SimpleMap

SimpleMap constructs high-density genetic linkage maps by selecting marker subsets based on recombination (repulsion) thresholds and integrating unmapped markers after mapping with external linkage mapping software to accelerate analysis of large datasets from modern high-throughput genotyping techniques.

Key Features:

• Perl-based implementation: SimpleMap is implemented as a Perl-based pipeline.
• Efficiency in processing: In wheat (Triticum aestivum L.) linkage groups derived from two different crosses, SimpleMap reduced processing time from approximately 8 hours to about 8 minutes for 13 of 15 genetic groups.
• Marker management: Generates a subset of markers where each marker pair exhibits a number of recombinants exceeding a user-defined repulsion threshold to limit duplicated and tightly linked molecular markers.
• Integration with external mapping tools: Maps the selected subset using external linkage mapping software and subsequently integrates remaining unmapped markers into the constructed map.
• User-defined repulsion threshold: The repulsion threshold can be adjusted by users, with a threshold equivalent to 1 centiMorgan (cM) typically producing manageable map lengths for analysis on standard personal computers.
• Scalability for high-throughput genotyping: Addresses challenges posed by large datasets generated through modern high-throughput genotyping techniques.

Scientific Applications:

• Plant and animal breeding programs: Supports construction of high-density linkage maps used in breeding research.
• Evolutionary studies: Facilitates generation of high-density linkage maps for evolutionary investigations.
• Genomic selection projects: Enables handling of large marker datasets required in genomic selection workflows.

Methodology:

Identify a subset of markers based on user-defined recombinant (repulsion) thresholds; map this subset using external linkage mapping software; and integrate the remaining unmapped markers into the constructed map.