· Added MorexV3 map + centromeres, PGSB and BaRT1.0 gene models and NCBI Entrez CDS sequence (see release notes
· Added POPSEQ map updated with 2017 data
· Added a dataset of NCBI genes to the Morex Genome map. This dataset includes genes like HvCO1, Int-c, Btr1, Vrs1, PhyB, HvCEN, etc... to a total of 894 entries.
· Support for the Illumina50K
markers, which can now be searched in the
and Morex Genome
released in 2017,
was designed to search the position of barley genetic markers
on the Barley Physical Map
,the POPSEQ map
(Mascher et al.
) and the
2017 Morex Genome.
The current version was updated to work with the MorexV3
genome (released in 2021)
All the public data used by Barleymap can be found at
, Barley RTD
and the NCBI
The Find markers
option allows to find the position of markers by using their identifiers as input.
Note that those markers must be part of one of the
precalculated datasets available (e.g.: Illumina 50K markers).
To use the Align sequences
option you must provide nucleotide sequences of the markers (in FASTA format).
These will be used to retrieve their positions through
to the selected map (IBSC2012, POPSEQ, MorexGenome or MorexV3).
The Locate by position
option allows to examine the map context of specific positions,
which must be provided as tuples with chromosome (or contig) and position (local position, within the chromosome or contig, in base pairs).
For example, an user could provide as input "chr1H 10000" to find out which genes are in that specific region of chromosome 1H.
In addition to locate a list of markers or sequences,
information of genes, genetic markers, and anchored features,
that enrich the context around or between the queries will be shown.
works on top of barleymap core API
, used also in a
that allows loading custom databases, maps and datasets, among other features.
Such application can be used with data from any organism for which sequences anchored to a genetic/physical background are available.
about how this tool works and help on using it can be found
Or you may wish to contact
the Computational and structural biology group
Carlos P Cantalapiedra
Cantalapiedra CP, Boudiar R, Casas AM, Igartua E, Contreras-Moreira B. BARLEYMAP: physical and genetic mapping of nucleotide sequences and annotation of surrounding loci in barley. Mol Breeding (2015) 35:13 DOI 10.1007/s11032-015-0253-1
A physical, genetic and functional sequence assembly of the barley genome.
Nature. 491:711-16. doi:10.1038/nature11543
Mascher et al. 2013.
Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ).
The Plant Journal, 76: 718-27. doi:10.1111/tpj.12319
Mascher et al. 2017
A chromosome conformation capture ordered sequence of the barley genome
Nature. 544:427-433. doi:10.1038/nature22043
Bayer et al. 2017
Development and Evaluation of a Barley 50k iSelect SNP Array
Frontiers in Plant Science. 8:1792. doi:10.3389/fpls.2017.01792
Mascher et al. 2021
Long-read sequence assembly: a technical evaluation in barley
The Plant Cell 33(6):1888–1906 doi:10.1093/plcell/koab077
Rapazote-Flores et al. 2019
BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq
BMC Genomics 20:968 doi:10.1186/s12864-019-6243-7