QTL IciMapping Version 4.2 released

QTL IciMapping is freely-available public software, capable of building high-density linkage genetic maps and mapping quantitative trait loci (QTL). The software is project based and has user-friendly interfaces. Version 4.2 of the software was released in July 2019.

Ten fully implemented functionalities in QTL IciMapping v4.2 are: (1) AOV: Analysis of variance for multi-environmental phenotyping trials; (2) 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 inbred parents are needed to use this functionality); (3) BIN: Binning of redundant markers; (4) MAP: Construction of genetic linkage maps in biparental populations; (5) CMP: Consensus map construction from multiple genetic linkage maps sharing common markers; (6) SDL: Mapping of segregation distortion loci in biparental populations; (7) BIP: Mapping of additive and digenic epistasis genes in biparental populations; (8) MET: QTL by environment interaction in biparental populations; (9) CSL: Mapping of additive and digenic epistasis genes with chromosome segment substitution lines; and (10) NAM: QTL mapping in nested association mapping populations. Three supplementary tools in QTL IciMapping v4.1 are: (1) MapShow: Display of completed genetic linkage maps; (2) 2pointREC: Estimation of recombination frequency between two loci in 20 biparental populations; and (3) ANOVA: Analysis of variance of multi-environmental trials.

What’s new in version 4.2?

1. In functionality AOV, genotype by environment stability analysis was implemented. Unbalanced data (or phenotypic data with missing) can also be analyzed.

2. 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 A, H, B, X which are required by the software. Users need to provide SNP genotypes of the two inbred parents to use this functionality.

3. In functionality MAP, 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.

4. In functionality MAP and functionality CMP, ordering algorithm was optimized.

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