Gene mapping

Gene Mapping And its Applications
Pratik Umesh Parikh
F. Y. M. Pharmacy 2nd semester
(pharmaceutical biotechnology)
Roll no.: 08
Email : pratikparik42@gmail.com
Seminar on
Guided by :
Dr. Namdev L. Dhas
Bioinformatics and Computational
Biotechnology
Sanjivani College of Pharmaceutical Education and Research,
Kopargaon
10/07/2021 SANJIVANI COLLEGE OF PHARMACEUTICAL EDUCATION & RESEARCH, KOPARGAON 1

Contents :
❖ Introduction
❖Types of Gene Mapping
❖Genetic Mapping
❖Physical Mapping
❖Various markers used in Gene Mapping
❖Applications of Gene Mapping
❖Factors affecting Gene Mapping
❖Limitations of Gene Mapping
❖Gene Expression
❖Reference
SANJIVANI COLLEGE OF PHARMACEUTICAL EDUCATION & RESEARCH, KOPARGAON
10/07/2021 2

•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.
Introduction :

•There are two types of gene mapping:
• Genetic Mapping - using linkage analysis to determine the relative position between two genes
on a chromosome.
•Genetic techniques include cross-breeding experiments or,
• Case of humans, the examination of family histories
• Physical Mapping - Physical mapping uses molecular biology techniques to examine DNA
molecules directly in order to construct maps showing the positions of sequence features,
including genes.
Types of 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".
Genetic Mapping :

• 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. 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.
Genetic 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.
Physical Mapping :

• 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.
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 can be generated by aligning the restriction maps of specific pieces of cloned
genomic DNA (for instance, inYAC or BAC vectors) along the chromosomes.
• These maps are extremely useful for the purpose of map-based gene cloning.
Physical Mapping :

• DNA sequence differences between polymorphic lines may create differences in the length
ofrestriction fragments derived from genomic DNA.
• Southern blot using as probe a DNA fragment corresponding to that region. The polymorphic
bands can then be used as genetic markers to distinguish the Multiple RFLP markers can be
identified and assembled into maps. 8 Restriction Fragment Length Polymorphisms (RFLPs)
• Identify the order and/or location of sequence landmarks on the DNA
Restriction Enzyme Digests
BamH1 – GGATCC
Restriction Fragment Length Polymorphism (RFLPs) :

•Sequence length polymorphisms (SSLPs)
• SSLPs are arrays of repeat sequences that display length variations, different alleles containing
different numbers of repeat units
• Unlike RFLPs that can have only two alleles, SSLPs can be multi-allelic as each SSLP can have a
number of different length variants. There are two types of SSLP, both of which were described
in
• Minisatellites, also known as variable number of tandem repeats (VNTRs), in which the repeat
unit is up to 25 bp in length;
• Microsatellites or simple tandem repeats (STRs), whose repeats are shorter, usually
dinucleotide or tetranucleotide units
Sequence Length Polymorphism (SSLPs) :

• Microsatellites are short segments of DNA that have a repeated sequence such as CACACACA,
and they tend to occur in non-coding DNA. In some microsatellites, the repeated unit (e.g. CA)
may occur four times, in others it may be seven, or two, or thirty.
• The most common way to detect microsatellites is to design PCR primers that are unique to one
locus in the genome and that base pair on either side of the repeated portion (See the Figure
below). Therefore, a single pair of PCR primers will work for every individual in the species and
produce different sized products for each of the different length microsatellites
Microsatellites :

Application of Microsatellites :
Genome Mapping
Genetic Diversity Analysis
Functional Genomics
Hybridization & breeding
Disease identification
Taxonomic & Phylogenetic Studies
Gene Tagging

•Fluorescent in situ hybridization (FISH) enables the
position of a marker on a chromosome or extended DNA
molecule to be directly visualized.
• In optical mapping the marker is a restriction site and it is
visualized as a gap in an extended DNA fiber.
• In FISH, the marker is a DNA sequence that is visualized by
hybridization with a fluorescent probe.
Fluorescent in situ hybridization (FISH) :

Mapping helps identify mutant genes that cause genetic disorders.
Gene map is the anatomy of human genome.
It is a prerequisite to understand functioning of human genome.
Helps in analysis of the heterogeneity and segregation of human genetic diseases.
Helps to develop methods for gene therapy.
Provides clinically useful information about linkage
Applications of Gene Mapping :

➢ Double Crossing Over : This phenomenon occurs between two genes which are situated by
long distance on the same chromosome. It has been observed, though there is double crossing
over yet the two genes are remaining on the same chromosome. There is no apparent sign of
crossing over. So, calculation of crossing over percentage may cause mistakes in the
chromosome map.
➢ Interference : One chiasma may interfere to form another chiasma formation in the vicinity. As
a result, one crossing over may reduces the crossing over in the vicinity.
➢ Temperature : High and low temperatures increase the frequency of crossing over. Hence, the
temperature causes fluctuations in the location of genes on chromosome.
Factors affecting Gene Mapping :

➢ X-ray : This ray increases the frequency of crossing over and disturb the location of genes on
chromosome mapping.
➢ Age : Experiment of Bridges shows that crossing over is more frequent in older females of
Drosophila. Thus age also affects the frequency of crossing over. Hence, ageing also cause
fluctuations in loci of genes on chromosome.
➢ Location : Crossing over is less frequent near centromere and near the terminal ends of
chromosome.
➢ Sex : The males of many organisms show less frequency of crossing over. In male Drosophila
there is no crossing over. Thus, sex may also affect the frequency of crossing over.
Factors affecting Gene Mapping :

➢ A map generated by genetic technique is really sufficient for directing the sequencing face of a
genome project this is for two reasons;
➢ The reduction of genetic map depending on the number of cross over that have been scored.
➢ Gene that are several tense of KB apart may appear at the same position of genetic map.
➢ Genetic map have limited accuracy .
➢ Presence of recombination hotspot means that the cross over are more likely to occur at some
points rather than at other.
➢ Physical mapping technique has been developed to address this problem.
Limitations of Gene Mapping :

➢Gene expression is the process by which information from a gene is used in the synthesis of a
functional gene product that enables it to produce end products, protein or non-coding RNA,
and ultimately affect a phenotype, as the final effect.
➢ These products are often proteins, but in non-protein-coding genes such as transfer RNA
(tRNA) and small nuclear RNA (snRNA), the product is a functional non-coding RNA.
➢ Gene expression is summarized in the central dogma of molecular biology first formulated
by Francis Crick in 1958,further developed in his 1970 article, and expanded by the subsequent
discoveries of reverse transcription and RNA replication.
➢The process of gene expression is used by all known life—eukaryotes (including multicellular
organisms), prokaryotes (bacteria and archaea ), and utilized by viruses—to generate
the macromolecular machinery for life.
Gene Expression :

➢In genetics, gene expression is the most fundamental level at which the genotype gives rise to
the phenotype, i.e. observable trait. The genetic information stored in DNA represents the
genotype, whereas the phenotype results from the "interpretation" of that information.
➢ Such phenotypes are often expressed by the synthesis of proteins that control the organism's
structure and development, or that act as enzymes catalyzing specific metabolic pathways.
➢ All steps in the gene expression process may be modulated (regulated), including
the transcription, RNA splicing, translation, and post-translational modification of a protein.
➢ Regulation of gene expression gives control over the timing, location, and amount of a given
gene product (protein or ncRNA) present in a cell and can have a profound effect on the cellular
structure and function.
Gene Expression :

➢Regulation of gene expression is the basis for cellular
differentiation, development, morphogenesis and the versatility and adaptability of
any organism. Gene regulation may therefore serve as a substrate for evolutionary change.
Gene Expression :

Reference :
1. Mader, Sylvia (2007). Biology Ninth Edition. New York: McGraw-Hill. p. 209. ISBN 978-0-07-
325839-3.
2. "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.
3. David W. mount, Bioinformatics Sequence and Genome Analysis, CBS Publishers and Distributors
4. https://www.slideshare.net/PrashantTripathi59/gene-mapping-ppt
5. https://www.slideshare.net/UsmanArshad53/gene-mapping-tools
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