IntroMap: A Pipeline and Set of Diagnostic DiploidArachisSNPs as a Tool for Mapping Alien Introgressions inArachis hypogaea

For crops with a narrow cultivated genetic base, incorporating beneficial alleles from related species through alien introgression widens the genetic base and provides key resistances to disease and abiotic stresses. Fine mapping of these introgressions can increase the efficiency of marker-assisted selection for breeding programs. To facilitate high resolution fine mapping of alien introgressions, we developed an automated pipeline, IntroMap. This pipeline was developed with accessibility and utility in mind, and does not present novel mapping algorithms. Using five diploid wild Arachis species, we identified diagnostic SNP sets for introgression mapping in Arachis hypogaea, cultivated peanut. IntroMap has applicability in all crops where alien introgression is used to bring in beneficial alleles from related species, so the pipeline includes an option to generate new diagnostic SNPs from any species/accession of interest for use in the pipeline. These user generated resources will be included f...