Genome-Wide Association Studies and Prediction of Tan Spot (<i>Pyrenophora tritici-repentis</i>) Infection in European Winter Wheat via Different Marker Platforms
Tan spot, caused by the fungus <i>Pyrenophora</i><i>tritici-repentis</i> (<i>Ptr</i>), is a severe foliar disease of wheat (<i>Triticum</i><i>aestivum</i> L.). Improving genetic resistance is a durable strategy to reduce <i>Ptr</i&...
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MDPI AG
2021-03-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/12/4/490 |
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| author | Quddoos H. Muqaddasi Roop Kamal Vilson Mirdita Bernd Rodemann Martin W. Ganal Jochen C. Reif Marion S. Röder |
| author_facet | Quddoos H. Muqaddasi Roop Kamal Vilson Mirdita Bernd Rodemann Martin W. Ganal Jochen C. Reif Marion S. Röder |
| author_sort | Quddoos H. Muqaddasi |
| collection | DOAJ |
| description | Tan spot, caused by the fungus <i>Pyrenophora</i><i>tritici-repentis</i> (<i>Ptr</i>), is a severe foliar disease of wheat (<i>Triticum</i><i>aestivum</i> L.). Improving genetic resistance is a durable strategy to reduce <i>Ptr</i>-related losses. Here, we dissected <i>Ptr</i>-infection’s genetic basis in 372 European wheat varieties via simple sequence repeats (SSRs) <i>plus</i> 35k and 90k single nucleotide polymorphism (SNP) marker platforms. In our phenotypic data analyses, <i>Ptr</i> infection showed a significant genotypic variance and a significant negative correlation with plant height. Genome-wide association studies revealed a highly quantitative nature of <i>Ptr</i> infection and identified two quantitative trait loci (QTL), viz., <i>QTs.ipk-7A</i> and <i>QTs.ipk-7B</i>, which imparted 21.23 and 5.84% of the genotypic variance, respectively. Besides, the <i>Rht-D1</i> gene showed a strong allelic influence on the infection scores. Due to the complex genetic nature of the <i>Ptr</i> infection, the potential of genome-wide prediction (GP) was assessed via three different genetic models on individual and combined marker platforms. The GP results indicated that the marker density and marker platforms do not considerably impact prediction accuracy (~40–42%) and that higher-order epistatic interactions may not be highly pervasive. Our results provide a further understanding of <i>Ptr</i>-infection’s genetic nature, serve as a resource for marker-assisted breeding, and highlight the potential of genome-wide selection for improved <i>Ptr</i> resistance. |
| first_indexed | 2024-03-10T12:50:07Z |
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| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T12:50:07Z |
| publishDate | 2021-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-3900a4b1b1e1437983c09cff19e078fd2023-11-21T13:05:32ZengMDPI AGGenes2073-44252021-03-0112449010.3390/genes12040490Genome-Wide Association Studies and Prediction of Tan Spot (<i>Pyrenophora tritici-repentis</i>) Infection in European Winter Wheat via Different Marker PlatformsQuddoos H. Muqaddasi0Roop Kamal1Vilson Mirdita2Bernd Rodemann3Martin W. Ganal4Jochen C. Reif5Marion S. Röder6Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, D-06466 Stadt Seeland OT Gatersleben, GermanyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, D-06466 Stadt Seeland OT Gatersleben, GermanyEuropean Wheat Breeding Center, BASF Agricultural Solutions GmbH, Am Schwabeplan 8, D-06466 Stadt Seeland OT Gatersleben, GermanyJulius-Kühn-Institute (JKI), D-38104 Braunschweig, GermanyTraitGenetics GmbH, Am Schwabeplan 1b, D-06466 Stadt Seeland OT Gatersleben, GermanyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, D-06466 Stadt Seeland OT Gatersleben, GermanyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, D-06466 Stadt Seeland OT Gatersleben, GermanyTan spot, caused by the fungus <i>Pyrenophora</i><i>tritici-repentis</i> (<i>Ptr</i>), is a severe foliar disease of wheat (<i>Triticum</i><i>aestivum</i> L.). Improving genetic resistance is a durable strategy to reduce <i>Ptr</i>-related losses. Here, we dissected <i>Ptr</i>-infection’s genetic basis in 372 European wheat varieties via simple sequence repeats (SSRs) <i>plus</i> 35k and 90k single nucleotide polymorphism (SNP) marker platforms. In our phenotypic data analyses, <i>Ptr</i> infection showed a significant genotypic variance and a significant negative correlation with plant height. Genome-wide association studies revealed a highly quantitative nature of <i>Ptr</i> infection and identified two quantitative trait loci (QTL), viz., <i>QTs.ipk-7A</i> and <i>QTs.ipk-7B</i>, which imparted 21.23 and 5.84% of the genotypic variance, respectively. Besides, the <i>Rht-D1</i> gene showed a strong allelic influence on the infection scores. Due to the complex genetic nature of the <i>Ptr</i> infection, the potential of genome-wide prediction (GP) was assessed via three different genetic models on individual and combined marker platforms. The GP results indicated that the marker density and marker platforms do not considerably impact prediction accuracy (~40–42%) and that higher-order epistatic interactions may not be highly pervasive. Our results provide a further understanding of <i>Ptr</i>-infection’s genetic nature, serve as a resource for marker-assisted breeding, and highlight the potential of genome-wide selection for improved <i>Ptr</i> resistance.https://www.mdpi.com/2073-4425/12/4/490wheattan spotGWASQTLgenome-wide prediction |
| spellingShingle | Quddoos H. Muqaddasi Roop Kamal Vilson Mirdita Bernd Rodemann Martin W. Ganal Jochen C. Reif Marion S. Röder Genome-Wide Association Studies and Prediction of Tan Spot (<i>Pyrenophora tritici-repentis</i>) Infection in European Winter Wheat via Different Marker Platforms Genes wheat tan spot GWAS QTL genome-wide prediction |
| title | Genome-Wide Association Studies and Prediction of Tan Spot (<i>Pyrenophora tritici-repentis</i>) Infection in European Winter Wheat via Different Marker Platforms |
| title_full | Genome-Wide Association Studies and Prediction of Tan Spot (<i>Pyrenophora tritici-repentis</i>) Infection in European Winter Wheat via Different Marker Platforms |
| title_fullStr | Genome-Wide Association Studies and Prediction of Tan Spot (<i>Pyrenophora tritici-repentis</i>) Infection in European Winter Wheat via Different Marker Platforms |
| title_full_unstemmed | Genome-Wide Association Studies and Prediction of Tan Spot (<i>Pyrenophora tritici-repentis</i>) Infection in European Winter Wheat via Different Marker Platforms |
| title_short | Genome-Wide Association Studies and Prediction of Tan Spot (<i>Pyrenophora tritici-repentis</i>) Infection in European Winter Wheat via Different Marker Platforms |
| title_sort | genome wide association studies and prediction of tan spot i pyrenophora tritici repentis i infection in european winter wheat via different marker platforms |
| topic | wheat tan spot GWAS QTL genome-wide prediction |
| url | https://www.mdpi.com/2073-4425/12/4/490 |
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