QTL IciMapping: Integrated Software for Building Linkage Maps and Mapping Quantitative Trait Genes

QTL IciMapping is freely-available public software, capable of building high-density genetic linkage maps and mapping quantitative trait loci (QTL). The latest released version has the following new features compared with previous versions. (1) Dominant/recessive markers are considered in recombination frequency estimation, map construction and QTL mapping. (2) A new functionality called IMP is implemented, which can be used to build the integrated map from multiple genetic linkage maps sharing common markers. (3) A new tool called 2pointREC is implemented, which can be used to estimate the pair-wise recombination frequency in bi-parental population. (4) Much more markers can be handled in the software. For example, map construction and QTL mapping can be done for more than 5000 markers. (5) Figures of linkage maps are improved.

Seven functionalities are fully implemented in QTL IciMapping v3.2. (1) MAP: Construction of genetic linkage maps in biparental populations. (2) BIP: Mapping of additive and digenic epistasis genes in biparental populations. (3) CSL: Mapping of additive and digenic epistasis genes with chromosome segment substitution lines. (4) MET: QTL by environment interaction in biparental populations. (5) NAM: QTL mapping in nested association mapping populations. (6) SDL: Mapping of segregation distortion loci in biparental populations. (7) IMP: Integration of multiple maps sharing common markers.

The software is project based, where kernel modules for building linkage maps were written by C#, those for QTL mapping was written by Fortran 90/95, and the interface was written by C#. It runs on 32 and 64-bit computers with Windows XP/Vista/7 and .NET Framework 2.0(x86)/3.0/3.5. Research and development of QTL IciMapping was mainly supported by the Generation Challenge Program, the National 863 Program, 973 Program, and Natural Science Foundation of China. The software can be accessed from http://www.isbreeding.net. Please contact Dr. Jiankang Wang (wangjk@caas.net.cn or jkwang@cgiar.org) for any enquires.