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

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.

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Acknowledgments

We thank Andrzej Kilian for his help with DArT markers. This work was funded by DGA—Obra Social La Caixa (Grant Number GA-LC-059-2011) and by the Spanish Ministry of Science and Innovation (Projects AGL2010-21929 and RTA2009-00006-C04-02). Carlos P. Cantalapiedra is funded by Spanish Ministry of Science and Innovation (Grant Number BES-2011-045905 linked to Project AGL2010-21929). Ridha Boudiar was supported by a Master’s fellowship from IAMZ-CIHEAM.

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Correspondence to Carlos P. Cantalapiedra or Bruno Contreras-Moreira.

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Cantalapiedra, C.P., Boudiar, R., Casas, A.M. et al. BARLEYMAP: physical and genetic mapping of nucleotide sequences and annotation of surrounding loci in barley. Mol Breeding 35, 13 (2015). https://doi.org/10.1007/s11032-015-0253-1

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Keywords

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