Fig. 1

Construction of two high-density haplotype maps. a W4M6 and DMRH pseudo one-way testcross populations were used to construct high-density haplotype maps in potato. b Using short nucleotide variants (SNVs) to calculate linkage disequilibrium (LD) within windows of 50 SNVs, we used high frequency linked alleles to reconstruct the two segregating haplotypes of the heterozygous parent. The reconstructed haplotypes were then used to assign haplotypes to individual SNVs in the progeny. A single crossover between SNV 3 and SNV 4 is illustrated for individual 3. c Haplotype map of the W4M6 and DMRH populations. Red and blue segments reflect the two alleles segregating in the W4M6 population (US-W4 alleles) with yellow segments in between to illustrate large crossover intervals (lack of intervening haplotype-differentiating SNVs). The green and orange segments represent the two alleles segregating in the DMRH population (RH alleles)