Data from: Genetic mapping and QTL analysis for peanut smut resistance. This collection contains supplementary information for the manuscript “Genetic mapping and QTL analysis for peanut smut resistance”, which reports the genetic map and quantitative trait loci associated with resistance to peanut smut, a disease caused by the fungus Thecaphora frezii. The information includes genotyping data of a 103 recombinant inbred line (RIL) population {susceptible Arachis hypogaea subsp. hypogaea × resistant synthetic amphidiploid [(A. correntina × A. cardenasii) × A. batizocoi]4×} and parental lines, generated with the Axiom_Arachis2 SNP array. Supplementary Data 1: SNP genotypes as called by the Axiom Analysis Suite File name: SD01_RILs_SNPs_whole_Axiom_Arachis2.txt Single nucleotide polymorphism genotyping of a 103 RIL population and parental lines generated with the Arachis_Axiom2 SNP array. Supplementary Data 2: Genotype calls stored in variant call format (VCF). File name: SD02_core_RILs_SNPs_Axiom_Arachis2.vcf Core SNP set used to characterize the RIL population and progenitors.