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Protocols

QTLMap specifications

Information


Unique identifier OMICS_07104
Name QTLMap
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A genetic map, a pedigree, some markers genotypes and traits values.
Output data A general listing.
Operating system Unix/Linux
Programming languages Fortran
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

QTLMap citations

 (42)
call_split

A genome scan for milk production traits in dairy goats reveals two new mutations in Dgat1 reducing milk fat content

2017
Sci Rep
PMCID: 5431851
PMID: 28500343
DOI: 10.1038/s41598-017-02052-0
call_split See protocol

[…] For QTL detection, both linkage analyses (LA) and linkage disequilibrium (LD) using interval mapping were applied to the data using the QTLMap software (ref. ; http://dga7.jouy.inra.fr/qtlmap/). For LA, interval mapping was performed with the likelihood ratio test (LRT) using within-sire linear regression. The QTL effect (average subs […]

library_books

Detection of QTL for traits related to adaptation to sub optimal climatic conditions in chickens

2017
PMCID: 5399330
PMID: 28427323
DOI: 10.1186/s12711-017-0314-5

[…] The position of the SNPs that flanked a QTL region was used to establish the correspondence between the results of QTLMap and those of GEMMA, by considering all SNP effects detected at a P value less than 0.05. Regions detected by both methods were found only on two chromosomes: GGA24 for BW04 and GGAZ for seven t […]

library_books

Deciphering mechanisms underlying the genetic variation of general production and liver quality traits in the overfed mule duck by pQTL analyses

2017
PMCID: 5396126
PMID: 28424047
DOI: 10.1186/s12711-017-0313-6

[…] e conserved for each mule duck, and the performance of each G2 female was computed as the average of the residual effects of her three male mule duck offspring.QTL detection was carried out using the QTLMap software [–] in order to implement linkage analysis according to the interval mapping method []. For each chromosome, first the probabilities of each possible phase of the G1 male founders were […]

library_books

Genome Wide Identification of the Mutation Underlying Fleece Variation and Discriminating Ancestral Hairy Species from Modern Woolly Sheep

2017
Mol Biol Evol
PMCID: 5455980
PMID: 28379502
DOI: 10.1093/molbev/msx114

[…] the major locus and identify the shortest woolly haplotype, we combined genotyping results from experimental and production populations. A linkage analysis within each ram family, performed with the QTLMap software (), showed that three out of eight sires were heterozygous for QTLOar25 (a, online). After phasing haplotypes for the region of interest, we used the software Plink () to identify seg […]

library_books

Regulatory Architecture of Gene Expression Variation in the Threespine Stickleback Gasterosteus aculeatus

2016
PMCID: 5217106
PMID: 27836907
DOI: 10.1534/g3.116.033241

[…] QTLMap input files are provided as Files Files S1-S5. Raw and normalized microarray data, in addition to R scripts describing the normalization procedure, are available in the ArrayExpress database (w […]

library_books

Genetic determinism of bone and mineral metabolism in meat type chickens: A QTL mapping study

2016
PMCID: 4926819
PMID: 28326346
DOI: 10.1016/j.bonr.2016.02.004

[…] QTL detection was carried out with the QTLMap software () using a half-sib model (, ) with interval mapping based on maximum likelihood estimations (). This model does not make assumptions on the number of QTL alleles segregating in the de […]

Citations

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QTLMap institution(s)
INRA Agrocampus Ouest, UMR0598, Rennes, France; INRA, UR0631, Castanet Tolosan, France; INRA AgroParisTech, UMR1313, Jouy en Josas, France

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