Figure 1

Schema of terms related to the HIPP. The total genotype of a tetraploid species consists of four chromosomes (Chromosome A-D) where two chromosomes come from the first parent (blue) and the other two from the second (green). A locus is a fixed position on a chromosome often consisting of many nucleotides. Four haplotypes (Haplotype A-D) represent the nucleotide sequence of the corresponding locus on the four chromosomes. The four haplotypes A*-D* represent the conflated data of genotype* and thus explain genotype* (see also Figure 2, Figure 3 and Figure 7). The example illustrates a population of one individual. A homozygous site of the presented individual and locus becomes a SNP site, if a second individual is added which is heterozygous at a site different from SNP1-4 (and vice versa).