QTL IciMapping: Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations
QTL IciMapping is freely available public software capable of building high-density linkage maps and mapping quantitative trait loci (QTL) in biparental populations. Eight functionalities are integrated in this software package: (1) BIN: binning of redundant markers; (2) MAP: construction of linkage maps in biparental populations; (3) CMP: consensus map construction from multiple linkage maps sharing common markers; (4) SDL: mapping of segregation distortion loci; (5) BIP: mapping of additive, dominant, and digenic epistasis genes; (6) MET: QTL-by-environment interaction analysis; (7) CSL: mapping of additive and digenic epistasis genes with chromosome segment substitution lines; and (8) NAM: QTL mapping in NAM populations. Input files can be arranged in plain text, MS Excel 2003, or MS Excel 2007 formats. Output files have the same prefix name as the input but with different extensions. As examples, there are two output files in BIN, one for summarizing the identified bin groups and deleted markers in each bin, and the other for using the MAP functionality. Eight output files are generated by MAP, including summary of the completed linkage maps, Mendelian ratio test of individual markers, estimates of recombination frequencies, LOD scores, and genetic distances, and the input files for using the BIP, SDL, and MET functionalities. More than 30 output files are generated by BIP, including results at all scanning positions, identified QTL, permutation tests, and detection powers for up to six mapping methods. Three supplementary tools have also been developed to display completed genetic linkage maps, to estimate recombination frequency between two loci, and to perform analysis of variance for multi-environmental trials.
Main Authors: | , , , |
---|---|
Format: | Article biblioteca |
Language: | English |
Published: |
Elsevier
2015
|
Subjects: | AGRICULTURAL SCIENCES AND BIOTECHNOLOGY, Biparental Populations, Map Construction, QTL Mapping, Software, CHROMOSOME MAPPING, QUANTITATIVE TRAIT LOCI, COMPUTER SOFTWARE, |
Online Access: | http://hdl.handle.net/10883/4536 |
Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
id |
dig-cimmyt-10883-4536 |
---|---|
record_format |
koha |
spelling |
dig-cimmyt-10883-45362021-02-18T21:01:24Z QTL IciMapping: Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations Meng, L. Huihui Li Luyan Zhang Jiankang Wang AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Biparental Populations Map Construction QTL Mapping Software CHROMOSOME MAPPING QUANTITATIVE TRAIT LOCI COMPUTER SOFTWARE QTL IciMapping is freely available public software capable of building high-density linkage maps and mapping quantitative trait loci (QTL) in biparental populations. Eight functionalities are integrated in this software package: (1) BIN: binning of redundant markers; (2) MAP: construction of linkage maps in biparental populations; (3) CMP: consensus map construction from multiple linkage maps sharing common markers; (4) SDL: mapping of segregation distortion loci; (5) BIP: mapping of additive, dominant, and digenic epistasis genes; (6) MET: QTL-by-environment interaction analysis; (7) CSL: mapping of additive and digenic epistasis genes with chromosome segment substitution lines; and (8) NAM: QTL mapping in NAM populations. Input files can be arranged in plain text, MS Excel 2003, or MS Excel 2007 formats. Output files have the same prefix name as the input but with different extensions. As examples, there are two output files in BIN, one for summarizing the identified bin groups and deleted markers in each bin, and the other for using the MAP functionality. Eight output files are generated by MAP, including summary of the completed linkage maps, Mendelian ratio test of individual markers, estimates of recombination frequencies, LOD scores, and genetic distances, and the input files for using the BIP, SDL, and MET functionalities. More than 30 output files are generated by BIP, including results at all scanning positions, identified QTL, permutation tests, and detection powers for up to six mapping methods. Three supplementary tools have also been developed to display completed genetic linkage maps, to estimate recombination frequency between two loci, and to perform analysis of variance for multi-environmental trials. 269-283 2015-10-26T16:35:42Z 2015-10-26T16:35:42Z 2015 Article http://hdl.handle.net/10883/4536 10.1016/j.cj.2015.01.001 English https://www.sciencedirect.com/science/article/pii/S2214514115000161?via%3Dihub#s0095 CIMMYT manages Intellectual Assets as International Public Goods. The user is free to download, print, store and share this work. In case you want to translate or create any other derivative work and share or distribute such translation/derivative work, please contact CIMMYT-Knowledge-Center@cgiar.org indicating the work you want to use and the kind of use you intend; CIMMYT will contact you with the suitable license for that purpose. Open Access PDF Amsterdam (Netherlands) Elsevier 3 3 The Crop Journal |
institution |
CIMMYT |
collection |
DSpace |
country |
México |
countrycode |
MX |
component |
Bibliográfico |
access |
En linea |
databasecode |
dig-cimmyt |
tag |
biblioteca |
region |
America del Norte |
libraryname |
CIMMYT Library |
language |
English |
topic |
AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Biparental Populations Map Construction QTL Mapping Software CHROMOSOME MAPPING QUANTITATIVE TRAIT LOCI COMPUTER SOFTWARE AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Biparental Populations Map Construction QTL Mapping Software CHROMOSOME MAPPING QUANTITATIVE TRAIT LOCI COMPUTER SOFTWARE |
spellingShingle |
AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Biparental Populations Map Construction QTL Mapping Software CHROMOSOME MAPPING QUANTITATIVE TRAIT LOCI COMPUTER SOFTWARE AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Biparental Populations Map Construction QTL Mapping Software CHROMOSOME MAPPING QUANTITATIVE TRAIT LOCI COMPUTER SOFTWARE Meng, L. Huihui Li Luyan Zhang Jiankang Wang QTL IciMapping: Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations |
description |
QTL IciMapping is freely available public software capable of building high-density linkage maps and mapping quantitative trait loci (QTL) in biparental populations. Eight functionalities are integrated in this software package: (1) BIN: binning of redundant markers; (2) MAP: construction of linkage maps in biparental populations; (3) CMP: consensus map construction from multiple linkage maps sharing common markers; (4) SDL: mapping of segregation distortion loci; (5) BIP: mapping of additive, dominant, and digenic epistasis genes; (6) MET: QTL-by-environment interaction analysis; (7) CSL: mapping of additive and digenic epistasis genes with chromosome segment substitution lines; and (8) NAM: QTL mapping in NAM populations. Input files can be arranged in plain text, MS Excel 2003, or MS Excel 2007 formats. Output files have the same prefix name as the input but with different extensions. As examples, there are two output files in BIN, one for summarizing the identified bin groups and deleted markers in each bin, and the other for using the MAP functionality. Eight output files are generated by MAP, including summary of the completed linkage maps, Mendelian ratio test of individual markers, estimates of recombination frequencies, LOD scores, and genetic distances, and the input files for using the BIP, SDL, and MET functionalities. More than 30 output files are generated by BIP, including results at all scanning positions, identified QTL, permutation tests, and detection powers for up to six mapping methods. Three supplementary tools have also been developed to display completed genetic linkage maps, to estimate recombination frequency between two loci, and to perform analysis of variance for multi-environmental trials. |
format |
Article |
topic_facet |
AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Biparental Populations Map Construction QTL Mapping Software CHROMOSOME MAPPING QUANTITATIVE TRAIT LOCI COMPUTER SOFTWARE |
author |
Meng, L. Huihui Li Luyan Zhang Jiankang Wang |
author_facet |
Meng, L. Huihui Li Luyan Zhang Jiankang Wang |
author_sort |
Meng, L. |
title |
QTL IciMapping: Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations |
title_short |
QTL IciMapping: Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations |
title_full |
QTL IciMapping: Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations |
title_fullStr |
QTL IciMapping: Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations |
title_full_unstemmed |
QTL IciMapping: Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations |
title_sort |
qtl icimapping: integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations |
publisher |
Elsevier |
publishDate |
2015 |
url |
http://hdl.handle.net/10883/4536 |
work_keys_str_mv |
AT mengl qtlicimappingintegratedsoftwareforgeneticlinkagemapconstructionandquantitativetraitlocusmappinginbiparentalpopulations AT huihuili qtlicimappingintegratedsoftwareforgeneticlinkagemapconstructionandquantitativetraitlocusmappinginbiparentalpopulations AT luyanzhang qtlicimappingintegratedsoftwareforgeneticlinkagemapconstructionandquantitativetraitlocusmappinginbiparentalpopulations AT jiankangwang qtlicimappingintegratedsoftwareforgeneticlinkagemapconstructionandquantitativetraitlocusmappinginbiparentalpopulations |
_version_ |
1756086551475912704 |