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When a genome is first investigated, this map is nonexistent. The map improves with the scientific progress and is perfect when the genomic DNA sequencing of the species has been completed. During this process, and for the investigation of differences in strain, the fragments are identified by small tags. These may be genetic markers (PCR products) or the unique sequence-dependent pattern of DNA-cutting enzymes. The ordering is derived from genetic observations (recombinant frequency) for these markers or in the second case from a computational integration of the fingerprinting data. The term "mapping" is used in two different but related contexts.
Two different ways of mapping are distinguished. Genetic mapping uses classical genetic techniques (e.g. pedigree analysis or breeding experiments) to determine sequence features within a genome. Using modern molecular biology techniques for the same purpose is usually referred to as physical mapping.
Genetic Mapping VS Physical Mapping
There are two distinctive types of "Maps" used in the field of genome mapping: genetic maps and physical maps. While both maps are a collection of genetic markers and gene loci, genetic maps distances are based on the genetic linkage information measured in Centi-Morgans(CM), while physical maps uses actual physical distances usually measured in number of base pairs. While the physical map could be a more "accurate" representation of the genome, genetic maps often offer insights into the nature of different regions of the chromosome, e.g. the genetic distance to physical distance ratio varies greatly at different genomic regions which reflects different recombination rates, and such rate is often indicative of euchromatic (usually gene-rich) vs heterochromatic(usually gene poor) regions of the genome.
The first steps of building a genetic map are the development of genetic markers and a mapping population. Since the closer the two markers are on the chromosome, the more likely they are to be passed on to the next generation together, therefore the "co-segregation" patterns of all markers can be used to reconstruct their order. With this in mind, the genotypes of each genetic marker is recorded for both parents, and in each individual in the following generations. The quality of the genetic maps are largely depended upon these two factors: the number of genetic markers on the map, and the size of the mapping population. The two factors are interlinked, as a larger mapping population could increase the "resolution" of the map and prevent the map being "saturated".
In physical mapping, the DNA is cut by a restriction enzyme. Once cut, the DNA fragments are separated by electrophoresis. The resulting pattern of DNA migration (i.e., its genetic fingerprint) is used to identify what stretch of DNA is in the clone. By analyzing the fingerprints, contigs are assembled by automated (FPC) or manual means (Pathfinders) into overlapping DNA stretches. Now a good choice of clones can be made to efficiently sequence the clones to determine the DNA sequence of the organism under study (seed picking).
Macrorestriction is a type of physical mapping wherein the high molecular weight DNA is digested with a restriction enzyme having a low number of restriction sites.
There are alternative ways to determine how DNA in a group of clones overlap without completely sequencing the clones. Once the map is determined, the clones can be used as a resource to efficiently contain large stretches of the genome. This type of mapping is more accurate than genetic maps.
Genome sequencing are sometimes mistakenly referred to as "genome mapping" by non-biologists. While the scope, purpose and process are totally different, a genome assembly can be viewed as the "ultimate" form of physical map, in that it provides all information that a traditional physical map can offer in a much better way.
The essense of all genome mapping approach is to place a collection of molecular markers onto their respective positions on the genome. Molecular markers come in all forms. Genes can be viewed as one special type of genetic markers in the construction of genome maps, and mapped the same way as any other markers.
In genetic mapping, any sequence feature that can be faithfully distinguished from the two parents can be used as a genetic marker. Genes, in this regard, are represented by "traits" that can be faithfully distinguished between two parents. Their linkage with other genetic markers are calculated same way as if they are common markers and the actual gene loci are then brackated in a region between the two nearest neighboring markers. This process are then repeated by looking at more markers that target that region to map the gene neighborhood to a higher resolution until the a specific causative locus can be identified. This process is often referred to as "positional cloning", and used extensively in the study of plant species.
In physical mapping, there are no direct ways of marking up a specific gene since the mapping do not include any information that concern traits and functions. Genetic markers can be linked to a physical map by processes in situ hybridization. By this approach, physical map contigs can be "anchored" onto a genetic map. The clones used in the physical map contigs can then be sequenced local scale to help new genetic marker design and identification of the causative loci.
The process to identify a genetic element that signs responsible for a disease is also referred to as "mapping". If the locus in which the search is performed is already considerably constrained, the search is called the "fine-mapping" of a gene. This information is derived from the investigation of disease-manifestations in large families (Genetic linkage) or from populations-based genetic association studies.
- Genome project
- Human Genome Project
- Quantitative trait locus
- Genetic fingerprinting
- Genetic linkage
- Sulston score
- Optical mapping
- "Gene mapping - Glossary Entry". Genetics Home Reference. Bethesda, MD: Lister Hill National Center for Biomedical Communications, an Intramural Research Division of the U.S. National Library of Medicine. 2013-09-03. Retrieved 2013-09-06.
- Brown, Terry A. (2007). Genomes 3. New York, NY: Garland Science Publishing. ISBN 9780815341383. OCLC 444522997.
- "Genetic Mapping Fact Sheet". Bethesda, MD: National Human Genome Research Institute, National Institutes of Health. Retrieved 2013-09-06.
- "Canada's Michael Smith Genome Sciences Centre". Vancouver, British Columbia. Retrieved 2013-09-06.
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