GACD: Integrated Software for Genetic Analysis in Clonal F1 and Double Cross Populations

J Hered. Nov-Dec 2015;106(6):741-4. doi: 10.1093/jhered/esv080. Epub 2015 Oct 26.


Clonal species are common among plants. Clonal F1 progenies are derived from the hybridization between 2 heterozygous clones. In self- and cross-pollinated species, double crosses can be made from 4 inbred lines. A clonal F1 population can be viewed as a double cross population when the linkage phase is determined. The software package GACD (Genetic Analysis of Clonal F1 and Double cross) is freely available public software, capable of building high-density linkage maps and mapping quantitative trait loci (QTL) in clonal F1 and double cross populations. Three functionalities are integrated in GACD version 1.0: binning of redundant markers (BIN); linkage map construction (CDM); and QTL mapping (CDQ). Output of BIN can be directly used as input of CDM. After adding the phenotypic data, the output of CDM can be used as input of CDQ. Thus, GACD acts as a pipeline for genetic analysis. GACD and example datasets are freely available from

Keywords: QTL mapping; clonal species; double cross design; linkage map construction.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromosome Mapping*
  • Crosses, Genetic*
  • Genetic Linkage
  • Hybridization, Genetic
  • Plant Breeding
  • Plants / genetics*
  • Quantitative Trait Loci
  • Software*