Representing SSR molecular marker profiles using concepts from Andean khipus

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cg.contributor.affiliationInternational Potato Center
cg.contributor.crpRoots, Tubers and Bananas
cg.creator.identifierPablo Carhuapoma: 0000-0003-0132-9775
cg.creator.identifierMarc Ghislain: 0000-0001-6485-1494
cg.creator.identifierStef de Haan: 0000-0001-8690-1886
cg.howPublishedFormally Published
cg.identifier.doihttps://doi.org/10.7287/peerj.preprints.522v1
cg.issn2167-8359
cg.journalPeerJ PrePrints
cg.subject.cipGENEBANK
cg.subject.cipBIODIVERSITY FOR THE FUTURE
dc.contributor.authorSimon, R.
dc.contributor.authorCarhuapoma, Pablo
dc.contributor.authorHualla, V.
dc.contributor.authorGhislain, M.
dc.contributor.authorMendiburu, F. de
dc.contributor.authorGómez, R.
dc.contributor.authorZorrilla, C.
dc.contributor.authorRoca, W.
dc.contributor.authorHaan, Stef de
dc.contributor.authorBonierbale, Merideth W.
dc.date.accessioned2015-04-02T11:48:05Zen
dc.date.available2015-04-02T11:48:05Zen
dc.identifier.urihttps://hdl.handle.net/10568/64923
dc.titleRepresenting SSR molecular marker profiles using concepts from Andean khipusen
dcterms.abstractGenebanks 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’.en
dcterms.accessRightsOpen Access
dcterms.bibliographicCitationSimon, 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.en
dcterms.extent9 p.
dcterms.issued2014
dcterms.languageen
dcterms.licenseCC-BY-4.0
dcterms.publisherPeerJ
dcterms.subjectpotatoesen
dcterms.subjectgene banksen
dcterms.subjectmicrosatellitesen
dcterms.subjectgenetic markersen
dcterms.typePreprint

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