GACD Version 1.1 released

GACD is freely-available public software, capable of building high-density linkage genetic maps and mapping quantitative trait loci (QTL) in clonal F₁ and double cross populations. The software is project based and has user-friendly interfaces. Version 1.1 of the software was released in January 2016. Three fully implemented functionalities in GACD v1.1 are: (1) BIN: Binning of redundant markers; (2) CDM: Construction of genetic linkage maps in clonal F₁ and double cross populations; (3) CDQ: Mapping of additive and dominance genes in clonal F₁ and double cross populations.

What’s new in version 1.1?

1. 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.

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

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

4. For output files from Simple Interval Mapping and Inclusive Composite Interval Mapping in CDQ functionality, the confidence intervals of QTL position were provided by the one-LOD drop criterion.

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