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JoinMap specifications


Unique identifier OMICS_19990
Name JoinMap
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Windows
Computer skills Advanced
Version 5.0
Stability Stable
Maintained Yes


  • MapChart




No version available

Publications for JoinMap

JoinMap citations


Identification of novel putative causative genes and genetic marker for male sterility in Japanese cedar (Cryptomeria japonica D.Don)

BMC Genomics
PMCID: 5914023
PMID: 29685102
DOI: 10.1186/s12864-018-4581-5

[…] A genetic linkage map was constructed using JoinMap 4.1 software (Kyazma, Wageningen, Netherlands) []. The marker segregation data were rescored as CP (cross between two heterogeneously heterozygous and homozygous diploid parents) population da […]


Genotyping by sequencing application on diploid rose and a resulting high density SNP based consensus map

PMCID: 5878828
PMID: 29619228
DOI: 10.1038/s41438-018-0021-6
call_split See protocol

[…] romosome 1 at position 19.680628 Mbp. Marker alleles were converted into genotype codes based on the possible CP population segregation types abxcd, efxeg, hkxhk, lmxll, and nnxnp as described in the JoinMap® v4.1 manual using a custom python script. […]


Molecular markers reliably predict post harvest deterioration of fresh cut lettuce in modified atmosphere packaging

PMCID: 5880813
PMID: 29619232
DOI: 10.1038/s41438-018-0022-5

[…] mapping population was genotyped with 257 SNPs. Molecular marker genotyping was conducted using the Illumina Golden Gate SNP assay (Illumina, San Diego, CA, USA). The linkage map was developed using JoinMap v. 2.0. RILs plus both parents of this mapping population were grown in two field experiments, processed for salad, and evaluated for the rate of deterioration.Fig. 2Eight accessions (Bandit, […]


Genome Wide Association Mapping Uncovers Fw1, a Dominant Gene Conferring Resistance to Fusarium Wilt in Strawberry

PMCID: 5940171
PMID: 29602808
DOI: 10.1534/g3.118.200129
call_split See protocol

[…] Because the parents and grandparents of the S1 populations were outbred, genetic mapping was performed using the full-sib mapping algorithm of JoinMap 4.1 (), which utilizes the general maximum-likelihood (ML) algorithm of for simultaneously estimating linkage and linkage phases in full-sib families. Because we selfed a single individual de […]


QTL Mapping of Genome Regions Controlling Manganese Uptake in Lentil Seed

PMCID: 5940135
PMID: 29588380
DOI: 10.1534/g3.118.200259
call_split See protocol

[…] JoinMap4.0 software described by was used for linkage mapping analysis. A maximum recombination frequency of 0.50 and the kosambi function were used as options in linkage mapping. Distorted markers w […]


Genome Wide Identification and Expression Profiling of Cytokinin Oxidase/Dehydrogenase (CKX) Genes Reveal Likely Roles in Pod Development and Stress Responses in Oilseed Rape (Brassica napus L.)

PMCID: 5867889
PMID: 29547590
DOI: 10.3390/genes9030168

[…] Chromosomal position information for the BnCKXs was obtained from the B. napus Genome Browser, and the genes were mapped onto chromosomal linkage groups with MapChart []. To investigate the exon/intron organization of the BnCKXs, the gene structures were analyzed using the Gene Structure Display Server ( []. Protein motifs were […]


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JoinMap institution(s)
Plant Research International, Wageningen, Netherlands

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