Integrated Software GACD for Linkage Map Construction and Gene Mapping in Clonal F1 and Double Cross Populations

Clonal F₁ hybrids are the progenies from the hybridization between two heterozygous clonal parents. In self- and cross-pollinated species, double crosses are commonly made between four inbred lines for genetic studies and breeding applications. A clonal F₁ population can be viewed as a double cross population when the linkage phase is determined. 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. The software runs on Windows XP/Vista/7/8/10, with Microsoft .NET Framework 4.0. GACD is project-based software. All operations and results will be properly saved when the software is closed. Three functionalities are integrated in GACD version 1.1: (1) BIN, binning of redundant markers; (2) CDM, construction of genetic linkage maps, including female, male and combined maps; (3) CDQ, mapping of additive and dominance genes of quantitative traits. Three mapping methods are implemented in CDQ, i.e., single marker analysis (SMA), interval mapping (IM), and inclusive composite interval mapping (ICIM). 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 www.isbreeding.net.