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Poudel RS, Belay K, Nelson B, Brueggeman R, Underwood W. Population and genome-wide association studies of Sclerotinia sclerotiorum isolates collected from diverse host plants throughout the United States. Front Microbiol 2023; 14:1251003. [PMID: 37829452 PMCID: PMC10566370 DOI: 10.3389/fmicb.2023.1251003] [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: 06/30/2023] [Accepted: 08/29/2023] [Indexed: 10/14/2023] Open
Abstract
Introduction Sclerotinia sclerotiorum is a necrotrophic fungal pathogen causing disease and economic loss on numerous crop plants. This fungus has a broad host range and can infect over 400 plant species, including important oilseed crops such as soybean, canola, and sunflower. S. sclerotiorum isolates vary in aggressiveness of lesion formation on plant tissues. However, the genetic basis for this variation remains to be determined. The aims of this study were to evaluate a diverse collection of S. sclerotiorum isolates collected from numerous hosts and U.S. states for aggressiveness of stem lesion formation on sunflower, to evaluate the population characteristics, and to identify loci associated with isolate aggressiveness using genome-wide association mapping. Methods A total of 219 S. sclerotiorum isolates were evaluated for stem lesion formation on two sunflower inbred lines and genotyped using genotyping-by-sequencing. DNA markers were used to assess population differentiation across hosts, regions, and climatic conditions and to perform a genome-wide association study of isolate aggressiveness. Results and discussion We observed a broad range of aggressiveness for lesion formation on sunflower stems, and only a moderate correlation between aggressiveness on the two lines. Population genetic evaluations revealed differentiation between populations from warmer climate regions compared to cooler regions. Finally, a genome-wide association study of isolate aggressiveness identified three loci significantly associated with aggressiveness on sunflower. Functional characterization of candidate genes at these loci will likely improve our understanding of the virulence strategies used by this pathogen to cause disease on a wide array of agriculturally important host plants.
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Affiliation(s)
- Roshan Sharma Poudel
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | - Kassaye Belay
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | - Berlin Nelson
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | - Robert Brueggeman
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - William Underwood
- Edward T. Schafer Agricultural Research Center, Sunflower and Plant Biology Research Unit, USDA Agricultural Research Service, Fargo, ND, United States
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Ribone AI, Fass M, Gonzalez S, Lia V, Paniego N, Rivarola M. Co-Expression Networks in Sunflower: Harnessing the Power of Multi-Study Transcriptomic Public Data to Identify and Categorize Candidate Genes for Fungal Resistance. PLANTS (BASEL, SWITZERLAND) 2023; 12:2767. [PMID: 37570920 PMCID: PMC10421300 DOI: 10.3390/plants12152767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023]
Abstract
Fungal plant diseases are a major threat to food security worldwide. Current efforts to identify and list loci involved in different biological processes are more complicated than originally thought, even when complete genome assemblies are available. Despite numerous experimental and computational efforts to characterize gene functions in plants, about ~40% of protein-coding genes in the model plant Arabidopsis thaliana L. are still not categorized in the Gene Ontology (GO) Biological Process (BP) annotation. In non-model organisms, such as sunflower (Helianthus annuus L.), the number of BP term annotations is far fewer, ~22%. In the current study, we performed gene co-expression network analysis using eight terabytes of public transcriptome datasets and expression-based functional prediction to categorize and identify loci involved in the response to fungal pathogens. We were able to construct a reference gene network of healthy green tissue (GreenGCN) and a gene network of healthy and stressed root tissues (RootGCN). Both networks achieved robust, high-quality scores on the metrics of guilt-by-association and selective constraints versus gene connectivity. We were able to identify eight modules enriched in defense functions, of which two out of the three modules in the RootGCN were also conserved in the GreenGCN, suggesting similar defense-related expression patterns. We identified 16 WRKY genes involved in defense related functions and 65 previously uncharacterized loci now linked to defense response. In addition, we identified and classified 122 loci previously identified within QTLs or near candidate loci reported in GWAS studies of disease resistance in sunflower linked to defense response. All in all, we have implemented a valuable strategy to better describe genes within specific biological processes.
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Affiliation(s)
| | | | | | | | | | - Máximo Rivarola
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CICVyA—Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Los Reseros y Nicolás Repetto, Hurlingham 1686, Argentina; (A.I.R.); (M.F.); (S.G.); (V.L.); (N.P.)
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Filippi CV, Corro Molas A, Dominguez M, Colombo D, Heinz N, Troglia C, Maringolo C, Quiroz F, Alvarez D, Lia V, Paniego N. Genome-Wide Association Studies in Sunflower: Towards Sclerotinia sclerotiorum and Diaporthe/Phomopsis Resistance Breeding. Genes (Basel) 2022; 13:2357. [PMID: 36553624 PMCID: PMC9777803 DOI: 10.3390/genes13122357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/24/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022] Open
Abstract
Diseases caused by necrotrophic fungi, such as the cosmopolitan Sclerotinia sclerotiorum and the Diaporthe/Phomopsis complex, are among the most destructive diseases of sunflower worldwide. The lack of complete resistance combined with the inefficiency of chemical control makes assisted breeding the best strategy for disease control. In this work, we present an integrated genome-wide association (GWA) study investigating the response of a diverse panel of sunflower inbred lines to both pathogens. Phenotypic data for Sclerotinia head rot (SHR) consisted of five disease descriptors (disease incidence, DI; disease severity, DS; area under the disease progress curve for DI, AUDPCI, and DS, AUDPCS; and incubation period, IP). Two disease descriptors (DI and DS) were evaluated for two manifestations of Diaporthe/Phomopsis: Phomopsis stem canker (PSC) and Phomopsis head rot (PHR). In addition, a principal component (PC) analysis was used to derive transformed phenotypes as inputs to a univariate GWA (PC-GWA). Genotypic data comprised a panel of 4269 single nucleotide polymorphisms (SNP), generated via genotyping-by-sequencing. The GWA analysis revealed 24 unique marker-trait associations for SHR, 19 unique marker-trait associations for Diaporthe/Phomopsis diseases, and 7 markers associated with PC1 and PC2. No common markers were found for the response to the two pathogens. Nevertheless, epistatic interactions were identified between markers significantly associated with the response to S. sclerotiorum and Diaporthe/Phomopsis. This suggests that, while the main determinants of resistance may differ for the two pathogens, there could be an underlying common genetic basis. The exploration of regions physically close to the associated markers yielded 364 genes, of which 19 were predicted as putative disease resistance genes. This work presents the first simultaneous evaluation of two manifestations of Diaporthe/Phomopsis in sunflower, and undertakes a comprehensive GWA study by integrating PSC, PHR, and SHR data. The multiple regions identified, and their exploration to identify candidate genes, contribute not only to the understanding of the genetic basis of resistance, but also to the development of tools for assisted breeding.
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Affiliation(s)
- Carla Valeria Filippi
- Laboratorio de Bioquímica, Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Avenida Garzón 780, Montevideo 12900, Uruguay
- Instituto de Agrobiotecnología y Biología Molecular–IABiMo–INTA-CONICET, Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, INTA, Hurlingham B1686, Argentina
| | - Andres Corro Molas
- Agencia De Extensión Rural General Pico, INTA, Calle 13 N° 857, Gral. Pico L6360, Argentina
| | - Matias Dominguez
- Estación Experimental Agropecuaria Pergamino, INTA, Av. Frondizi Km 4.5, Pergamino B2700, Argentina
| | - Denis Colombo
- Estación Experimental Agropecuaria Anguil, INTA, Ruta Nacional 5 Km 580, Anguil L6326, Argentina
| | - Nicolas Heinz
- Estación Experimental Agropecuaria Manfredi, INTA, Ruta Nac. nro. 9 km 636, Manfredi X5988, Argentina
| | - Carolina Troglia
- Estación Experimental Agropecuaria Balcarce, INTA, Ruta 226 Km 73.5, Balcarce B7620, Argentina
| | - Carla Maringolo
- Estación Experimental Agropecuaria Balcarce, INTA, Ruta 226 Km 73.5, Balcarce B7620, Argentina
| | - Facundo Quiroz
- Estación Experimental Agropecuaria Balcarce, INTA, Ruta 226 Km 73.5, Balcarce B7620, Argentina
| | - Daniel Alvarez
- Estación Experimental Agropecuaria Manfredi, INTA, Ruta Nac. nro. 9 km 636, Manfredi X5988, Argentina
| | - Veronica Lia
- Instituto de Agrobiotecnología y Biología Molecular–IABiMo–INTA-CONICET, Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, INTA, Hurlingham B1686, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Autónoma de Buenos Aires C1428, Argentina
| | - Norma Paniego
- Instituto de Agrobiotecnología y Biología Molecular–IABiMo–INTA-CONICET, Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, INTA, Hurlingham B1686, Argentina
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Talukder ZI, Underwood W, Misar CG, Seiler GJ, Cai X, Li X, Qi L. A Quantitative Genetic Study of Sclerotinia Head Rot Resistance Introgressed from the Wild Perennial Helianthus maximiliani into Cultivated Sunflower ( Helianthus annuus L.). Int J Mol Sci 2022; 23:ijms23147727. [PMID: 35887074 PMCID: PMC9321925 DOI: 10.3390/ijms23147727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 11/27/2022] Open
Abstract
Sclerotinia head rot (HR), caused by Sclerotinia sclerotiorum, is an economically important disease of sunflower with known detrimental effects on yield and quality in humid climates worldwide. The objective of this study was to gain insight into the genetic architecture of HR resistance from a sunflower line HR21 harboring HR resistance introgressed from the wild perennial Helianthus maximiliani. An F2 population derived from the cross of HA 234 (susceptible-line)/HR21 (resistant-line) was evaluated for HR resistance at two locations during 2019−2020. Highly significant genetic variations (p < 0.001) were observed for HR disease incidence (DI) and disease severity (DS) in both individual and combined analyses. Broad sense heritability (H2) estimates across environments for DI and DS were 0.51 and 0.62, respectively. A high-density genetic map of 1420.287 cM was constructed with 6315 SNP/InDel markers developed using genotype-by-sequencing technology. A total of 16 genomic regions on eight sunflower chromosomes, 1, 2, 10, 12, 13, 14, 16 and 17 were associated with HR resistance, each explaining between 3.97 to 16.67% of the phenotypic variance for HR resistance. Eleven of these QTL had resistance alleles from the HR21 parent. Molecular markers flanking the QTL will facilitate marker-assisted selection breeding for HR resistance in sunflower.
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Affiliation(s)
- Zahirul I. Talukder
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USA; (Z.I.T.); (X.L.)
| | - William Underwood
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, 1616 Albrecht Blvd. N., Fargo, ND 58102, USA; (W.U.); (C.G.M.); (G.J.S.)
| | - Christopher G. Misar
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, 1616 Albrecht Blvd. N., Fargo, ND 58102, USA; (W.U.); (C.G.M.); (G.J.S.)
| | - Gerald J. Seiler
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, 1616 Albrecht Blvd. N., Fargo, ND 58102, USA; (W.U.); (C.G.M.); (G.J.S.)
| | - Xiwen Cai
- USDA-Agricultural Research Service, Wheat, Sorghum and Forage Research Unit, 251 Filley Hall, 1625 Arbor Drive, Lincoln, NE 68583, USA;
| | - Xuehui Li
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USA; (Z.I.T.); (X.L.)
| | - Lili Qi
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, 1616 Albrecht Blvd. N., Fargo, ND 58102, USA; (W.U.); (C.G.M.); (G.J.S.)
- Correspondence: ; Tel.: +1-701-239-1351
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Talukder ZI, Underwood W, Misar CG, Seiler GJ, Cai X, Li X, Qi L. Genomic Insights Into Sclerotinia Basal Stalk Rot Resistance Introgressed From Wild Helianthus praecox Into Cultivated Sunflower ( Helianthus annuus L.). FRONTIERS IN PLANT SCIENCE 2022; 13:840954. [PMID: 35665155 PMCID: PMC9158519 DOI: 10.3389/fpls.2022.840954] [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: 01/13/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Crop wild relatives of the cultivated sunflower (Helianthus annuus L.) are a valuable resource for its sustainable production. Helianthus praecox ssp. runyonii is a wild sunflower known for its resistance against diseases caused by the fungus, Sclerotinia sclerotiorum (Lib.) de Bary, which infects over 400 broadleaf hosts including many important food crops. The objective of this research was to dissect the Sclerotinia basal stalk rot (BSR) resistance introgressed from H. praecox ssp. runyonii into cultivated sunflower. An advanced backcross quantitative trait loci (AB-QTL) mapping population was developed from the cross of a H. praecox accession with cultivated sunflower lines. The AB-QTL population was evaluated for BSR resistance in the field during the summers of 2017-2018 and in the greenhouse in the spring of 2018. Highly significant genetic variations (p < 0.001) were observed for the BSR disease in the field and greenhouse with a moderately high broad-sense heritability (H 2) ranging from 0.66 to 0.73. Genotyping-by-sequencing approach was used to genotype the parents and the progeny lines of the AB-QTL population. A genetic linkage map spanning 1,802.95 cM was constructed using 1,755 single nucleotide polymorphism (SNP) markers mapped on 17 sunflower chromosomes. A total of 19 BSR resistance QTL were detected on nine sunflower chromosomes, each explaining 2.21%-16.99% of the phenotypic variance for resistance in the AB-QTL population. Sixteen of the 19 QTL had alleles conferring increased BSR resistance derived from the H. praecox parent. SNP markers flanking the identified QTL will facilitate marker-assisted breeding to combat the disease in sunflower.
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Affiliation(s)
- Zahirul I. Talukder
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - William Underwood
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Christopher G. Misar
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Gerald J. Seiler
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Xiwen Cai
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Xuehui Li
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Lili Qi
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
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Talukder ZI, Underwood W, Misar CG, Seiler GJ, Liu Y, Li X, Cai X, Qi L. Unraveling the Sclerotinia Basal Stalk Rot Resistance Derived From Wild Helianthus argophyllus Using a High-Density Single Nucleotide Polymorphism Linkage Map. FRONTIERS IN PLANT SCIENCE 2021; 11:617920. [PMID: 33613588 PMCID: PMC7886805 DOI: 10.3389/fpls.2020.617920] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/21/2020] [Indexed: 05/30/2023]
Abstract
Basal stalk rot (BSR), caused by the fungus Sclerotinia sclerotiorum, is a serious disease of sunflower (Helianthus annuus L.) in the humid temperate growing areas of the world. BSR resistance is quantitative and conditioned by multiple genes. Our objective was to dissect the BSR resistance introduced from the wild annual species Helianthus argophyllus using a quantitative trait loci (QTL) mapping approach. An advanced backcross population (AB-QTL) with 134 lines derived from the cross of HA 89 with a H. argophyllus Torr. and Gray accession, PI 494573, was evaluated for BSR resistance in three field and one greenhouse growing seasons of 2017-2019. Highly significant genetic variations (p < 0.001) were observed for BSR disease incidence (DI) in all field screening tests and disease rating and area under the disease progress curve in the greenhouse. The AB-QTL population and its parental lines were genotyped using the genotyping-by-sequencing method. A genetic linkage map spanning 2,045.14 cM was constructed using 3,110 SNP markers mapped on 17 sunflower chromosomes. A total of 21 QTL associated with BSR resistance were detected on 11 chromosomes, each explaining a phenotypic variation ranging from 4.5 to 22.6%. Of the 21 QTL, eight were detected for BSR DI measured in the field, seven were detected for traits measured in the greenhouse, and six were detected from both field and greenhouse tests. Thirteen of the 21 QTL had favorable alleles from the H. argophyllus parent conferring increased BSR resistance.
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Affiliation(s)
- Zahirul I. Talukder
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - William Underwood
- United States Department of Agriculture – Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Christopher G. Misar
- United States Department of Agriculture – Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Gerald J. Seiler
- United States Department of Agriculture – Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Yuan Liu
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Xuehui Li
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Xiwen Cai
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Lili Qi
- United States Department of Agriculture – Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
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