Gene mapping
Encyclopedia
Gene mapping, also called genome mapping, is the creation of a genetic map assigning DNA
fragments to chromosome
s.
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 marker
s (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.
. 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 analysing the fingerprints, contig
s 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.
Genes can be mapped prior to the complete sequencing by independent approaches like in situ hybridization
.
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.
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
fragments to 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...
s.
When a genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
is first investigated, this map is nonexistent. The map improves with the scientific progress and is perfect when the genomic DNA sequencing
DNA sequencing
DNA sequencing includes several methods and technologies that are used for determining the order of the nucleotide bases—adenine, guanine, cytosine, and thymine—in a molecule of DNA....
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 marker
Genetic marker
A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify cells, individuals or species. It can be described as a variation that can be observed...
s (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
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
. Using modern molecular biology techniques for the same purpose is usually referred to as physical mapping.
Physical Mapping
In physical mapping, the DNA is cut by a restriction enzymeRestriction enzyme
A Restriction Enzyme is an enzyme that cuts double-stranded DNA at specific recognition nucleotide sequences known as restriction sites. Such enzymes, found in bacteria and archaea, are thought to have evolved to provide a defense mechanism against invading viruses...
. Once cut, the DNA fragments are separated by electrophoresis
Electrophoresis
Electrophoresis, also called cataphoresis, is the motion of dispersed particles relative to a fluid under the influence of a spatially uniform electric field. This electrokinetic phenomenon was observed for the first time in 1807 by Reuss , who noticed that the application of a constant electric...
. The resulting pattern of DNA migration (i.e., its genetic fingerprint) is used to identify what stretch of DNA is in the clone. By analysing the fingerprints, contig
Contig
A contig is a set of overlapping DNA segments that together represent a consensus region of DNA. In bottom-up sequencing projects, a contig refers to overlapping sequence data ; in top-down sequencing projects, contig refers to the overlapping clones that form a physical map of the genome that is...
s 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
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
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.
Genes can be mapped prior to the complete sequencing by independent approaches like in situ hybridization
In situ hybridization
In situ hybridization is a type of hybridization that uses a labeled complementary DNA or RNA strand to localize a specific DNA or RNA sequence in a portion or section of tissue , or, if the tissue is small enough , in the entire tissue...
.
Disease-association
The process to identify a genetic element that signs responsible for a diseaseDisease
A disease is an abnormal condition affecting the body of an organism. It is often construed to be a medical condition associated with specific symptoms and signs. It may be caused by external factors, such as infectious disease, or it may be caused by internal dysfunctions, such as autoimmune...
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
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:...
) or from populations-based genetic association
Genetic association
Genetic association is the occurrence, more often than can be readily explained by chance, of two or more traits in a population of individuals, of which at least one trait is known to be genetic....
studies.
See also
- Genome projectGenome projectGenome projects are scientific endeavours that ultimately aim to determine the complete genome sequence of an organism and to annotate protein-coding genes and other important genome-encoded features...
- Human Genome ProjectHuman Genome ProjectThe Human Genome Project is an international scientific research project with a primary goal of determining the sequence of chemical base pairs which make up DNA, and of identifying and mapping the approximately 20,000–25,000 genes of the human genome from both a physical and functional...
- Quantitative trait locusQuantitative trait locusQuantitative traits refer to phenotypes that vary in degree and can be attributed to polygenic effects, i.e., product of two or more genes, and their environment. Quantitative trait loci are stretches of DNA containing or linked to the genes that underlie a quantitative trait...
- Genetic fingerprintingGenetic fingerprintingDNA profiling is a technique employed by forensic scientists to assist in the identification of individuals by their respective DNA profiles. DNA profiles are encrypted sets of numbers that reflect a person's DNA makeup, which can also be used as the person's identifier...
- Genetic linkageGenetic linkageGenetic 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:...
- Sulston scoreSulston scoreThe Sulston Score is an equation used in DNA mapping to numerically assess the likelihood that a given "fingerprint" similarity between two DNA clones is merely a result of chance. Used as such, it is a test of statistical significance...
- Optical mappingOptical mappingOptical mapping is a technique for constructing ordered, genome-wide, high-resolution restriction maps from single, stained molecules of DNA, called "optical maps". By mapping the location of restriction enzyme sites along the unknown DNA of an organism, the spectrum of resulting DNA fragments...