Molecular Breeding

, 35:13 | Cite as

BARLEYMAP: physical and genetic mapping of nucleotide sequences and annotation of surrounding loci in barley

Article

Abstract

The BARLEYMAP pipeline was designed to map both genomic sequences and transcripts against sequence-enriched genetic/physical frameworks, with plant breeders as the main target users. It reports the most probable genomic locations of queries after merging results from different resources so that diversity obtained from re-sequencing experiments can be exploited. In addition, the application lists surrounding annotated genes and markers, facilitating downstream analyses. Pre-computed marker datasets can also be created and browsed to facilitate searches and cross referencing. Performance is evaluated by mapping two sets of long transcripts and by locating the physical and genetic positions of four marker collections widely used for high-throughput genotyping of barley cultivars. In addition, genome positions retrieved by BARLEYMAP are compared to positions within a conventional genetic map for a population of recombinant inbred lines, yielding a gene-order accuracy of 96 %. These results reveal advantages and drawbacks of current in silico approaches for barley genomics. A web application to make use of barley data is available at http://floresta.eead.csic.es/barleymap. The pipeline can be set up for any species with similar sequence resources, for which a fully functional standalone version is available for download.

Keywords

Barley Marker Genetic and physical maps Genotyping-by-sequencing Gene annotation Sequence mapping 

Supplementary material

11032_2015_253_MOESM1_ESM.pdf (149 kb)
Supplementary material 1 (PDF 148 kb)
11032_2015_253_MOESM2_ESM.zip (3.6 mb)
Supplementary material 2 (ZIP 3704 kb)

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Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  • Carlos P. Cantalapiedra
    • 1
    • 2
  • Ridha Boudiar
    • 1
  • Ana M. Casas
    • 1
  • Ernesto Igartua
    • 1
  • Bruno Contreras-Moreira
    • 1
    • 3
  1. 1.Estación Experimental de Aula Dei (EEAD-CSIC)ZaragozaSpain
  2. 2.Plant Biology and Biotechnology PhD ProgramUniversitat Autònoma de BarcelonaBarcelonaSpain
  3. 3.Fundación ARAIDZaragozaSpain

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