GACD: Integrated Software for Building Genetic Linkage Maps and Mapping Quantitative Trait Genes in Clonal F₁ and Double Cross Populations

Current version: V1.1; Released 14 January 2016

Version history: v1.0 released July 2014

What is new in V4.1? (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.

Technical development of GACD: 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/7/10, with .NET Framework 4.0.

Contacts: Drs. Jiankang Wang (wangjiankang@caas.cn), or Luyan Zhang (zhangluyan@caas.cn)