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MAPMAKER specifications


Unique identifier OMICS_19991
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
Programming languages C
Computer skills Advanced
Version 1.1
Maintained Yes


No version available


Publication for MAPMAKER

MAPMAKER citations


QTLs underlying the genetic interrelationship between efficient compatibility of Bradyrhizobium strains with soybean and genistein secretion by soybean roots

PLoS One
PMCID: 5884529
PMID: 29617389
DOI: 10.1371/journal.pone.0194671
call_split See protocol

[…] ics 20.0 (SPSS, USA). One-way ANOVA for the analysis of each phenotype was performed.We reconstructed the linkage map for 93 RILs (F14) using 227 polymorphic SSR (simple sequence repeat) markers with MAPMAKER/EXE v. 3.0 software [] based on the linkage map for F8 plants consisting of 344 polymorphic SSR markers []. Quantitative trait locus mapping was performed by means of composite interval mappi […]


Haplotype based allele mining in the Japan MAGIC rice population

Sci Rep
PMCID: 5847589
PMID: 29531264
DOI: 10.1038/s41598-018-22657-3

[…] corrected with Bonferroni’s adjustment and were used to produce Q-Q plots.For QTL analysis for glutinous endosperm and CL in the four types of RILs, we constructed genetic maps using version 3.0b of MAPMAKER/EXP software. The QTL analysis was performed by interval composite mapping using version 2.5 of QTL Cartographer software, and the threshold was calculated from 1,000 permutations. […]


Large effect quantitative trait loci for salicinoid phenolic glycosides in Populus: Implications for gene discovery

Ecol Evol
PMCID: 5901179
PMID: 29686853
DOI: 10.1002/ece3.3932
call_split See protocol

[…] used to construct a framework linkage map composed of 326 AFLP markers distributed among nineteen linkage groups (Woolbright et al., ). Chromosome assignments and marker order were established using MapMaker 3.0 (Lander et al., ) with “default linkage criteria” of LOD = 8.0 and recombination fraction (rf) = 0.37. One hundred eleven microsatellite (SSR) markers conserved across Populus species wer […]


AtHMA4 Drives Natural Variation in Leaf Zn Concentration of Arabidopsis thaliana

Front Plant Sci
PMCID: 5839161
PMID: 29545819
DOI: 10.3389/fpls.2018.00270
call_split See protocol

[…] n and marker information were integrated for QTL mapping performed using R/qtl in R program (; ). The contribution of each marker accounting for the variation of Zn concentration was determined using MapMaker ().To determine the relationship between Zn concentration and HMA4, we also conducted bulk segregant analysis (BSA) using an F2 population from a cross between Col-0 × Fab-2. We chose 100 F2 […]


Genetic loci simultaneously controlling lignin monomers and biomass digestibility of rice straw

Sci Rep
PMCID: 5827516
PMID: 29483532
DOI: 10.1038/s41598-018-21741-y
call_split See protocol

[…] A total of 177 simple sequence repeat (SSR) markers and four insertion deletion (InDel) markers were employed to construct the genetic map of the RIL population using MAPMAKER/EXP version 3.0b software, in which 145 SSR and all InDel markers have been described previously. In this study, an additional 32 markers were added to the map using the SSR assay as describe […]


Genome Based Prediction of Time to Curd Induction in Cauliflower

Front Plant Sci
PMCID: 5807883
PMID: 29467774
DOI: 10.3389/fpls.2018.00078

[…] air temperatures Ti as follows:kij was added up until the cumulative kj became ≥ 1, i.e., when the adult vegetative phase was completed and curd development started.A linkage map was constructed with MapMaker 3 by simultaneous multipoint-analysis using the Haldane function (; ). On basis of the results of parameterization trials, QTL analyses were conducted on LAR, S, and T0 using PlabQTL 1.2 (). […]


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MAPMAKER institution(s)
Whitehead Institute for Biomedical Research, Cambridge Center, Cambridge, MA, USA; Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard University, Cambridge, MA, USA; Human Genetics Department, Collaborative Research, inc., Bedford, MA, USA
MAPMAKER funding source(s)
Supported in part by grants from the National Science Foundation and System Development Foundation.

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