Haplotype
A haplotype is a specific combination of alleles that occur in linkage. In the case of markers, if such a string of closely linked markers surround a gene of interest, the chance is considerable that the haplotype is "diagnostic" (unique), allowing the breeder to follow the presence of the gene of interest in descendants of the donor that contributes the gene.
In this example, the haplotype M1m2M3m4M5M6 is typical for the desirable allele A of the gene; haplotype m1M2m3M4m5m6 is typical for the undesirable allele of the gene. Note that descendants that carry the A allele but have a recombination between for example M3 and m4 will probably form a novel and aberrant haplotype, and cannot be recognized for sure to carry allele A. If the constituent markers are tightly linked, the chance for such a recombination is very small.
The advantage is that, across a range of possible accessions, the multi-marker haplotype has a much larger chance to be diagnostic for the favorable allele than a single marker or a pair of markers flanking the gene of interest. The haplotype may be used to screen the elite lines or cultivars of a breeding program for having the desired allele A and subsequently use these as parents in crosses. If we use a parent carrying allele A and the marker haplotype as donor in a complex crossing programme involving various other parents, we may monitor the presence of allele A by scoring all six markers. It is extremely unlikely that another accession of the crop would be by chance M1m2AM3m4M5M6, without carrying allele A. If another genotype for example has M1m2M3M4m5m6, then this is a third haplotype. For this third haplotype it is not known whether it carries the A or a allele; only the known haplotype provides sufficient certainty.
A prerequisite for selection on the basis of haplotypes is that you need to be able to run large numbers of markers (e.g. on SNP platforms).
Summary
→ Haplotyping addresses several specific marker alleles to a desirable allele of a gene and diagnostic for the gene that they are used for
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