The phenotypic differences observed between individuals of the same species are the consequence of both genetic and environmental variation. The cause of natural genetic variation is random mutations, which alter an individual’s genomic DNA sequence at single nucleotide positions (point mutations) or over DNA stretches from a few nucleotides to whole chromosome arms (insertions, deletions, inversions, translocations). Neutral mutations do not have any detectable phenotypic effect in a given environmental context in the individuals that carry them. The majority of DNA-based markers

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result from mutations in this category. On the other hand, non-deleterious mutations in genes that are causal for a given phenotype must be responsible for the genetic portion of the phenotypic variation among individuals. These mutations may affect coding and/or regulatory portions of a gene and give rise to alleles that modify the phenotype in one or another direction. Let’s assume the DNA sequences of all gene(s) that control a particular phenotype are known. In this case, the natural molecular variation of these genes can be evaluated in populations of individuals, which have been examined for their phenotype values. The causal DNA variants will then be directly associated with the phenotypic variation (Kerem et al. 1989). In potato, there is presently no example for this ideal situation. However, not only causal DNA variants in causal gene(s) show association with the phenotype but also physically linked DNA polymorphisms within the gene(s) itself or in the chromosomal regions fl anking the gene, which do not have a direct functional role in producing the phenotype. This is due to the common transmission of physically linked DNA polymorphisms through successive meiotic generations (linkage disequilibrium = LD). LD is a function of the recombination frequency between polymorphic loci and the number of meiotic generations separating the ancestral haplotype (the combination of DNA polymorphisms present on a chromosome) from the haplotypes in the population analyzed, assuming random mating among the individuals (Hartl and Clark 1997). With each generation, the common transmission of physically linked DNA polymorphisms is reduced in proportion to the recombination fraction until linkage equilibrium (LE) is reached, that is, recombinant and non-recombinant haplotypes are equally distributed in the population (Fig. 7-1). The tighter the physical linkage between two loci, the longer linkage disequilibrium persists over multiple meiotic generations in a population due to the low recombination frequency. A DNA-based marker linked, for example, to an unknown gene underlying a quantitative trait locus (QTL) for pathogen resistance, might be but is not necessarily in LD with that gene in a population of individuals descending from common ancestors (related by descent). If the marker is in LD with the gene underlying the QTL, specifi c marker alleles distributed at a given frequency in such a population will be associated with the variation of disease resistance. Marker-trait associations as compared to marker-trait linkages have the advantage that a marker associated with a particular phenotype is diagnostic in wide germplasm pools, whereas a linked marker is diagnostic primarily in progeny descending from a specifi c carrier of a specifi c trait allele.