GENE Mapping - Lecture notes 2-10 PDF

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GENE MAPPING FOR SECOND YEAR STUDENTS -PHARM.D...

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GENE MAPPING  Gene mapping describes the methods used to identify the locus of a gene and the distances between genes.  The essence of all genome mapping 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. GENOME MAPPING  Genetic mapping is based on the use of genetic techniques to construct maps showing the positions of genes and other sequence features on a genome.  Genetic techniques include cross-breeding experiments or,  Case of humans, the examination of family histories (pedigrees).  Physical mapping uses molecular biology techniques to examine DNA molecules directly in order to construct maps showing the positions of sequence features, including genes. GENETIC MAPPING 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. The genotypes of each genetic marker are recorded for both parents, and in each individual in the following generations. The quality of the genetic maps is largely dependent upon these two factors: the number of genetic markers on the map and the size of the mapping population. In gene mapping, any sequence feature that can be faithfully distinguished from the two parents can be used as a genetic marker. Genes are represented by "traits" that can be 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 bracketed in a region between the two nearest neighbouring markers. The entire process is then repeated by looking at more markers which target that region to map the gene neighbourhood 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. PHYSICAL MAPPING  Restriction mapping, which locates the relative positions on a DNA molecule of the recognition sequences for restriction endonucleases;  Fluorescent in situ hybridization (FISH), in which marker locations are mapped by hybridizing a probe containing the marker to intact chromosomes;  Sequence tagged site (STS) mapping, in which the positions of short sequences are mapped by PCR and/or hybridization analysis of genome fragments. Physical maps  Physical maps can be generated by aligning the restriction maps of specific pieces of cloned genomic DNA (for instance, in YAC or BAC vectors) along the chromosomes.  These maps are extremely useful for the purpose of map-based gene cloning.

Genetic vs. Physical Distance  Map distances based on recombination frequencies are not a direct measurement of physical distance along a chromosome  Recombination “hot spots” overestimate physical length  Low rates in heterochromatin and centromeres underestimate actual physical length Uses of Gene Mapping  Identify genes responsible for diseases.  Heritable diseases  Cancer  Identify genes responsible for traits.  Plants or Animals  Disease resistance  Meat or Milk Production Human Genome Project  The Human Genome Project (HGP) is an international scientific research project with the goal of determining the sequence of chemical base pairs which make up human DNA, and of identifying and mapping all of the genes of the human genome from both a physical and a functional standpoint.  The Human Genome Project originally aimed to map the nucleotides contained in a human haploid reference genome (more than three billion). The "genome" of any given individual is unique; mapping the "human genome" involves sequencing multiple variations of each gene. In May 2016, scientists considered extending the HGP to include creating a synthetic human genome. LIMITATIONS  A map generated by genetic techniques is rarely sufficient for directing the sequencing phase of a genome project. This is for two reasons:  The resolution of a genetic map depends on the number of crossovers that have been scored .  Genes that are several tens of kb apart may appear at the same position on the genetic map.  Genetic maps have limited accuracy .  Presence of recombination hotspots means that crossovers are more likely to occur at some points rather than at others.  physical mapping techniques has been developed to address this problem....