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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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Kashiwa T, Suzuki T. High-quality genome assembly of the soybean fungal pathogen Cercospora kikuchii. G3 (BETHESDA, MD.) 2021; 11:jkab277. [PMID: 34568928 PMCID: PMC8496228 DOI: 10.1093/g3journal/jkab277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 07/29/2021] [Indexed: 11/12/2022]
Abstract
Plant diseases caused by the Cercospora genus of ascomycete fungi are a major concern for commercial agricultural practices. Several Cercospora species can affect soybeans, such as Cercospora kikuchii which causes soybean leaf blight. Speciation in Cercospora on soybean has not been adequately studied. Some cryptic groups of Cercospora also cause diseases on soybean. Moreover, it has been known C. kikuchii population genetic structure is different between countries. Consequently, further genomic information could help to elucidate the covert differentiation of Cercospora diseases in soybean. Here, we report for the first time, a chromosome-level genome assembly for C. kikuchii. The genome assembly of 9 contigs was 34.44 Mb and the N50 was 4.19 Mb. Based on ab initio gene prediction, several candidates for pathogenicity-related genes, including 242 genes for putative effectors, 55 secondary metabolite gene clusters, and 399 carbohydrate-active enzyme genes were identified. The genome sequence and the features described in this study provide a solid foundation for comparative and evolutionary genomic analysis for Cercospora species that cause soybean diseases worldwide.
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Affiliation(s)
- Takeshi Kashiwa
- Biological Resources and Post-harvest Division, Japan International Research
Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki 305-8686,
Japan
| | - Tomohiro Suzuki
- Center for Bioscience Research and Education, Utsunomiya
University, Utsunomiya, Tochigi 321-8505, Japan
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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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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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Kim H, Newell AD, Cota-Sieckmeyer RG, Rupe JC, Fakhoury AM, Bluhm BH. Mating-type distribution and genetic diversity of Cercospora sojina populations on soybean from Arkansas: evidence for potential sexual reproduction. PHYTOPATHOLOGY 2013; 103:1045-51. [PMID: 23721180 DOI: 10.1094/phyto-09-12-0229-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Cercospora sojina causes frogeye leaf spot of soybean, which can cause serious economic losses in the United States. In this study, 132 C. sojina isolates were collected from six fields (from two counties, Cross and Crawford) in Arkansas. To determine mating type, a multiplex polymerase chain reaction assay was developed with primers specific for C. sojina. Of the 132 isolates, 68 isolates had the MAT1-1-1 idiomorph and 64 isolates had the MAT1-2 idiomorph; no isolates possessed both idiomorphs. Both mating types were present in a variety of spatial scales, including separate lesions on individual leaves. Clone-corrected data from eight microsatellites indicated that mating-type loci were present in approximately equal proportions in all populations analyzed, which suggests that Arkansas populations of C. sojina are undergoing cryptic sexual reproduction. All six populations evaluated had high genotypic diversity of 26 to 79%. In addition, among strains isolated from a single leaf, multiple and distinct haplotypes were associated with both mating types, supporting the hypothesis that sexual reproduction occurs within the populations. Most populations showed significant gametic disequilibrium but levels of disequilibrium were relatively low, particularly in populations from Crawford County. A low differentiation index (GST) was observed for all simple-sequence repeat markers across all populations. Furthermore, the value of G statistics between populations suggests that significant genetic exchange exists among the populations. Taken together, these results demonstrate that C. sojina populations from Arkansas are genetically diverse and most likely undergoing sexual reproduction.
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Cai G, Schneider RW, Padgett GB. Assessment of Lineages of Cercospora kikuchii in Louisiana for Aggressiveness and Screening Soybean Cultivars for Resistance to Cercospora Leaf Blight. PLANT DISEASE 2009; 93:868-874. [PMID: 30754540 DOI: 10.1094/pdis-93-9-0868] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Cercospora leaf blight (CLB) became much more prevalent in Louisiana beginning in 1999. A previous study showed that the Louisiana population of Cercospora kikuchii, the causal agent, was dominated by a new lineage that differed from those collected in other locations at earlier times. In this study, we tested whether the dominance of the new lineage was caused by higher aggressiveness and screened soybean cultivars for resistance to CLB. Representative isolates from both lineages were used individually to inoculate six soybean cultivars in the greenhouse. Contrary to expectations, the new lineage was less aggressive. Three virulence groups were defined in this pathogen based on correlation of the aggressiveness of individual isolates on soybean cultivars. Other possible causes that led to the dominance of the new lineage in Louisiana are discussed. Eleven soybean cultivars were tested for disease reaction at two locations over 3 years in the field. Two cultivars, AG5701 (Asgrow) and TV59R85 (Terral), were among the more resistant cultivars to CLB both in the greenhouse and in the field.
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Affiliation(s)
- Guohong Cai
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge 70803
| | - Raymond W Schneider
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge 70803
| | - Guy B Padgett
- Macon Ridge Research Station, Louisiana State University Agricultural Center, Winnsboro 71295
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Cai G, Schneider RW. Population structure of Cercospora kikuchii, the causal agent of Cercospora leaf blight and purple seed stain in soybean. PHYTOPATHOLOGY 2008; 98:823-9. [PMID: 18943259 DOI: 10.1094/phyto-98-7-0823] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Random amplified polymorphic DNA (RAPD) and microsatellite-primed polymerase chain reaction (MP-PCR) were used to characterize 164 isolates of Cercospora kikuchii, most of which were collected from Louisiana. Plant tissue (seeds versus leaves), but not host cultivar, had a significant impact on pathogen population differentiation. Cluster analysis showed that the Louisiana population was dominated by a primary lineage (group I) with only a few Louisiana isolates belonging to the minor lineage that also included the non-Louisiana isolates (group II). A previous study showed that isolates could be differentiated according to vegetative compatibility groups (VCGs). However, RAPD and MP-PCR data demonstrated that isolates of C. kikuchii were not generally clustered according to these VCGs. Furthermore, genetic relationships within and between VCGs were examined using sequences of the intergenic spacer region of rDNA. These analyses showed that VCG is not an indicator of evolutionary lineage in this fungus. Our results suggest the likely existence of a cryptically functioning sexual stage in some portion of the C. kikuchii population.
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Affiliation(s)
- G Cai
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
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