Map distances and markers
Maps can be used to find markers linked to or in the region of genes for traits of interest. The marker loci are usually not evenly distributed over the chromosome, but they appear more clustered in some regions and absent in others (gaps in maps). Markers in clusters may be removed from the data set, to obtain a skeletal linkage map for application in mapping. Markers that have (nearly) the same segregation pattern, because of (near-) identical position are redundant: they do not add much power or precision to the outcome of the mapping study, but may increase computional time for analyses. In addition, in the case of even a low percentage of errors in genotyping, a large number of markers may drastically overestimate the map length of linkage groups because such errors cause an overestimation of the number of recombinations.
The recombination frequency is not equal along chromosomes: there are recombination 'hot spots' and 'cold spots'. Higher levels of recombination correspond to larger genetic map distances (more cM). Hot spots will therefore result in relatively large distances between adjacent marker loci. Cold spots will be 'condensed' on the linkage map: marker locus intervals are small, and markers tend to cluster. In many organisms, centromeric regions are cold spots, and often stand out in linkage maps as clusters of marker loci. In such cold spots there is hardly any relationship anymore between physical distance in base pairs (may be quite large) and genetic distance (0 or close to 0). In general, because the recombination frequency varies along chromosomes, the distances on a linkage map do not correspond to physical distances between markers measured in nucleotide base pairs.
Map distances are expressed in centiMorgan units (cM). When map distances are small (<10 cM), the map distance in cM is almost equal to the recombination frequency in percentage (per meiosis). However, when map distances are greater than approximately 10 cM, the map distance deviates more and more from the recombination frequency. This is because of the higher probability of multiple recombinations (see paragraph on 'Linkage, recombination and map distance') and interference caused by other cross-over events. The recombination frequency in a diploid cannot be higher than 50% (apart from some sampling variation), while the length of a linkage group corresponding to a single chromosome might be more than 100 cM.
Many of the markers observed in the population under study might be absent (or better: not polymorphic) in other populations. Therefore, they will not show up in linkage maps from other populations. Markers that are present in several maps can be used as reference for the location of other markers; these are called 'anchor markers' (will be treated in more detail later).
The accuracy of the map (marker order and distances) is directly related to the size of the mapping population. Mapping populations should consist of a minimum of 50 individuals (or lines) for constructing linkage maps. However, for application of mapping genes for traits of interest, especially mapping of genes with small effects (QTLs) a mapping population of about 200 genotypes is required. The larger the population the larger the power for detection of QTLs.
Interference
Interference means that crossover events in adjacent intervals interfere: the occurrence of an event in a given interval may reduce or enhance the chance for occurrence of an event in its neighborhood. Negative interference refers to the 'enhancement' of crossover events around a given one. Positive interference refers to the 'suppression' of crossover events in the neighborhood of a given one. In most organisms positive interference has been observed, to various degrees of intensity. Positive interference results in fewer double recombinants (over adjacent intervals) than would be expected on the basis of independence of recombination events.
Summary
→ The strength of evidence of linkage between markers is often expressed as a LOD score
→ Map distances are calculated from recombination frequencies and expressed in centiMorgan units
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