GACD Version 1.2 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 1.2 of the software was released in July 2019.

Four fully implemented functionalities in GACD v1.2 are: (1) SNP: Converting the SNP genotyping data to the software format (i.e. from AA, TT, CC, GG, AT, AC, AG, TC, TG, GT to A, B, H. SNP genotypes of the two heterozygous parents of clonal F₁ or four inbred parents of double cross are needed to use this functionality); (2) BIN: Binning of redundant markers; (3) CDM: Construction of genetic linkage maps in clonal F₁ and double cross populations; (4) CDQ: Gene detection in clonal F₁ and double cross populations.

What’s new in version 1.2?

1. A new functionality was added to convert the SNP genotypic data to the software format, which was called SNP, and listed as the second functionality of the software. By using the SNP functionality, genotypes AA, TT, CC, GG, AT, AC, AG, TC, TG and GT will be converted to genotypes which are required by the software. Users need to provide SNP genotypes of the two heterozygous parents of clonal F₁ or four inbred parents of double cross to use this functionality.

2. In functionality CDM, the estimated recombination frequency and LOD score were recorded in a temporary external file, in order to increase the capability to handle the large number of markers. In current version, the maximum number of markers can reach 20,000 to 40,000. For markers more than 10,000, we suggest to use functionality BIN to remove the redundancy.

3. In functionality CDM, ordering algorithm was optimized.

4. Both 32-bit and 64-bit versions were provided.