MAPMAKER protocols

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MAPMAKER statistics

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MAPMAKER specifications

Information


Unique identifier OMICS_19991
Name MAPMAKER
Alternative names MAPMAKER/QTL, MAPMAKER/EXP
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

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Documentation


Publication for MAPMAKER

MAPMAKER in pipelines

 (6)
2016
PMCID: 4757802
PMID: 26743902
DOI: 10.14348/molcells.2016.2264

[…] the selected primer sets were used for virtual pcr analysis of the km and melon sequence data to distinguish nw-specific marker candidates ()., an oriental melon genetic map was constructed using mapmaker 3.0/exp () with 234 dcaps () and 25 ssr markers. f2 population nw and km specimens were used for mapping. recombination fractions were converted to map distances in centimorgans (cm) using […]

2016
PMCID: 5124567
PMID: 27965677
DOI: 10.3389/fpls.2016.01714

[…] marker were chosen for molecular mapping of the shr locus. total 769 f2 plants of shr x s. pimpinellifolium were genotyped and analyzed by chi-square test. map construction was carried out using the mapmaker/exe v.3.0 (lander et al., ; lincoln and lander, ) program following kosambi function (kosambi, ). linkage groups were determined using “group” and “error detection on” commands with a lod […]

2015
PMCID: 4323067
PMID: 25596612
DOI: 10.1093/jhered/esu086

[…] biased allele distribution and missing data in the worker offspring, 1415 markers remained that were used to construct a genomic linkage map. this map was assembled using kosambi’s map function with mapmaker 3.0b (), according to previously described procedures (; ). we combined de novo linkage analysis with information from the marker order on the physical honey bee genome (ncbi taxid: 7460), […]

2015
PMCID: 4507776
PMID: 26022253
DOI: 10.1093/jxb/erv246

[…] further details of the genomic data processing have been given by ., analysis of the phenotype data was performed using spss version 19 (ibm). linkage maps were constructed from the genotype data by mapmaker/exp 3.0 software (). qtl analysis was conducted using qtlnetwork (v.2.0) based on the mixed-model based composite interval mapping (mcim) method (, ). an f-statistic based on the henderson […]

2014
PMCID: 4157721
PMID: 25056774
DOI: 10.1093/jxb/eru306

[…] gene-specific primers tatef-1f/r, tatef-2f/r, tatef-3f/r, and tatef-6f/r for tatef-7a localization were used for pcr. tatef-7a was mapped on a mapping population (hanxuan 10×lumai 14) using the mapmaker/exp 3.0 ()., full-length protein sequences of tatef-7a from triticum aestivum (ta), brachypodium distachyon (bd), oryza sativa (os), setaria italica (si), zea mays (zm), sorghum bicolour […]


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MAPMAKER in publications

 (460)
PMCID: 5938815
PMID: 29739415
DOI: 10.1186/s12942-018-0129-9

[…] work for other groups possibly due to differences in population size and distribution. for producing disease maps that incorporate the population age structure, e.g., directly age-adjusted maps, the mapmaker must be careful not to choose different threshold values for each age strata as this could lead to the use of inconsistent spatial supports. generally, spatial supports must be consistently […]

PMCID: 5893511
PMID: 29637380
DOI: 10.1186/s12284-018-0217-2

[…] to detect allele can increase kongyu 131’s grain length, we measured grain length and analyzed genotype with an f2 populations constructed by kongyu 131 and gkbr, and made qtl analysis according to mapmaker/qtl 1.1b (lincoln et al. ). we detected a qtl related to grain length on the chromosome 3 (fig. ), nearby gs3 locus, presumably this qtl is gs3 locus. and also we noticed another qtl […]

PMCID: 5889531
PMID: 29625552
DOI: 10.1186/s12870-018-1269-6

[…] for 10 s and 72 °c for 1 min; final extension at 72 °c for 5 min. in all other pcr reactions thermocycling was as above except annealing temperature varied as indicated in additional file ., using mapmaker/exp 3.0 [] the lpdhs1, lphss1 and lphss2 genes were mapped by genetic linkage analysis in an f1 population comprised of 94 perennial ryegrass individuals, using gene markers that reveal […]

PMCID: 5884529
PMID: 29617389
DOI: 10.1371/journal.pone.0194671

[…] 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 […]

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

[…] 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., , […]


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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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