HAPPY Mapping, first proposed by Paul H. Dear and Peter R. Cook in 1989, is a method used in molecular biology

Molecular biology

Molecular biology is the branch of biology that deals with the molecular basis of biological activity. This field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry...

 to study the linkage

Genetic linkage

Genetic linkage is the tendency of certain loci or alleles to be inherited together. Genetic loci that are physically close to one another on the same chromosome tend to stay together during meiosis, and are thus genetically linked.-Background:...

 between two or more DNA sequences. According to the Single Molecule Genomics Group, it is "Mapping based on the analysis of approximately HAPloid DNA samples using the PolYmerase chain reaction". In genomics

Genomics

Genomics is a discipline in genetics concerning the study of the genomes of organisms. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. The field also includes studies of intragenomic phenomena such as heterosis,...

, HAPPY mapping can be applied to assess the synteny

Synteny

In classical genetics, synteny describes the physical co-localization of genetic loci on the same chromosome within an individual or species. The concept is related to genetic linkage: Linkage between two loci is established by the observation of lower-than-expected recombination frequencies...

 and orientation of various DNA sequences across a particular genome - the generation of a "genomic" map.

As with linkage mapping, HAPPY mapping relies on the differential probability of two or more DNA sequences being separated. In genetic mapping, the probability of a recombination

Genetic recombination

Genetic recombination is a process by which a molecule of nucleic acid is broken and then joined to a different one. Recombination can occur between similar molecules of DNA, as in homologous recombination, or dissimilar molecules, as in non-homologous end joining. Recombination is a common method...

 event between two genetic loci

Locus (genetics)

In the fields of genetics and genetic computation, a locus is the specific location of a gene or DNA sequence on a chromosome. A variant of the DNA sequence at a given locus is called an allele. The ordered list of loci known for a particular genome is called a genetic map...

 on the same chromosome

Chromosome

A chromosome is an organized structure of DNA and protein found in cells. It is a single piece of coiled DNA containing many genes, regulatory elements and other nucleotide sequences. Chromosomes also contain DNA-bound proteins, which serve to package the DNA and control its functions.Chromosomes...

 is directly proportional to the distance between them. HAPPY mapping replaces recombination with fragmentation - instead of relying on recombination to separate genetic loci, the entire genome is fragmented, for example, by radiation or mechanical shearing. If the DNA is broken on a random basis, the longer the distance between two DNA sequences, the higher the chances of it to break between the two, and vice versa.

HAPPY mapping retains the benefits of genetic mapping while removing some of the problems associated with recombination. I.e., the need for polymorphism

Polymorphism (biology)

Polymorphism in biology occurs when two or more clearly different phenotypes exist in the same population of a species — in other words, the occurrence of more than one form or morph...

, and breeding. Also, recombination can be locale specific whereas breakage of genomic DNA by radiation or mechanical shearing seems to be more random.