Representing SSR molecular marker profiles using concepts from Andean khipus
Genebanks increasingly use molecular markers for routine characterization of ex-situ collections and farmer managed diversity. The International Potato Center presently uses a SSR marker-kit to create molecular profiles for potato accessions. We identified a need for a compact graphical representati...
| Main Authors: | , , , , , , , , , |
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| Format: | Preprint |
| Language: | Inglés |
| Published: |
PeerJ
2014
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/64923 |
| _version_ | 1855535756829786112 |
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| author | Simon, R. Carhuapoma, Pablo Hualla, V. Ghislain, M. Mendiburu, F. de Gómez, R. Zorrilla, C. Roca, W. Haan, Stef de Bonierbale, Merideth W. |
| author_browse | Bonierbale, Merideth W. Carhuapoma, Pablo Ghislain, M. Gómez, R. Haan, Stef de Hualla, V. Mendiburu, F. de Roca, W. Simon, R. Zorrilla, C. |
| author_facet | Simon, R. Carhuapoma, Pablo Hualla, V. Ghislain, M. Mendiburu, F. de Gómez, R. Zorrilla, C. Roca, W. Haan, Stef de Bonierbale, Merideth W. |
| author_sort | Simon, R. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Genebanks increasingly use molecular markers for routine characterization of ex-situ collections and farmer managed diversity. The International Potato Center presently uses a SSR marker-kit to create molecular profiles for potato accessions. We identified a need for a compact graphical representation that allows comparative presentation of molecular diversity and accession characteristics - thereby permitting biologists and collection curators to have a simple means to interpret molecular data. Inspired by the ancient Andean qipus we devised a graph that standardizes representation while leaving room for updates of the marker kit and the collection of accessions. The molecular khipu permits combining and annotating a set of SSR loci with allele frequency and allele size distribution information. The design is flexible to incorporate updates on genetic diversity information. Graphical means facilitate reading of allele diversity information. As a compact graphical view it facilitates information storage and exchange. The SSR khipu will be useful to other genebanks and breeders. Software to create graphics in single or batch mode is available as R package ’khipu’. |
| format | Preprint |
| id | CGSpace64923 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2014 |
| publishDateRange | 2014 |
| publishDateSort | 2014 |
| publisher | PeerJ |
| publisherStr | PeerJ |
| record_format | dspace |
| spelling | CGSpace649232025-11-06T13:37:44Z Representing SSR molecular marker profiles using concepts from Andean khipus Simon, R. Carhuapoma, Pablo Hualla, V. Ghislain, M. Mendiburu, F. de Gómez, R. Zorrilla, C. Roca, W. Haan, Stef de Bonierbale, Merideth W. potatoes gene banks microsatellites genetic markers Genebanks increasingly use molecular markers for routine characterization of ex-situ collections and farmer managed diversity. The International Potato Center presently uses a SSR marker-kit to create molecular profiles for potato accessions. We identified a need for a compact graphical representation that allows comparative presentation of molecular diversity and accession characteristics - thereby permitting biologists and collection curators to have a simple means to interpret molecular data. Inspired by the ancient Andean qipus we devised a graph that standardizes representation while leaving room for updates of the marker kit and the collection of accessions. The molecular khipu permits combining and annotating a set of SSR loci with allele frequency and allele size distribution information. The design is flexible to incorporate updates on genetic diversity information. Graphical means facilitate reading of allele diversity information. As a compact graphical view it facilitates information storage and exchange. The SSR khipu will be useful to other genebanks and breeders. Software to create graphics in single or batch mode is available as R package ’khipu’. 2014 2015-04-02T11:48:05Z 2015-04-02T11:48:05Z Preprint https://hdl.handle.net/10568/64923 en Open Access application/pdf PeerJ Simon, R.; Carhuapoma, P.; Hualla, V.; Ghislain, M.; Mendiburu, F. de; Gomez, R.; Zorrilla, C.; Roca, W.; Haan, S. de; Bonierbale, M. 2014. Representing SSR molecular marker profiles using concepts from Andean khipus. PeerJ PrePrints. 2:e522v1:9 p. |
| spellingShingle | potatoes gene banks microsatellites genetic markers Simon, R. Carhuapoma, Pablo Hualla, V. Ghislain, M. Mendiburu, F. de Gómez, R. Zorrilla, C. Roca, W. Haan, Stef de Bonierbale, Merideth W. Representing SSR molecular marker profiles using concepts from Andean khipus |
| title | Representing SSR molecular marker profiles using concepts from Andean khipus |
| title_full | Representing SSR molecular marker profiles using concepts from Andean khipus |
| title_fullStr | Representing SSR molecular marker profiles using concepts from Andean khipus |
| title_full_unstemmed | Representing SSR molecular marker profiles using concepts from Andean khipus |
| title_short | Representing SSR molecular marker profiles using concepts from Andean khipus |
| title_sort | representing ssr molecular marker profiles using concepts from andean khipus |
| topic | potatoes gene banks microsatellites genetic markers |
| url | https://hdl.handle.net/10568/64923 |
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