Identifying genetically redundant accessions in the world’s largest cassava collection
Crop diversity conserved in genebanks facilitates the development of superior varieties, improving yields, nutrition, adaptation to climate change and resilience against pests and diseases. Cassava ( Manihot esculenta ) plays a vital role in providing carbohydrates to approximately 500 million peopl...
| Autores principales: | , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Frontiers Media
2024
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| Acceso en línea: | https://hdl.handle.net/10568/139417 |
| _version_ | 1855530967816470528 |
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| author | Carvajal-Yepes, Monica Ospina, Jessica Alejandra Aranzales Rondón, Ericson Velez-Tobon, Monica Correa-Abondano, Miguel Manrique-Carpintero, Norma Constanza Wenzl, Peter |
| author_browse | Aranzales Rondón, Ericson Carvajal-Yepes, Monica Correa-Abondano, Miguel Manrique-Carpintero, Norma Constanza Ospina, Jessica Alejandra Velez-Tobon, Monica Wenzl, Peter |
| author_facet | Carvajal-Yepes, Monica Ospina, Jessica Alejandra Aranzales Rondón, Ericson Velez-Tobon, Monica Correa-Abondano, Miguel Manrique-Carpintero, Norma Constanza Wenzl, Peter |
| author_sort | Carvajal-Yepes, Monica |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Crop diversity conserved in genebanks facilitates the development of superior varieties, improving yields, nutrition, adaptation to climate change and resilience against pests and diseases. Cassava ( Manihot esculenta ) plays a vital role in providing carbohydrates to approximately 500 million people in Africa and other continents. The International Center for Tropical Agriculture (CIAT) conserves the largest global cassava collection, housing 5,963 accessions of cultivated cassava and wild relatives within its genebank. Efficient genebank management requires identifying and eliminating genetic redundancy within collections. In this study, we optimized the identification of genetic redundancy in CIAT’s cassava genebank, applying empirical distance thresholds, and using two types of molecular markers (single-nucleotide polymorphism (SNP) and SilicoDArT) on 5,302 Manihot esculenta accessions. A series of quality filters were applied to select the most informative and high-quality markers and to exclude low-quality DNA samples. The analysis identified a total of 2,518 and 2,526 (47 percent) distinct genotypes represented by 1 to 87 accessions each, using SNP or SilicoDArT markers, respectively. A total of 2,776 (SNP) and 2,785 (SilicoDArT) accessions were part of accession clusters with up to 87 accessions. Comparing passport and historical characterization data, such as pulp color and leaf characteristic, we reviewed clusters of genetically redundant accessions. This study provides valuable guidance to genebank curators in defining minimum genetic-distance thresholds to assess redundancy within collections. It aids in identifying a subset of genetically distinct accessions, prioritizing collection management activities such as cryopreservation and provides insights for follow-up studies in the field, potentially leading to removal of duplicate accessions. |
| format | Journal Article |
| id | CGSpace139417 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | Frontiers Media |
| publisherStr | Frontiers Media |
| record_format | dspace |
| spelling | CGSpace1394172025-12-08T10:29:22Z Identifying genetically redundant accessions in the world’s largest cassava collection Carvajal-Yepes, Monica Ospina, Jessica Alejandra Aranzales Rondón, Ericson Velez-Tobon, Monica Correa-Abondano, Miguel Manrique-Carpintero, Norma Constanza Wenzl, Peter cassava gene banks-genebanks genetic redundacy curators diversity Crop diversity conserved in genebanks facilitates the development of superior varieties, improving yields, nutrition, adaptation to climate change and resilience against pests and diseases. Cassava ( Manihot esculenta ) plays a vital role in providing carbohydrates to approximately 500 million people in Africa and other continents. The International Center for Tropical Agriculture (CIAT) conserves the largest global cassava collection, housing 5,963 accessions of cultivated cassava and wild relatives within its genebank. Efficient genebank management requires identifying and eliminating genetic redundancy within collections. In this study, we optimized the identification of genetic redundancy in CIAT’s cassava genebank, applying empirical distance thresholds, and using two types of molecular markers (single-nucleotide polymorphism (SNP) and SilicoDArT) on 5,302 Manihot esculenta accessions. A series of quality filters were applied to select the most informative and high-quality markers and to exclude low-quality DNA samples. The analysis identified a total of 2,518 and 2,526 (47 percent) distinct genotypes represented by 1 to 87 accessions each, using SNP or SilicoDArT markers, respectively. A total of 2,776 (SNP) and 2,785 (SilicoDArT) accessions were part of accession clusters with up to 87 accessions. Comparing passport and historical characterization data, such as pulp color and leaf characteristic, we reviewed clusters of genetically redundant accessions. This study provides valuable guidance to genebank curators in defining minimum genetic-distance thresholds to assess redundancy within collections. It aids in identifying a subset of genetically distinct accessions, prioritizing collection management activities such as cryopreservation and provides insights for follow-up studies in the field, potentially leading to removal of duplicate accessions. 2024-01-18 2024-02-15T09:43:13Z 2024-02-15T09:43:13Z Journal Article https://hdl.handle.net/10568/139417 en Open Access application/pdf Frontiers Media Carvajal-Yepes, M.; Ospina, J.A.; Aranzales, E.; Velez-Tobon, M.; Correa-Abondano, M.; Manrique-Carpintero, N.C.; Wenzl, P. (2024) Identifying genetically redundant accessions in the world’s largest cassava collection. Frontiers in Plant Science 14: 1338377. ISSN: 1664-462X |
| spellingShingle | cassava gene banks-genebanks genetic redundacy curators diversity Carvajal-Yepes, Monica Ospina, Jessica Alejandra Aranzales Rondón, Ericson Velez-Tobon, Monica Correa-Abondano, Miguel Manrique-Carpintero, Norma Constanza Wenzl, Peter Identifying genetically redundant accessions in the world’s largest cassava collection |
| title | Identifying genetically redundant accessions in the world’s largest cassava collection |
| title_full | Identifying genetically redundant accessions in the world’s largest cassava collection |
| title_fullStr | Identifying genetically redundant accessions in the world’s largest cassava collection |
| title_full_unstemmed | Identifying genetically redundant accessions in the world’s largest cassava collection |
| title_short | Identifying genetically redundant accessions in the world’s largest cassava collection |
| title_sort | identifying genetically redundant accessions in the world s largest cassava collection |
| topic | cassava gene banks-genebanks genetic redundacy curators diversity |
| url | https://hdl.handle.net/10568/139417 |
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