Genome-Wide Association Studies in Sunflower: Towards Sclerotinia sclerotiorum and Diaporthe/Phomopsis Resistance Breeding
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...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-12-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/13/12/2357 |
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| author | Carla Valeria Filippi Andres Corro Molas Matias Dominguez Denis Colombo Nicolas Heinz Carolina Troglia Carla Maringolo Facundo Quiroz Daniel Alvarez Veronica Lia Norma Paniego |
| author_facet | Carla Valeria Filippi Andres Corro Molas Matias Dominguez Denis Colombo Nicolas Heinz Carolina Troglia Carla Maringolo Facundo Quiroz Daniel Alvarez Veronica Lia Norma Paniego |
| author_sort | Carla Valeria Filippi |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T16:28:22Z |
| format | Article |
| id | doaj.art-5464fd14419240e588af6445a75a7283 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-09T16:28:22Z |
| publishDate | 2022-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-5464fd14419240e588af6445a75a72832023-11-24T15:05:35ZengMDPI AGGenes2073-44252022-12-011312235710.3390/genes13122357Genome-Wide Association Studies in Sunflower: Towards Sclerotinia sclerotiorum and Diaporthe/Phomopsis Resistance BreedingCarla Valeria Filippi0Andres Corro Molas1Matias Dominguez2Denis Colombo3Nicolas Heinz4Carolina Troglia5Carla Maringolo6Facundo Quiroz7Daniel Alvarez8Veronica Lia9Norma Paniego10Laboratorio de Bioquímica, Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Avenida Garzón 780, Montevideo 12900, UruguayAgencia De Extensión Rural General Pico, INTA, Calle 13 N° 857, Gral. Pico L6360, ArgentinaEstación Experimental Agropecuaria Pergamino, INTA, Av. Frondizi Km 4.5, Pergamino B2700, ArgentinaEstación Experimental Agropecuaria Anguil, INTA, Ruta Nacional 5 Km 580, Anguil L6326, ArgentinaEstación Experimental Agropecuaria Manfredi, INTA, Ruta Nac. nro. 9 km 636, Manfredi X5988, ArgentinaEstación Experimental Agropecuaria Balcarce, INTA, Ruta 226 Km 73.5, Balcarce B7620, ArgentinaEstación Experimental Agropecuaria Balcarce, INTA, Ruta 226 Km 73.5, Balcarce B7620, ArgentinaEstación Experimental Agropecuaria Balcarce, INTA, Ruta 226 Km 73.5, Balcarce B7620, ArgentinaEstación Experimental Agropecuaria Manfredi, INTA, Ruta Nac. nro. 9 km 636, Manfredi X5988, ArgentinaInstituto de Agrobiotecnología y Biología Molecular–IABiMo–INTA-CONICET, Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, INTA, Hurlingham B1686, ArgentinaInstituto de Agrobiotecnología y Biología Molecular–IABiMo–INTA-CONICET, Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, INTA, Hurlingham B1686, ArgentinaDiseases 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.https://www.mdpi.com/2073-4425/13/12/2357sunflowerSclerotinia sclerotiorumDiaporthe/PhomopsisGWAS |
| spellingShingle | Carla Valeria Filippi Andres Corro Molas Matias Dominguez Denis Colombo Nicolas Heinz Carolina Troglia Carla Maringolo Facundo Quiroz Daniel Alvarez Veronica Lia Norma Paniego Genome-Wide Association Studies in Sunflower: Towards Sclerotinia sclerotiorum and Diaporthe/Phomopsis Resistance Breeding Genes sunflower Sclerotinia sclerotiorum Diaporthe/Phomopsis GWAS |
| title | Genome-Wide Association Studies in Sunflower: Towards Sclerotinia sclerotiorum and Diaporthe/Phomopsis Resistance Breeding |
| title_full | Genome-Wide Association Studies in Sunflower: Towards Sclerotinia sclerotiorum and Diaporthe/Phomopsis Resistance Breeding |
| title_fullStr | Genome-Wide Association Studies in Sunflower: Towards Sclerotinia sclerotiorum and Diaporthe/Phomopsis Resistance Breeding |
| title_full_unstemmed | Genome-Wide Association Studies in Sunflower: Towards Sclerotinia sclerotiorum and Diaporthe/Phomopsis Resistance Breeding |
| title_short | Genome-Wide Association Studies in Sunflower: Towards Sclerotinia sclerotiorum and Diaporthe/Phomopsis Resistance Breeding |
| title_sort | genome wide association studies in sunflower towards sclerotinia sclerotiorum and diaporthe phomopsis resistance breeding |
| topic | sunflower Sclerotinia sclerotiorum Diaporthe/Phomopsis GWAS |
| url | https://www.mdpi.com/2073-4425/13/12/2357 |
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