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Representing SSR molecular marker profiles using concepts from Andean khipus

International Potato Center Dataverse OAI Archive

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Title Representing SSR molecular marker profiles using concepts from Andean khipus
 
Identifier https://doi.org/10.21223/P3/VOSMTS
 
Creator Simon, Reinhard
Carhuapoma, Pablo
Nuñez, Jorge
Hualla, Vilma
De Haan, Stef
Ghislain, Marc
Zorrilla, Cinthya
Gomez, Rene
De Mendiburu, Felipe
Roca, William
Bonierbale, Merideth
 
Publisher International Potato Center
 
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’.
 
Subject Agricultural Sciences
Computer and Information Science
Potatoes
Gene Banks
Microsatellites
Genetic markers
 
Language English
 
Date 2014-04-22
 
Contributor Administrator, CIP
International Potato Center
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