Representing SSR molecular marker profiles using concepts from Andean khipus
- Published
- Accepted
- Subject Areas
- Anthropology, Biodiversity, Molecular Biology, Statistics, Computational Science
- Keywords
- molecular diversity, potato, microsatellite, SSR, khipu
- Copyright
- © 2014 Simon et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.
- Cite this article
- 2014. Representing SSR molecular marker profiles using concepts from Andean khipus. PeerJ PrePrints 2:e522v1 https://doi.org/10.7287/peerj.preprints.522v1
Abstract
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’.
Author Comment
This will be a submission for PeerJ for review.