Barleymap was designed to search the position of barley genetic markers on the Barley Physical Map (IBSC[1]), the POPSEQ map (Mascher et al.[2]) and the 2017 Morex Genome. The current version uses by default the MorexV3 genome[5]. Since 2026 markers can also be mapped to pangenome graphs.
All the public data used by Barleymap can be found at PGSB , IPK , e!DAL , Barley RTD , the NCBI, and barley_pangenes.
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 sequence alignment to the selected map (IBSC2012, POPSEQ, MorexGenome or MorexV3).
The Align to graph also requires nucleotide sequences of the markers (in FASTA format).
These will be used to retrieve their positions through alignment to the selected pangenome graph (Pan20, Med13).
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 and pangenes, genetic markers, and anchored features, that enrich the context around or between the queries will be shown.
Further information about how this tool works and help on using it can be found here, the source is on GitHub.
Or you may wish to contact the Computational and structural biology group at EEAD-CSIC.
Funding: This work was funded by DGA-Obra Social La Caixa [GA-LC-059-2011], the Spanish Ministry of Science and Innovation [AGL2010-21929,RTA2009-00006-C04-02, PID2022-142116OB-I00], Horizon 2020 [PRIMA GENDIBAR, PCI2019-103526], Government of Aragon [A08_23R] and CSIC [FAS2022_052, INFRA24018].
Citation: 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
[1]IBSC. 2012. A physical, genetic and functional sequence assembly of the barley genome. Nature. 491:711-16. doi:10.1038/nature11543
[2]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
[3]Mascher et al. 2017 A chromosome conformation capture ordered sequence of the barley genome Nature. 544:427-433. doi:10.1038/nature22043
[4]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 [5]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 [6]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 [7]Contreras-Moreira et al. 2023 GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation Genome Biol 24, 223 doi: 10.1186/s13059-023-03071-z