QTL Cartographer protocols

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QTL Cartographer specifications

Information


Unique identifier OMICS_07101
Name QTL Cartographer
Alternative names WinQTL Cartogarpher, WinQTL Cart, Windows QTL Cartographer
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Windows
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for QTL Cartographer

QTL Cartographer in pipeline

2010
PMCID: 3095315
PMID: 20923552
DOI: 10.1186/1471-2229-10-215

[…] [] and a minimum lod of 3.0 and using the genetic map from blair et al. []., qtl were detected first with composite interval mapping (cim) analysis that was carried out using the software program qtl cartographer v. 2.5 [] and the genetic map for the dor364 × g19833 used in blair et al. [] along with the markers for iron reductase genes described above. the following parameters were used […]


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QTL Cartographer in publications

 (269)
PMCID: 5946024
PMID: 29780395
DOI: 10.3389/fpls.2018.00573

[…] error variance, r is the number of replicates per line, and y is the number of years., both conditional and traditional qtl analyses were conducted using composite interval mapping (cim) using qtl cartographer 2.5 (). the lod value was set at 3.0 after 1,000 permutations to declare of putative qtl. the qtl (2.5 < lod < 3.0) were also reported for other environments […]

PMCID: 5909218
PMID: 29673320
DOI: 10.1186/s12870-018-1287-4

[…] qtl analysis of rhr in rh hotspot regions. in each hotspot, the rhr for each line was treated as a phenotype for qtl analysis. the composite interval mapping procedure [] implemented in windows qtl cartographer v.2.5 software was employed []. we chose an lod score of 3 as the threshold to declare the significance of a qtl. the confidence interval of a qtl was defined as a two-lod drop […]

PMCID: 5878199
PMID: 29623004
DOI: 10.1007/s11032-018-0804-3

[…] heritability (h2) estimate of vernalization requirements (in days) calculated from variance components (czyczyło-mysza et al. ) was 92%. composite interval mapping analysis was performed using qtl cartographer 2.5 software (wang et al. ). after performing a 1000-permutation test, a lod threshold was set individually to 2.9 to declare a qtl as significant. a walk speed of 1.0 cm was chosen […]

PMCID: 5865336
PMID: 29566663
DOI: 10.1186/s12870-018-1268-7

[…] conditional phenotypic values for each trait collected in each environment were employed for qtl mapping analyses and named as unconditional qtls and conditional qtls, respectively, by the windows qtl cartographer 2.5 using the composite interval mapping model []. a stringent lod threshold (2.8–3.1) of putative qtls were determined by selecting 1000-fold permutation tests (α = 0.05), […]

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

[…] 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., , electronic supplementary material , supplementary information accompanies this paper […]


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QTL Cartographer institution(s)
Department of Statistics, North Carolina State University, Raleigh, North Carolina, NC, USA; Department of Zoology, Duke University, Durham, NC, USA
QTL Cartographer funding source(s)
Supported by U.S. Public Health Service Grants GM-47292 and GM-45344.

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