Ten recombinant inbred line (RIL) populations were generated for the Arabidopsis thaliana accession crosses Col x C24 (233 lines, F9), C24 x Col (249 lines, F9), Nd x C24 (248 lines, F8), C24 x Nd (250 lines, F8), Bch-1 x C24 (248 lines, F8), C24 x Bch-1 (249 lines, F8), Ak-1 x C24 (232 lines, F8), C24 x Ak-1 (224 lines, F8), Ler x C24 (250 lines, F5), C24 x Ler (249 lines, F5). The Col x C24 and C24 x Col lines have been genotyped with a framework marker set of 112 SNP markers, which has been made available for general use. Furthermore, two sets of genetic substitution lines (nearly isogenic lines, NILs) were created and genotyped: 80 lines of Col (recurrent parent) / C24 (donor parent) and 64 lines of C24 (recurrent parent) / Col (donor parent).