Version history: v1.0 released February 2007; v1.4 released June 2007; v2.0 released November 2007; v2.1 released August 2008; v2.2 released December 2008; v3.0 released September 2010; v3.1 released May 2011; v3.2 released April 2012

What is new in V3.3? (1) BIN is implemented as a new functionality; (2) CMP is given for the consensus map construction of multiple maps sharing common markers. This functionality was called IMP in previous versions; (3) Much effort is spent on re-structuring the Fortran code. As a result, the efficiency and stability of the software are much improved; (4) Efficiency in loading EXCEL input files is improved.

Eight fully implemented functionalities in QTL IciMapping v3.3 are: (1) BIN: Binning of redundant markers; (2) MAP: Construction of genetic linkage maps in biparental populations; (3) BIP: Mapping of additive and digenic epistasis genes in biparental populations; (4) CSL: Mapping of additive and digenic epistasis genes with chromosome segment substitution lines; (5) MET: QTL by environment interaction in biparental populations; (6) NAM: QTL mapping in nested association mapping populations; (7) SDL: Mapping of segregation distortion loci in biparental populations; and (8) CMP: Consensus map construction from multiple genetic linkage maps sharing common markers.

Two supplementary tools in QTL IciMapping v3.3 are: (1) 2pointREC: Estimation of recombination frequency between two loci in 20 biparental populations; and (2) ANOVA: Analysis of variance of multi-environmental trials.

Technical development of QTL IciMapping: 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 Windows XP/Vista/7, with .NET Framework 2.0(x86)/3.0/3.5.