QTL IciMapping Version 4.1 released

QTL IciMapping is freely-available public software, capable of building high-density linkage genetic maps and mapping quantitative trait loci (QTL). The software is project based and has user-friendly interfaces. Version 4.1 of the software was released in January 2016. Nine fully implemented functionalities in QTL IciMapping v4.1 are: (1) AOV: Analysis of variance for multi-environmental phenotyping trials; (2) BIN: Binning of redundant markers; (3) MAP: Construction of genetic linkage maps in biparental populations; (4) CMP: Consensus map construction from multiple genetic linkage maps sharing common markers; (5) SDL: Mapping of segregation distortion loci in biparental populations; (6) BIP: Mapping of additive and digenic epistasis genes in biparental populations; (7) MET: QTL by environment interaction in biparental populations; (8) CSL: Mapping of additive and digenic epistasis genes with chromosome segment substitution lines; and (9) NAM: QTL mapping in nested association mapping populations. Three supplementary tools in QTL IciMapping v4.1 are: (1) MapShow: Display of completed genetic linkage maps; (2) 2pointREC: Estimation of recombination frequency between two loci in 20 biparental populations; and (3) ANOVA: Analysis of variance of multi-environmental trials.

What’s new in version 4.1?

1. Change the tool ANOVA to the first functionality AOV. Additional methods such as correlation analysis between traits and environments, bi-plot analysis were added.

2. More options were provided for missing phenotypic values. In the current version, missing phenotypic values can be represented by “NA”, “na”, “*”, or “.”. Previous “-100” option is still valid.

3. In BIN functionality, markers can be deleted by their distortions, represented by P values.

4. In MAP functionality, a new grouping algorithm was added for a given group number. Parameter-setting window was re-arranged.

5. In output files from Simple Interval Mapping and Inclusive Composite Interval Mapping, the confidence intervals of QTL position were provided by the one-LOD drop criterion.

6. For all QTL mapping method, PVE (phenotypic variation explained) of individual QTL were adjusted once QTL mapping was done. The adjusted PVE are additive.