Graph-based pangenomics maximizes genotyping density and reveals structural impacts on fungal resistance in melon
The power of pangenomic graphs to improve genetic mapping is still unclear. Here, the authors demonstrate its value in identification of genetic variants associated with disease resistance traits in melon using PanPipes, a pangenome construction and low-coverage genotype-by-sequencing pipeline.
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2022-12-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-022-35621-7 |
| _version_ | 1797977324574998528 |
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| author | Justin N. Vaughn Sandra E. Branham Brian Abernathy Amanda M. Hulse-Kemp Adam R. Rivers Amnon Levi William P. Wechter |
| author_facet | Justin N. Vaughn Sandra E. Branham Brian Abernathy Amanda M. Hulse-Kemp Adam R. Rivers Amnon Levi William P. Wechter |
| author_sort | Justin N. Vaughn |
| collection | DOAJ |
| description | The power of pangenomic graphs to improve genetic mapping is still unclear. Here, the authors demonstrate its value in identification of genetic variants associated with disease resistance traits in melon using PanPipes, a pangenome construction and low-coverage genotype-by-sequencing pipeline. |
| first_indexed | 2024-04-11T05:06:08Z |
| format | Article |
| id | doaj.art-2edc9b2e0e0a44ccb0e3ceffeaa28fb8 |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-04-11T05:06:08Z |
| publishDate | 2022-12-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-2edc9b2e0e0a44ccb0e3ceffeaa28fb82022-12-25T12:21:50ZengNature PortfolioNature Communications2041-17232022-12-0113111410.1038/s41467-022-35621-7Graph-based pangenomics maximizes genotyping density and reveals structural impacts on fungal resistance in melonJustin N. Vaughn0Sandra E. Branham1Brian Abernathy2Amanda M. Hulse-Kemp3Adam R. Rivers4Amnon Levi5William P. Wechter6Genomics and Bioinformatics Research Unit, The Agricultural Research Service of U.S. Department of AgriculturePlant and Environmental Sciences Department, Coastal Research and Education Center, Clemson UniversityDepartment of Crop and Soil Sciences, University of GeorgiaGenomics and Bioinformatics Research Unit, The Agricultural Research Service of U.S. Department of AgricultureGenomics and Bioinformatics Research Unit, The Agricultural Research Service of U.S. Department of AgricultureUS Vegetable Laboratory, The Agricultural Research Service of U.S. Department of AgriculturePlant and Environmental Sciences Department, Coastal Research and Education Center, Clemson UniversityThe power of pangenomic graphs to improve genetic mapping is still unclear. Here, the authors demonstrate its value in identification of genetic variants associated with disease resistance traits in melon using PanPipes, a pangenome construction and low-coverage genotype-by-sequencing pipeline.https://doi.org/10.1038/s41467-022-35621-7 |
| spellingShingle | Justin N. Vaughn Sandra E. Branham Brian Abernathy Amanda M. Hulse-Kemp Adam R. Rivers Amnon Levi William P. Wechter Graph-based pangenomics maximizes genotyping density and reveals structural impacts on fungal resistance in melon Nature Communications |
| title | Graph-based pangenomics maximizes genotyping density and reveals structural impacts on fungal resistance in melon |
| title_full | Graph-based pangenomics maximizes genotyping density and reveals structural impacts on fungal resistance in melon |
| title_fullStr | Graph-based pangenomics maximizes genotyping density and reveals structural impacts on fungal resistance in melon |
| title_full_unstemmed | Graph-based pangenomics maximizes genotyping density and reveals structural impacts on fungal resistance in melon |
| title_short | Graph-based pangenomics maximizes genotyping density and reveals structural impacts on fungal resistance in melon |
| title_sort | graph based pangenomics maximizes genotyping density and reveals structural impacts on fungal resistance in melon |
| url | https://doi.org/10.1038/s41467-022-35621-7 |
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