
| | - Qingsheng Wang
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture Harmful Biology of Crop Scientific Monitoring Station Jiamusi Experiment Station, China Agriculture Research System of MOF and MARA, Jiamusi, 154007, China
| | - Zengjie Li
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture Harmful Biology of Crop Scientific Monitoring Station Jiamusi Experiment Station, China Agriculture Research System of MOF and MARA, Jiamusi, 154007, China
| | - Zhimin Li
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture Harmful Biology of Crop Scientific Monitoring Station Jiamusi Experiment Station, China Agriculture Research System of MOF and MARA, Jiamusi, 154007, China
| | - Qingying Meng
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture Harmful Biology of Crop Scientific Monitoring Station Jiamusi Experiment Station, China Agriculture Research System of MOF and MARA, Jiamusi, 154007, China
| | - Shuai Yang
- Potato Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Chao Wang
- Key Laboratory of Crop Biotechnology Breeding of the Ministry of Agriculture, Beidahuang Kenfeng Seed Co., Ltd., Harbin, 150030, China
| | - Xiping Hu
- Key Laboratory of Crop Biotechnology Breeding of the Ministry of Agriculture, Beidahuang Kenfeng Seed Co., Ltd., Harbin, 150030, China.
| | - Junjie Ding
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture Harmful Biology of Crop Scientific Monitoring Station Jiamusi Experiment Station, China Agriculture Research System of MOF and MARA, Jiamusi, 154007, China.
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Harrelson BC, Kemerait RC, Culbreath AK, Ghimire B, Li Z, Severns PM, Buck JW. Assessment of Quinone Outside Inhibitor Sensitivity and Frogeye Leaf Spot Race of Cercospora sojina in Georgia Soybean. PLANT DISEASE 2021; 105:2946-2954. [PMID: 33779250 DOI: 10.1094/pdis-02-21-0236-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Frogeye leaf spot (FLS), caused by the fungal pathogen Cercospora sojina K. Hara, is a foliar disease of soybean (Glycine max L. [Merr.]) responsible for yield reductions throughout the major soybean-producing regions of the world. In the United States, management of FLS relies heavily on the use of resistant cultivars and in-season fungicide applications, specifically within the class of quinone outside inhibitors (QoIs), which has resulted in the development of fungicide resistance in many states. In 2018 and 2019, 80 isolates of C. sojina were collected from six counties in Georgia and screened for QoI fungicide resistance using molecular and in vitro assays, with resistant isolates being confirmed from three counties. Additionally, 50 isolates, including a "baseline isolate" with no prior fungicide exposure, were used to determine the percent reduction of mycelial growth to two fungicides, azoxystrobin and pyraclostrobin, at six concentrations: 0.0001, 0.001, 0.01, 0.1, 1, and 10 μg ml-1. Mycelial growth observed for resistant isolates varied significantly from both sensitive isolates and baseline isolate for azoxystrobin concentrations of 10, 1, 0.1, and 0.01 μg ml-1 and for pyraclostrobin concentrations of 10, 1, 0.1, 0.01, and 0.001 μg ml-1. Moreover, 40 isolates were used to evaluate pathogen race on six soybean differential cultivars by assessing susceptible or resistant reactions. Isolate reactions suggested 12 races of C. sojina present in Georgia, 4 of which have not been previously described. Species richness indicators (rarefaction and abundance-based coverage estimators) indicated that within-county C. sojina race numbers were undersampled in this study, suggesting the potential for the presence of either additional undescribed races or known but unaccounted for races in Georgia. However, no isolates were pathogenic on 'Davis', a differential cultivar carrying the Rcs3 resistance allele, suggesting that the gene is still an effective source of resistance in Georgia.
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Affiliation(s)
| | - Robert C Kemerait
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793
| | | | - Bikash Ghimire
- Department of Plant Pathology, University of Georgia, Griffin, GA 30223
| | - Zenglu Li
- Institute of Plant Breeding, Genetics and Genomics/Department of Crop and Soil Sciences, University of Georgia, Athens, GA 30602
| | - Paul M Severns
- Department of Plant Pathology, University of Georgia, Athens, GA 30602
| | - James W Buck
- Department of Plant Pathology, University of Georgia, Griffin, GA 30223
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Nsibo DL, Barnes I, Omondi DO, Dida MM, Berger DK. Population genetic structure and migration patterns of the maize pathogenic fungus, Cercospora zeina in East and Southern Africa. Fungal Genet Biol 2021; 149:103527. [PMID: 33524555 DOI: 10.1016/j.fgb.2021.103527] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 12/13/2020] [Accepted: 12/20/2020] [Indexed: 11/16/2022]
Abstract
Cercospora zeina is a causal pathogen of gray leaf spot (GLS) disease of maize in Africa. This fungal pathogen exhibits a high genetic diversity in South Africa. However, little is known about the pathogen's population structure in the rest of Africa. In this study, we aimed to assess the diversity and gene flow of the pathogen between major maize producing countries in East and Southern Africa (Kenya, Uganda, Zambia, Zimbabwe, and South Africa). A total of 964 single-spore isolates were made from GLS lesions and confirmed as C.zeina using PCR diagnostics. The other causal agent of GLS, Cercospora zeae-maydis, was absent. Genotyping all the C.zeina isolates with 11 microsatellite markers and a mating-type gene diagnostic revealed (i) high genetic diversity with some population structure between the five African countries, (ii) cryptic sexual recombination, (iii) that South Africa and Kenya were the greatest donors of migrants, and (iv) that Zambia had a distinct population. We noted evidence of human-mediated long-distance dispersal, since four haplotypes from one South African site were also present at five sites in Kenya and Uganda. There was no evidence for a single-entry point of the pathogen into Africa. South Africa was the most probable origin of the populations in Kenya, Uganda, and Zimbabwe. Continuous annual maize production in the tropics (Kenya and Uganda) did not result in greater genetic diversity than a single maize season (Southern Africa). Our results will underpin future management of GLS in Africa through effective monitoring of virulent C.zeina strains.
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Affiliation(s)
- David L Nsibo
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa
| | - Irene Barnes
- Department of Biochemistry, Genetics and Microbiology, FABI, University of Pretoria, South Africa
| | | | | | - Dave K Berger
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa.
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Gu X, Ding J, Liu W, Yang X, Yao L, Gao X, Zhang M, Yang S, Wen J. Comparative genomics and association analysis identifies virulence genes of Cercospora sojina in soybean. BMC Genomics 2020; 21:172. [PMID: 32075575 PMCID: PMC7032006 DOI: 10.1186/s12864-020-6581-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 02/13/2020] [Indexed: 03/01/2023] Open
Abstract
BACKGROUND Recently, a new strain of Cercospora sojina (Race15) has been identified, which has caused the breakdown of resistance in most soybean cultivars in China. Despite this serious yield reduction, little is known about why this strain is more virulent than others. Therefore, we sequenced the Race15 genome and compared it to the Race1 genome sequence, as its virulence is significantly lower. We then re-sequenced 30 isolates of C. sojina from different regions to identifying differential virulence genes using genome-wide association analysis (GWAS). RESULTS The 40.12-Mb Race15 genome encodes 12,607 predicated genes and contains large numbers of gene clusters that have annotations in 11 different common databases. Comparative genomics revealed that although these two genomes had a large number of homologous genes, their genome structures have evolved to introduce 245 specific genes. The most important 5 candidate virulence genes were located on Contig 3 and Contig 1 and were mainly related to the regulation of metabolic mechanisms and the biosynthesis of bioactive metabolites, thereby putatively affecting fungi self-toxicity and reducing host resistance. Our study provides insight into the genomic basis of C. sojina pathogenicity and its infection mechanism, enabling future studies of this disease. CONCLUSIONS Via GWAS, we identified five candidate genes using three different methods, and these candidate genes are speculated to be related to metabolic mechanisms and the biosynthesis of bioactive metabolites. Meanwhile, Race15 specific genes may be linked with high virulence. The genes highly prevalent in virulent isolates should also be proposed as candidates, even though they were not found in our SNP analysis. Future work should focus on using a larger sample size to confirm and refine candidate gene identifications and should study the functional roles of these candidates, in order to investigate their potential roles in C. sojina pathogenicity.
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Affiliation(s)
- Xin Gu
- Department of Plant Protection, College of Agriculture, Northeast Agricultural University, Harbin, China
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Junjie Ding
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Wei Liu
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Xiaohe Yang
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Liangliang Yao
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Xuedong Gao
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Maoming Zhang
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Shuai Yang
- Potato Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Jingzhi Wen
- Department of Plant Protection, College of Agriculture, Northeast Agricultural University, Harbin, China.
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9
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Brito FSD, Santos JRP, Azevedo VCR, Peixouto YS, de Oliveira SA, Ferreira CF, Haddad F, Amorim EP, Fraaije B, Miller RNG. Genetic Diversity and Azole Fungicide Sensitivity in Pseudocercospora musae Field Populations in Brazil. Front Microbiol 2020; 11:99. [PMID: 32117129 PMCID: PMC7011104 DOI: 10.3389/fmicb.2020.00099] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 01/17/2020] [Indexed: 11/21/2022] Open
Abstract
Pseudocercospora musae, causal agent of Sigatoka leaf spot, or yellow Sigatoka disease, is considered a major pathogen of banana (Musa spp.). Widely disseminated in Brazil, this study explored the genetic diversity in field populations of the pathogen from production areas in the Distrito Federal and the States of Bahia, Minas Gerais, and Rio Grande do Norte. Resistance to demethylation inhibitor (DMI) fungicides was also examined. For 162 isolates from 10 banana growing regions, analysis of mating type idiomorph frequency was conducted, together with estimation of genetic diversity at 15 microsatellite loci. A total of 149 haplotypes were identified across the examined populations, with an average genetic diversity of 4.06. In general, populations displayed 1:1 proportions of idiomorphs MAT1-1 and MAT1-2, providing evidence for sexual recombination. Multilocus linkage disequilibrium also indicated asexual reproduction contributing to the genetic structure of certain populations. AMOVA revealed that 86.3% of the genetic differentiation of the pathogen occurred among isolates within populations. Discriminant Analysis of Principal Components (DAPC) identified six most probable genetic groups, with no population structure associated with geographic origin or collection site. Although genetic similarity was observed among certain populations from different states, data revealed increasing genetic differentiation with increasing geographic distance, as validated by Mantel’s test (r = 0.19, P < 0.001). On the basis of DMI fungicide sensitivity testing and CYP51 gene sequence polymorphism, isolates from the Distrito Federal separated into two main groups, one with generally higher EC50 values against eight DMI fungicides. A clear phenotype-to-genotype relationship was observed for isolates carrying the CYP51 alteration Y461N. Conventionally adopted fungicides for control of Sigatoka leaf spot are likely to be overcome by combined sexual and asexual reproduction mechanisms in P. musae driving genetic variability. Continued analysis of pathogen genetic diversity and monitoring of DMI sensitivity profiles of Brazilian field populations is essential for the development of integrated control strategies based on host resistance breeding and rational design of fungicide regimes.
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Affiliation(s)
| | - Jansen R P Santos
- Department of Phytopathology, University of Brasília, Brasília, Brazil
| | - Vânia C R Azevedo
- Department of Plant Genetics, Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil
| | - Yslai S Peixouto
- Department of Plant Breeding and Phytopathology, Embrapa Mandioca e Fruticultura, Cruz das Almas, Brazil
| | - Saulo A de Oliveira
- Department of Plant Breeding and Phytopathology, Embrapa Mandioca e Fruticultura, Cruz das Almas, Brazil
| | - Cláudia F Ferreira
- Department of Plant Breeding and Phytopathology, Embrapa Mandioca e Fruticultura, Cruz das Almas, Brazil
| | - Fernando Haddad
- Department of Plant Breeding and Phytopathology, Embrapa Mandioca e Fruticultura, Cruz das Almas, Brazil
| | - Edson P Amorim
- Department of Plant Breeding and Phytopathology, Embrapa Mandioca e Fruticultura, Cruz das Almas, Brazil
| | - Bart Fraaije
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, United Kingdom
| | - Robert N G Miller
- Department of Phytopathology, University of Brasília, Brasília, Brazil
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10
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Mengistu A, Ray JD, Kelly HM, Lin B, Yu H, Smith JR, Arelli PR, Bellaloui N. Pathotype Grouping of Cercospora sojina Isolates on Soybean and Sensitivity to QoI Fungicides. PLANT DISEASE 2020; 104:373-380. [PMID: 31841377 DOI: 10.1094/pdis-02-19-0368-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: 06/10/2023]
Abstract
Frogeye leaf spot (FLS), caused by Cercospora sojina, is a common disease of soybean in the southern and northern United States and causes significant yield loss. The use of the current race scheme for classification for C. sojina does not take into account the range of disease severity reactions within each differential. The objective of this research was to better understand the diversity among C. sojina isolates through the development and use of pathogenicity groups. In this study, 83 isolates acquired from 2006 to 2009 were screened using 12 soybean (Glycine max) differentials. Disease severity on the 12 differentials ranged from 0 to 9, where 0 is immune and 9 is very susceptible. The average severity for each isolate across differentials ranged from 1 to 7. The 83 isolates were grouped into five pathogenicity groups (PG): PG1, PG2, PG3, PG4, and PG5, reflecting the severity grouping. Using the 12 differentials, PG1 isolates were differentiated by the lack of infection on Davis, Peking, Kent, Palmetto, Hood, CNS, Tracy, and Richland. PG2 had a range of infections on a scale of 1 to 2 on all differentials except on Davis; PG3 isolates had severity ranging from 3 to 4 except on Davis. PG4 isolates caused no infection on Davis, a maximum disease severity of 5 on Peking, while the rest of differentials had severities from 5 to 6. PG5 isolates caused no infection on Davis, severity of 7 on CNS, and severity of 8 on Kent, Hood, and Palmetto. The remaining seven differentials had severities of 9. Across the geographical locations, the predominant pathotypes were PG3 and PG4 and represented 84% of the tested isolates. Azoxystrobin fungicide sensitivity tests showed that 88% of the isolates were sensitive and dominated the population, while only 6% had a high level of fungicide resistance, suggesting that FLS resistance to the QoI fungicide group was not yet completely developed and had not spread to other areas at the time when these isolates were acquired. The overall virulence profile of the isolates indicated that there was variation in disease severity, suggesting that selection of resistance for each PG may produce lines with more precisely defined interactions to specific pathotypes of C. sojina. This may improve the screening and selection of useful resistance genes that could be pyramided for resistance to each pathogenicity group.
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Affiliation(s)
- Alemu Mengistu
- USDA, Agricultural Research Service, Crop Genetics Research Unit, Jackson, TN 38301
| | - Jeffery D Ray
- USDA, Agricultural Research Service, Crop Genetics Research Unit, Stoneville, MS 38776-0350
| | - Heather M Kelly
- University of Tennessee, Entomology and Plant Pathology, Jackson, TN 38301
| | - Binbin Lin
- University of Tennessee, Entomology and Plant Pathology, Jackson, TN 38301
| | - Hao Yu
- University of Tennessee, Entomology and Plant Pathology, Jackson, TN 38301
| | - James R Smith
- USDA, Agricultural Research Service, Crop Genetics Research Unit, Stoneville, MS 38776-0350
| | - Prakash R Arelli
- USDA, Agricultural Research Service, Crop Genetics Research Unit, Jackson, TN 38301
| | - Nacer Bellaloui
- USDA, Agricultural Research Service, Crop Genetics Research Unit, Stoneville, MS 38776-0350
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11
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Dai Y, Gan L, Ruan H, Shi N, Du Y, Chen F, Yang X. Characterization of Natural Isolates of Bipolaris maydis Associated with Mating Types, Genetic Diversity, and Pathogenicity in Fujian Province, China. PLANT DISEASE 2020; 104:323-329. [PMID: 31841376 DOI: 10.1094/pdis-03-19-0650-re] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Due to the natural destructiveness and persistence of the southern corn leaf blight (SCLB) fungus Bipolaris maydis (Nisikado et Miyake) Shoem, the characterization of B. maydis field isolates is essential to guide the rational distribution of resistant materials in corn-growing regions. In the present study, 102 field isolates collected from seven locations covering the entire region of Fujian Province, China, were assessed for mating type distribution, genetic diversity, and pathogenicity toward local sweet corn cultivars. Mating type detection via polymerase chain reaction indicated that 36.3 and 63.7% of isolates were MAT1-1 and MAT1-2, respectively; more than 80% of these isolates were confirmed using cross assays with known mating type isolates. Thirteen intersimple sequence repeat (ISSR) markers within and among two mating type populations revealed a high level of DNA polymorphism for all combined isolates and between MAT1-1 and MAT1-2 populations. The MAT1-2 population was more diverse based on DNA polymorphism than the MAT1-1 population. The value of GST was 0.0070, ranging from 0.0399 to 0.3044 based on analysis of combined isolates and individual regional populations, respectively, suggesting the presence of genetic differentiation in the two mating type populations from different locations. Pathogenicity assays revealed that both MAT1-1 and MAT1-2 populations were pathogenic to all 11 local sweet corn cultivars tested in this study. The potential of sexual reproduction, existence of genetic diversity in the two mating type populations, and pathogenicity suggest that B. maydis populations have independently clonally adapted under natural field conditions during corn cultivation.
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Affiliation(s)
- Yuli Dai
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian Province 350013, China
| | - Lin Gan
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian Province 350013, China
| | - Hongchun Ruan
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian Province 350013, China
| | - Niuniu Shi
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian Province 350013, China
| | - Yixin Du
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian Province 350013, China
| | - Furu Chen
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian Province 350013, China
| | - Xiujuan Yang
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian Province 350013, China
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12
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Nsibo DL, Barnes I, Kunene NT, Berger DK. Influence of farming practices on the population genetics of the maize pathogen Cercospora zeina in South Africa. Fungal Genet Biol 2019; 125:36-44. [DOI: 10.1016/j.fgb.2019.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 12/11/2018] [Accepted: 01/11/2019] [Indexed: 12/14/2022]
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13
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Luo X, Cao J, Huang J, Wang Z, Guo Z, Chen Y, Ma S, Liu J. Genome sequencing and comparative genomics reveal the potential pathogenic mechanism of Cercospora sojina Hara on soybean. DNA Res 2018; 25:25-37. [PMID: 28985305 PMCID: PMC5824798 DOI: 10.1093/dnares/dsx035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 08/16/2017] [Indexed: 01/10/2023] Open
Abstract
Frogeye leaf spot, caused by Cercospora sojina Hara, is a common disease of soybean in most soybean-growing countries of the world. In this study, we report a high-quality genome sequence of C. sojina by Single Molecule Real-Time sequencing method. The 40.8-Mb genome encodes 11,655 predicated genes, and 8,474 genes are revealed by RNA sequencing. Cercospora sojina genome contains large numbers of gene clusters that are involved in synthesis of secondary metabolites, including mycotoxins and pigments. However, much less carbohydrate-binding module protein encoding genes are identified in C. sojina genome, when compared with other phytopathogenic fungi. Bioinformatics analysis reveals that C. sojina harbours about 752 secreted proteins, and 233 of them are effectors. During early infection, the genes for metabolite biosynthesis and effectors are significantly enriched, suggesting that they may play essential roles in pathogenicity. We further identify 13 effectors that can inhibit BAX-induced cell death. Taken together, our results provide insights into the infection mechanisms of C. sojina on soybean.
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Affiliation(s)
- Xuming Luo
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jidong Cao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Junkai Huang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zongyi Wang
- Beijing Key Laboratory of Agricultural Product Detection and Control for Spoilage Organisms and Pesticides, Beijing University of Agriculture, Beijing 102206, China
| | - Zhengyan Guo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yihua Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shumei Ma
- Department of Plant Protection, College of Agriculture Resources and Environment, Heilongjiang University, Harbin 150080, China
| | - Jun Liu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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14
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Shrestha SK, Cochran A, Mengistu A, Lamour K, Castro-Rocha A, Young-Kelly H. Genetic diversity, QoI fungicide resistance, and mating type distribution of Cercospora sojina-Implications for the disease dynamics of frogeye leaf spot on soybean. PLoS One 2017; 12:e0177220. [PMID: 28486517 PMCID: PMC5423647 DOI: 10.1371/journal.pone.0177220] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 04/24/2017] [Indexed: 11/19/2022] Open
Abstract
Frogeye leaf spot (FLS), caused by Cercospora sojina, causes significant damage to soybean in the U.S. One control strategy is the use of quinone outside inhibitor (QoI) fungicides. QoI resistant isolates were first reported in Tennessee (TN) in 2010. To investigate the disease dynamics of C. sojina, we collected 437 C. sojina isolates in 2015 from Jackson and Milan, TN and used 40 historical isolates collected from 2006-2009 from TN and ten additional states for comparison. A subset of 186 isolates, including historical isolates, were genotyped for 49 single nucleotide polymorphism (SNP) markers and the QoI resistance locus, revealing 35 unique genotypes. The genotypes clustered into three groups with two groups containing only sensitive isolates and the remaining group containing all resistant isolates and a dominant clonal lineage of 130 isolates. All 477 C. sojina isolates were genotyped for the QoI locus revealing 344 resistant and 133 sensitive isolates. All isolates collected prior to 2015 were QoI sensitive. Both mating type alleles (MAT1-1-1 and MAT1-2) were found in Jackson and Milan, TN and recovered from single lesions suggesting sexual recombination may play a role in the epidemiology of field populations. Analysis of C. sojina isolates using SNP markers proved useful to investigate population diversity and to elaborate on diversity as it relates to QoI resistance and mating type.
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Affiliation(s)
- Sandesh Kumar Shrestha
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Alicia Cochran
- Department of Entomology and Plant Pathology, University of Tennessee, Jackson, Tennessee, United States of America
| | - Alemu Mengistu
- United States Department of Agriculture, Agriculture Research Service, Jackson, Tennessee, United States of America
| | - Kurt Lamour
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Arturo Castro-Rocha
- Departamento de Ciencias Químico-Biológicas, Universidad Autónoma de Cd. Juárez, Chihuahua, Mexico
| | - Heather Young-Kelly
- Department of Entomology and Plant Pathology, University of Tennessee, Jackson, Tennessee, United States of America
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15
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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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16
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Human MP, Barnes I, Craven M, Crampton BG. Lack of Population Structure and Mixed Reproduction Modes in Exserohilum turcicum from South Africa. PHYTOPATHOLOGY 2016; 106:1386-1392. [PMID: 27392177 DOI: 10.1094/phyto-12-15-0311-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Exserohilum turcicum is the causal agent of northern corn leaf blight, a destructive foliar disease of maize that results in yield losses worldwide. In South Africa, typical yield losses range from 15 to 30%. Previous studies found high haplotypic diversity with evidence for sexual recombination in E. turcicum populations from tropical climates such as Kenya. However, the population genetic structure and method of reproduction of E. turcicum in South Africa is unknown and, therefore, was investigated. Twelve polymorphic microsatellite markers were screened on 258 E. turcicum isolates from maize collected during 2012 and 2013 from three maize fields in South Africa. A multiplex polymerase chain reaction assay amplifying both mating type idiomorphs was applied to investigate the distribution of mating types. No distinct genetic clusters were observed. Shared haplotypes were identified between isolates separated by distances of up to 762 km, which provided evidence of migration. High haplotypic diversity indicated that sexual reproduction is occurring among E. turcicum isolates, although mating type ratios and linkage disequilibrium analyses did not support the hypothesis of random mating. The population genetic structure of E. turcicum in South Africa is likely due to the direct movement and spread of isolates undergoing a mixed reproductive lifecycle.
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Affiliation(s)
- Maria Petronella Human
- First and fourth authors: Department of Plant and Soil Sciences, and second author: Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0002, South Africa; and third author: Agricultural Research Council-Grain Crops Institute, Potchefstroom, 2520, South Africa
| | - Irene Barnes
- First and fourth authors: Department of Plant and Soil Sciences, and second author: Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0002, South Africa; and third author: Agricultural Research Council-Grain Crops Institute, Potchefstroom, 2520, South Africa
| | - Maryke Craven
- First and fourth authors: Department of Plant and Soil Sciences, and second author: Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0002, South Africa; and third author: Agricultural Research Council-Grain Crops Institute, Potchefstroom, 2520, South Africa
| | - Bridget Genevieve Crampton
- First and fourth authors: Department of Plant and Soil Sciences, and second author: Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0002, South Africa; and third author: Agricultural Research Council-Grain Crops Institute, Potchefstroom, 2520, South Africa
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17
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Muller MF, Barnes I, Kunene NT, Crampton BG, Bluhm BH, Phillips SM, Olivier NA, Berger DK. Cercospora zeina from Maize in South Africa Exhibits High Genetic Diversity and Lack of Regional Population Differentiation. PHYTOPATHOLOGY 2016; 106:1194-1205. [PMID: 27392176 DOI: 10.1094/phyto-02-16-0084-fi] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
South Africa is one of the leading maize-producing countries in sub-Saharan Africa. Since the 1980s, Cercospora zeina, a causal agent of gray leaf spot of maize, has become endemic in South Africa, and is responsible for substantial yield reductions. To assess genetic diversity and population structure of C. zeina in South Africa, 369 isolates were collected from commercial maize farms in three provinces (KwaZulu-Natal, Mpumalanga, and North West). These isolates were evaluated with 14 microsatellite markers and species-specific mating type markers that were designed from draft genome sequences of C. zeina isolates from Africa (CMW 25467) and the United States (USPA-4). Sixty alleles were identified across 14 loci, and gene diversity values within each province ranged from 0.18 to 0.35. High levels of gene flow were observed (Nm = 5.51), and in a few cases, identical multilocus haplotypes were found in different provinces. Overall, 242 unique multilocus haplotypes were identified with a low clonal fraction of 34%. No distinct population clusters were identified using STRUCTURE, principal coordinate analysis, or Weir's theta θ statistic. The lack of population differentiation was supported by analysis of molecular variance tests, which indicated that only 2% of the variation was attributed to variability between populations from each province. Mating type ratios of MAT1-1 and MAT1-2 idiomorphs from 335 isolates were not significantly different from a 1:1 ratio in all provinces, which provided evidence for sexual reproduction. The draft genome of C. zeina CMW 25467 exhibited a complete genomic copy of the MAT1-1 idiomorph as well as exonic fragments of MAT genes from both idiomorphs. The high level of gene diversity, shared haplotypes at different geographical locations within South Africa, and presence of both MAT idiomorphs at all sites indicates widespread dispersal of C. zeina between maize fields in the country as well as evidence for sexual recombination. The outcomes of this genome-enabled study are important for disease management since the high diversity has implications for dispersal of fungicide resistance should it emerge and the need for diversified resistance breeding.
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Affiliation(s)
- Mischa F Muller
- First, third, fourth, sixth, seventh, and eighth authors: Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa; second author: Department of Genetics, FABI, University of Pretoria, Pretoria 0028, South Africa; fifth author: Department of Plant Pathology, University of Arkansas; and seventh author: Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa
| | - Irene Barnes
- First, third, fourth, sixth, seventh, and eighth authors: Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa; second author: Department of Genetics, FABI, University of Pretoria, Pretoria 0028, South Africa; fifth author: Department of Plant Pathology, University of Arkansas; and seventh author: Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa
| | - Ncobile T Kunene
- First, third, fourth, sixth, seventh, and eighth authors: Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa; second author: Department of Genetics, FABI, University of Pretoria, Pretoria 0028, South Africa; fifth author: Department of Plant Pathology, University of Arkansas; and seventh author: Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa
| | - Bridget G Crampton
- First, third, fourth, sixth, seventh, and eighth authors: Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa; second author: Department of Genetics, FABI, University of Pretoria, Pretoria 0028, South Africa; fifth author: Department of Plant Pathology, University of Arkansas; and seventh author: Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa
| | - Burton H Bluhm
- First, third, fourth, sixth, seventh, and eighth authors: Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa; second author: Department of Genetics, FABI, University of Pretoria, Pretoria 0028, South Africa; fifth author: Department of Plant Pathology, University of Arkansas; and seventh author: Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa
| | - Sonia M Phillips
- First, third, fourth, sixth, seventh, and eighth authors: Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa; second author: Department of Genetics, FABI, University of Pretoria, Pretoria 0028, South Africa; fifth author: Department of Plant Pathology, University of Arkansas; and seventh author: Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa
| | - Nicholas A Olivier
- First, third, fourth, sixth, seventh, and eighth authors: Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa; second author: Department of Genetics, FABI, University of Pretoria, Pretoria 0028, South Africa; fifth author: Department of Plant Pathology, University of Arkansas; and seventh author: Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa
| | - Dave K Berger
- First, third, fourth, sixth, seventh, and eighth authors: Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa; second author: Department of Genetics, FABI, University of Pretoria, Pretoria 0028, South Africa; fifth author: Department of Plant Pathology, University of Arkansas; and seventh author: Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa
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18
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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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19
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Zeng F, Arnao E, Zhang G, Olaya G, Wullschleger J, Sierotzki H, Ming R, Bluhm BH, Bond JP, Fakhoury AM, Bradley CA. Characterization of Quinone Outside Inhibitor Fungicide Resistance in Cercospora sojina and Development of Diagnostic Tools for its Identification. PLANT DISEASE 2015; 99:544-550. [PMID: 30699555 DOI: 10.1094/pdis-05-14-0460-re] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Frogeye leaf spot of soybean, caused by the fungus Cercospora sojina, reduces soybean yields in most of the top-producing countries around the world. Control strategies for frogeye leaf spot can rely heavily on quinone outside inhibitor (QoI) fungicides. In 2010, QoI fungicide-resistant C. sojina isolates were identified in Tennessee for the first time. As the target of QoI fungicides, the cytochrome b gene present in fungal mitochondria has played a key role in the development of resistance to this fungicide class. The cytochrome b genes from three QoI-sensitive and three QoI-resistant C. sojina isolates were cloned and sequenced. The complete coding sequence of the cytochrome b gene was identified and found to encode 396 amino acids. The QoI-resistant C. sojina isolates contained the G143A mutation in the cytochrome b gene, a guanidine to cytosine transversion at the second position in codon 143 that causes an amino acid substitution of alanine for glycine. C. sojina-specific polymerase chain reaction primer sets and TaqMan probes were developed to efficiently discriminate QoI-resistant and -sensitive isolates. The molecular basis of QoI fungicide resistance in field isolates of C. sojina was identified as the G143A mutation, and specific molecular approaches were developed to discriminate and to track QoI-resistant and -sensitive isolates of C. sojina.
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Affiliation(s)
- F Zeng
- Department of Plant Biology, University of Illinois, Urbana 61801, and State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, China
| | - E Arnao
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale 62901
| | - G Zhang
- Department of Crop Sciences, University of Illinois
| | - G Olaya
- Syngenta Crop Protection, Vero Beach, FL 32967
| | | | - H Sierotzki
- Syngenta Crop Protection, Stein, Switzerland
| | - R Ming
- Department of Plant Biology, University of Illinois
| | - B H Bluhm
- Department of Plant Pathology, University of Arkansas, Fayetteville 72701
| | - J P Bond
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University
| | - A M Fakhoury
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University
| | - C A Bradley
- Department of Crop Sciences, University of Illinois
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20
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Nascimento KJT, Debona D, França SKS, Gonçalves MGM, DaMatta FM, Rodrigues FÁ. Soybean Resistance to Cercospora sojina Infection Is Reduced by Silicon. PHYTOPATHOLOGY 2014; 104:1183-91. [PMID: 24805073 DOI: 10.1094/phyto-02-14-0047-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Frogeye leaf spot, caused by Cercospora sojina, is one of the most important leaf diseases of soybean worldwide. Silicon (Si) is known to increase the resistance of several plant species to pathogens. The cultivars Bossier and Conquista, which are susceptible and resistant, respectively, to frogeye leaf spot, supplied and nonsupplied with Si were examined for the activities of defense enzymes and the concentrations of total soluble phenolics (TSP) and lignin-thioglycolic acid (LTGA) derivatives at 8, 14, and 16 days after inoculation (dai) with C. sojina. The importance of cell wall degrading enzymes (CWDE) to the infection process of C. sojina and the effect of Si on their activities were also determined. Soybean plants were grown in hydroponic culture containing either 0 or 2 mM Si (-Si and +Si, respectively) and noninoculated or C. sojina inoculated. Severity of frogeye leaf spot was higher in cultivar Bossier plants than cultivar Conquista and also in the +Si plants compared with their -Si counterparts. Except for the concentrations of TSP and LTGA derivatives, activities of defense enzymes and the CWDE did not change for +Si noninoculated plants regardless of the cultivar. The activities of lipoxygenases, phenylalanine ammonia-lyases, chitinases, and polyphenoloxidases as well as the activities of CWDE decreased for the +Si inoculated plants. The results from this study demonstrated that defense enzyme activities decreased in soybean plants supplied with Si, which compromised resistance to C. sojina infection.
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