IntroMap: A Pipeline and Set of Diagnostic Diploid Arachis SNPs as a Tool for Mapping Alien Introgressions in Arachis hypogaea

ABSTRACT 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 for distribution with IntroMap to increase the SNP resources for all users. We demonstrate the efficacy of IntroMap by fine mapping three alien introgressions in an elite peanut breeding line with superior disease resistance. IntroMap works well even at low coverage, recovering at 2x coverage almost 50% of the diagnostic SNPs found at 10x coverage. The true benefit of IntroMap is the availability and generation of shared public resources, specifically for Arachis spp. IntroMap is freely distributed at https://sourceforge.net/projects/intromap/.