User:Southgatea/Gene mapping

Thomas Hunt Morgan's Drosophila melanogaster genetic linkage map. This was the first successful gene mapping work and provides important evidence for the Boveri–Sutton chromosome theory of inheritance. The map shows the relative positions of allelic characteristics on the second Drosophila chromosome. The distance between the genes (map units) are equal to the percentage of crossing-over events that occurs between different alleles.

Gene mapping describes the methods used to identify the position of a gene in a genome and the distances between genes. Methods of gene mapping have changed over time with the application of new molecular biology-based technologies (cloning, DNA sequencing, etc). and can varied between different species, i.e. Human genes are mapped differently than Drosophila genes.

Gene mapping results in the production of either genetic or physical maps depending on the methodologies being used. Gene mapping often starts with assigning a particular gene to a given chromosome.

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 gene loci, and genetic markers, genetic maps' distances are based on the genetic linkage information, while physical maps use 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.

Linkage (cosegregation) or independent assortment can be used to identify the chromosomal position of a gene responsible for a particular trait. Thomas Hunt Morgan created the first genetic map for the X chromosome in Drosophila melanogaster using such an approach. His studies with his student Edward Sturtevant lead to the chromosomal theory of heredity in 1905.

Gene mapping

Researchers begin a genetic map by collecting samples of blood., saliva, or tissue from family members that carry a prominent disease or trait and family members that don't. The most common sample used in gene mapping, especially in personal genomic tests is saliva. Scientists then isolate DNA from the samples and closely examine it, looking for unique patterns in the DNA of the family members who do carry the disease that the DNA of those who don't carry the disease don't have. These unique molecular patterns in the DNA are referred to as polymorphisms, or markers.

The first steps of building a genetic map are the development of genetic markers and a mapping population. The closer 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 are recorded for both parents and each individual in the following generations. The quality of the genetic maps is largely dependent upon these 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 from being "saturated".

In gene 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 is calculated in the same way as if they are common markers and the actual gene loci are then bracketed in a region between the two nearest neighboring markers. The entire process is then repeated by looking at more markers that target that region to map the gene neighborhood to a higher resolution until a specific causative locus can be identified. This process is often referred to as "positional cloning", and it is used extensively in the study of plant species. One plant species, in particular in which positional cloning is utilized is in maize.ref>Gallvetti, Andrea; Whipple, Clinton J. (2015). "Positional cloning in maize (Zea mays subsp. mays, Poaceae)". Applications in Plant Sciences. 3 (1): 1400092. doi:10.3732/apps.1400092. PMC 4298233. PMID 25606355.</ref> The great advantage of genetic mapping is that it can identify the relative position of genes based solely on their phenotypic effect.

Genetic mapping is a way to identify exactly which chromosome has which gene and exactly pinpointing where that gene lies on that particular chromosome. Mapping also acts as a method in determining which gene is most likely recombine based on the distance between two genes. The distance between two genes is measured in units known as centimorgan. A centimorgan is a distance between genes for which one product of meiosis in one hundred is recombinant. The further two genes are from each other, the more likely they are going to recombine. If it were closer, the opposite would occur.

Physical mapping

Since actual base-pair distances are generally hard or impossible to directly measure, physical maps are actually constructed by first shattering the genome into hierarchically smaller pieces. By characterizing each single piece and assembling back together, the overlapping path or "tiling path" of these small fragments would allow researchers to infer physical distances between genomic features. The fragmentation of the genome can be achieved by restriction enzyme cutting or by physically shattering the genome by processes like sonication. 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.

In physical mapping, there are no direct ways of marking up a specific gene since the mapping does not include any information that concerns traits and functions. Genetic markers can be linked to a physical map by processes like 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 on a local scale to help new genetic marker design and identification of the causative loci.

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 overlaps 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

Genome sequencing is sometimes mistakenly referred to as "genome mapping" by non-biologists. The process of "shotgun sequencing" resembles the process of physical mapping: it shatters the genome into small fragments, characterizes each fragment, then puts them back together (more recent sequencing technologies are drastically different). 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 in a much better way all the information that a traditional physical map can offer.

Use

Identification of genes is usually the first step in understanding a genome of a species; mapping of the gene is usually the first step of identification of the gene. Gene mapping is usually the starting point of many important downstream studies.

Disease association

The process to identify a genetic element that is 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.

See also

• Genetic fingerprinting
• Genetic linkage
• Genome project
• Human Genome Project
• Optical mapping
• Quantitative trait locus
• Sulston score