Genetic markers are heritable traits, which occur in at least two variants (alleles) in populations of individuals of the same species. They correspond to single genetic loci and segregate in progeny of parents differing in their alleles according toMendelian rules. The molecular basis of all genetic markers is DNA mutations, either point mutations (exchange of a single nucleotide) or insertions/deletions of one or more nucleotides in one allele versus another. Whereas Mendel analysed the inheritance of DNA mutations by observing morphological variation, molecular techniques are used today to detect DNA polymorphisms directly, for example by restriction fragment length analysis or DNA sequencing (DNA-based markers). Genetic markers located on the same chromosome are physically linked. The distance between the marker loci and their linear order can be determined by estimating the pair wise recombination frequency between all markers located on that chromosome in a segregating population. This results in a genetic linkage map of the chromosome. Such linkage maps can be constructed for all chromosomes of a species. In the FI progeny of heterozygous, diploid parents such as diploid potatoes, two linkage maps are constructed derived from meiotic recombination events in the seed and pollen parent. The precision and resolution of linkage rnaps depends on the number of marker loci and the number of recombination events (population size) analysed. The true physical distance between marker loci is determined by genomic sequencing. The genome sequence of a species is therefore the map with ultimate precision and resolution.
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