Data for: Identifying genetically redundant accessions in the globally largest cassava collection
A diverse panel of cultivated cassava landraces and improved lines were genotyped using DArTSeq Technology to identify genetic redundancy within the genebank collection. Methodology: Leaf samples were collected from in vitro plants for DNA extraction. The extracted DNA samples were subsequently s...
| Main Authors: | , , , , , , |
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| Format: | Conjunto de datos |
| Language: | Inglés |
| Published: |
2025
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/173881 |
| _version_ | 1855532868275535872 |
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| author | Carvajal-Yepes, Monica Ospina Colorado, Jessica Alejandra Aranzales Rondon, Ericson Velez Tobon, Monica Lorena Correa Abondano, Miguel Angel Barbosa Torres, Norma Constanza Wenzl, Peter |
| author_browse | Aranzales Rondon, Ericson Barbosa Torres, Norma Constanza Carvajal-Yepes, Monica Correa Abondano, Miguel Angel Ospina Colorado, Jessica Alejandra Velez Tobon, Monica Lorena Wenzl, Peter |
| author_facet | Carvajal-Yepes, Monica Ospina Colorado, Jessica Alejandra Aranzales Rondon, Ericson Velez Tobon, Monica Lorena Correa Abondano, Miguel Angel Barbosa Torres, Norma Constanza Wenzl, Peter |
| author_sort | Carvajal-Yepes, Monica |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | A diverse panel of cultivated cassava landraces and improved lines were genotyped using DArTSeq Technology to identify genetic redundancy within the genebank collection.
Methodology: Leaf samples were collected from in vitro plants for DNA extraction. The extracted DNA samples were subsequently sent to DArT P/L and genotyped using the DArTseq platform and sequencing, resulting in approximately 2.5 million reads per sample. Libraries were generated using the PstI and MseI restriction enzymes. To call SNPs and SilicoDArT genomic variants, the DS14 software was implemented. Genomic variants were reported in .csv files. SilicoDArT Format: SilicoDArTs are scored in a binary fashion, representing genetically 'dominant' markers, with '1' indicating the presence and '0' indicating the absence of a restriction fragment with the marker sequence in the genomic representation of the sample. 'NA' is used for missing data. SNP Format: '0' represents a reference allele homozygote, '2' represents an SNP allele homozygote, '1' represents a heterozygote, and 'NA' represents a double null/null allele homozygote (absence of a fragment with SNP in the genomic representation) |
| format | Conjunto de datos |
| id | CGSpace173881 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| record_format | dspace |
| spelling | CGSpace1738812025-04-11T10:10:02Z Data for: Identifying genetically redundant accessions in the globally largest cassava collection Carvajal-Yepes, Monica Ospina Colorado, Jessica Alejandra Aranzales Rondon, Ericson Velez Tobon, Monica Lorena Correa Abondano, Miguel Angel Barbosa Torres, Norma Constanza Wenzl, Peter cassava A diverse panel of cultivated cassava landraces and improved lines were genotyped using DArTSeq Technology to identify genetic redundancy within the genebank collection. Methodology: Leaf samples were collected from in vitro plants for DNA extraction. The extracted DNA samples were subsequently sent to DArT P/L and genotyped using the DArTseq platform and sequencing, resulting in approximately 2.5 million reads per sample. Libraries were generated using the PstI and MseI restriction enzymes. To call SNPs and SilicoDArT genomic variants, the DS14 software was implemented. Genomic variants were reported in .csv files. SilicoDArT Format: SilicoDArTs are scored in a binary fashion, representing genetically 'dominant' markers, with '1' indicating the presence and '0' indicating the absence of a restriction fragment with the marker sequence in the genomic representation of the sample. 'NA' is used for missing data. SNP Format: '0' represents a reference allele homozygote, '2' represents an SNP allele homozygote, '1' represents a heterozygote, and 'NA' represents a double null/null allele homozygote (absence of a fragment with SNP in the genomic representation) 2025-03 2025-03-26T12:45:28Z 2025-03-26T12:45:28Z Dataset https://hdl.handle.net/10568/173881 en Open Access Carvajal-Yepes, M.; Ospina Colorado, J.A.; Aranzales Rondon, E.; Velez Tobon, M.L.; Correa Abondano, M.A.; Barbosa Torres, N.C.; Wenzl, P. (2025) Data for: Identifying genetically redundant accessions in the globally largest cassava collection. https://doi.org/10.7910/DVN/JWNYFA |
| spellingShingle | cassava Carvajal-Yepes, Monica Ospina Colorado, Jessica Alejandra Aranzales Rondon, Ericson Velez Tobon, Monica Lorena Correa Abondano, Miguel Angel Barbosa Torres, Norma Constanza Wenzl, Peter Data for: Identifying genetically redundant accessions in the globally largest cassava collection |
| title | Data for: Identifying genetically redundant accessions in the globally largest cassava collection |
| title_full | Data for: Identifying genetically redundant accessions in the globally largest cassava collection |
| title_fullStr | Data for: Identifying genetically redundant accessions in the globally largest cassava collection |
| title_full_unstemmed | Data for: Identifying genetically redundant accessions in the globally largest cassava collection |
| title_short | Data for: Identifying genetically redundant accessions in the globally largest cassava collection |
| title_sort | data for identifying genetically redundant accessions in the globally largest cassava collection |
| topic | cassava |
| url | https://hdl.handle.net/10568/173881 |
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