SimpleMap: A Pipeline to Streamline High-Density Linkage Map Construction

The recent development in high-throughput genotyping techniques requires new statistical methods to analyze large datasets. The current available linkage mapping software are time consuming and limited in terms of the maximum number of markers that can be mapped on a single linkage group. In this paper, we propose the Perl pipeline, SimpleMap. This tool can significantly improve the speed of currently available linkage mapping software with minimal impact on marker order and map length by limiting the consideration of duplicated and tightly linked molecular markers during linkage group development. SimpleMap works with the following three main steps: (i) generating a subset of markers for which each pair has a number of recombinants higher than a threshold determined by the user (the repulsion threshold), (ii) mapping this subset with any external mapping tool, and (iii) intersecting the remaining unmapped markers to the constructed map. The script was tested on 15 wheat (Triticum aestivum L.) linkage groups derived from two different crosses. In 13 genetic groups, the computational time was reduced from similar to 8 h to similar to 8 min, while it was impossible to map the remaining two linkage groups without applying SimpleMap first. SimpleMap is a very time-efficient tool, and considering a repulsion threshold equivalent to 1 cM results in a number of markers similar to map lengths that can be analyzed on a simple personal computer. SimpleMap can be downloaded from http://simplemap-aj.sourceforge.net/.