Genetic mapping is based on recombination frequencies between genetic loci during meiosis. Physical mapping determines the actual distances in base pairs between sequences on a chromosome using overlapping DNA fragments. Before whole genome sequencing, physical maps were created using techniques like restriction mapping of large-insert clones, probing genomic libraries with end fragments, and chromosome walking to build contigs of overlapping sequences. This allowed sequencing of individual fragments which could then be assembled into a complete genome sequence.
What is Genome,Genome mapping,types of Genome mapping,linkage or genetic mapping,Physical mapping,Somatic cell hybridization
Radiation hybridization ,Fish( =fluorescence in - situ hybridization),Types of probes for FISH,applications,Molecular markers,Rflp(= Restriction fragment length polymorphism),RFLPs may have the following Applications;Advantages of rflp,disAdvantages of rflp, Rapd(=Random amplification of polymorphic DNA),Process of rapd, Difference between rflp &rapd
What is Genome,Genome mapping,types of Genome mapping,linkage or genetic mapping,Physical mapping,Somatic cell hybridization
Radiation hybridization ,Fish( =fluorescence in - situ hybridization),Types of probes for FISH,applications,Molecular markers,Rflp(= Restriction fragment length polymorphism),RFLPs may have the following Applications;Advantages of rflp,disAdvantages of rflp, Rapd(=Random amplification of polymorphic DNA),Process of rapd, Difference between rflp &rapd
Introduction
History
Genetic mapping
DNA Markers
Physical mapping
Importance
Drawback
Conclusion
References
uses genetic techniques to construct maps showing the positions of genes and other sequence features on a genome.
Genetic techniques include cross-breeding experiments or, in the case of humans, the examination of family histories (pedigrees).
BAC & YAC are artificially prepared chromosomes to clone DNA sequences.yeast artificial chromosome is capable of carrying upto 1000 kbp of inserted DNA sequence
Creation of a cDNA library starts with mRNA instead of DNA. Messenger RNA carries encoded information from DNA to ribosomes for translation into protein. To create a cDNA library, these mRNA molecules are treated with the enzyme reverse transcriptase, which is used to make a DNA copy of an mRNA (i.e., cDNA). A cDNA library represents a sampling of the transcribed genes, but a genomic library includes untranscribed regions.
STS stands for sequence tagged site which is short DNA sequence, generally between 100 and 500 bp in length, that is easily recognizable and occurs only once in the chromosome or genome being studied.
Introduction
History
Genetic mapping
DNA Markers
Physical mapping
Importance
Drawback
Conclusion
References
uses genetic techniques to construct maps showing the positions of genes and other sequence features on a genome.
Genetic techniques include cross-breeding experiments or, in the case of humans, the examination of family histories (pedigrees).
BAC & YAC are artificially prepared chromosomes to clone DNA sequences.yeast artificial chromosome is capable of carrying upto 1000 kbp of inserted DNA sequence
Creation of a cDNA library starts with mRNA instead of DNA. Messenger RNA carries encoded information from DNA to ribosomes for translation into protein. To create a cDNA library, these mRNA molecules are treated with the enzyme reverse transcriptase, which is used to make a DNA copy of an mRNA (i.e., cDNA). A cDNA library represents a sampling of the transcribed genes, but a genomic library includes untranscribed regions.
STS stands for sequence tagged site which is short DNA sequence, generally between 100 and 500 bp in length, that is easily recognizable and occurs only once in the chromosome or genome being studied.
In shotgun sequencing the genome is broken randomly into short fragments (1 to 2 kbp long) suitable for sequencing. The fragments are ligated into a suitable vector and then partially sequenced. Around 400–500 bp of sequence can be generated from each fragment in a single sequencing run. In some cases, both ends of a fragment are sequenced. Computerized searching for overlaps between individual sequences then assembles the complete sequence.
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.
Genome evolution - tales of scales DNA to crops,months to billions of years, ...Pat (JS) Heslop-Harrison
Pat Heslop-Harrison: Lecture to University of Malaya, Kuala Lumpur, Malaysia December 2013
Some DNA sequences are recognizable in all organisms and originated with the start of life. Others are unique to a single species. Some sequences are present in single copies in genomes, while others are present as millions of copies. The total amount of DNA in cells of an advanced eukaryotic species can vary over three orders of magnitude, and chromosome number can vary similarly. How can such huge variations be accommodated within the constraints of organism growth, development and reproduction? What are the evolutionary implications of these huge variations? How can we use the information to understand plant evolution, cytogenetics, genetics and epigenetics? What are the implications for future evolution, biodiversity and responses of plants during plant breeding or climate change?
How to Make a Field invisible in Odoo 17Celine George
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Synthetic Fiber Construction in lab .pptxPavel ( NSTU)
Synthetic fiber production is a fascinating and complex field that blends chemistry, engineering, and environmental science. By understanding these aspects, students can gain a comprehensive view of synthetic fiber production, its impact on society and the environment, and the potential for future innovations. Synthetic fibers play a crucial role in modern society, impacting various aspects of daily life, industry, and the environment. ynthetic fibers are integral to modern life, offering a range of benefits from cost-effectiveness and versatility to innovative applications and performance characteristics. While they pose environmental challenges, ongoing research and development aim to create more sustainable and eco-friendly alternatives. Understanding the importance of synthetic fibers helps in appreciating their role in the economy, industry, and daily life, while also emphasizing the need for sustainable practices and innovation.
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Model Attribute Check Company Auto PropertyCeline George
In Odoo, the multi-company feature allows you to manage multiple companies within a single Odoo database instance. Each company can have its own configurations while still sharing common resources such as products, customers, and suppliers.
The French Revolution, which began in 1789, was a period of radical social and political upheaval in France. It marked the decline of absolute monarchies, the rise of secular and democratic republics, and the eventual rise of Napoleon Bonaparte. This revolutionary period is crucial in understanding the transition from feudalism to modernity in Europe.
For more information, visit-www.vavaclasses.com
The Art Pastor's Guide to Sabbath | Steve ThomasonSteve Thomason
What is the purpose of the Sabbath Law in the Torah. It is interesting to compare how the context of the law shifts from Exodus to Deuteronomy. Who gets to rest, and why?
2024.06.01 Introducing a competency framework for languag learning materials ...Sandy Millin
http://sandymillin.wordpress.com/iateflwebinar2024
Published classroom materials form the basis of syllabuses, drive teacher professional development, and have a potentially huge influence on learners, teachers and education systems. All teachers also create their own materials, whether a few sentences on a blackboard, a highly-structured fully-realised online course, or anything in between. Despite this, the knowledge and skills needed to create effective language learning materials are rarely part of teacher training, and are mostly learnt by trial and error.
Knowledge and skills frameworks, generally called competency frameworks, for ELT teachers, trainers and managers have existed for a few years now. However, until I created one for my MA dissertation, there wasn’t one drawing together what we need to know and do to be able to effectively produce language learning materials.
This webinar will introduce you to my framework, highlighting the key competencies I identified from my research. It will also show how anybody involved in language teaching (any language, not just English!), teacher training, managing schools or developing language learning materials can benefit from using the framework.
2. CONTENTS
Genetic mapping: Virtual or
relational mapping
Physical mapping: systematic
analysis
Chromosome walking: find a gene
on chromosome
New techniques for mapping .
3. WHY MAP BEFORE SEQUENCING?
Major problem in large-scale sequencing:
Current technologies can only sequence 600–800
bases at a time. We need to sequence 30 billion bp in
order to perfectly sequence human genome
One solution: make a physical map of overlapping
DNA fragments: Top-Down approach
Chromosomal libraries: 46 chromosomes/23 pairs
Genomic library for many fragments from each
chromosome
Determine sequence of each fragment
Then assemble to form contiguous sequence
4. MAPPING I
Mapping is
identifying
relationships
between genes on
chromosomes
Just as a road map
shows relationships
between towns on
highway: fine maps
Two types of
mapping: genetic
and physical
5. MAPPING II
Genetic mapping
Based on differences in recombination
frequency between genetic loci: meiosis
Physical mapping
Based on actual distances in base pairs between
specific sequences found on the chromosome
Most powerful when genetic and physical mapping
are combined
6. GENETIC MAPPING
Based on recombination frequencies
The further away two points are on a
chromosome, the more recombination there is
between them
Because recombination frequencies vary along a
chromosome, we can obtain a relative position
for the loci
Distance between the markers
7. GENETIC MAPPING
Genetic mapping requires that a cross be
performed between two related organisms
The organism should have phenotypic
differences (contrasting characters like red
and white or tall and short etc) resulting from
allele differences at two or more loci
The frequency of recombination is determined
by counting the F2 progeny with each phenotype
8. GENETIC MAPPING EXAMPLE I
Genes on two
different
chromosomes
Independent
assortment
during meiosis
(Mendel)
No linkage
Dihybrid ratio
F1
9 : 3 : 3 : 1
F2
P
9. GENETIC MAPPING EXAMPLE II
Genes very
close together
on same
chromosome
Will usually
end up
together after
meiosis
Tightly linked
F1
1 : 2 : 1
F2
P
10. GENETIC MAPPING EXAMPLE III
Genes on same
chromosome, but not
very close together
Recombination will
occur
Frequency of
recombination
proportional to
distance between
genes
Measured in
centiMorgans =cM
Recombinants
Non-parental features
One map unit = one centimorgan (cM) = 1%
recombination between loci
12. GENETIC MARKERS
Genetic mapping between positions on
chromosomes
Positions can be genes
Responsible for phenotype
Examples: eye color or disease trait:
limited
Positions can be physical markers
DNA sequence variation
13. PHYSICAL MARKERS
Physical markers are DNA sequences that vary
between two related genomes
Referred to as a DNA polymorphism
Usually not in a gene
Examples
RFLP
SSLP
SNP
14. RFLP
Restriction-fragment length polymorphism
Cut genomic DNA from two individuals with
restriction enzyme
Run Southern blot
Probe with different pieces of DNA
Sequence difference creates different band pattern
GGATCC
CCTAGG
GTATCC
GATAGG
GGATCC
CCTAGG
200 400
GGATCC
CCTAGG
GCATCC
GGTAGG
GGATCC
CCTAGG
200 400*
*
200
400
600
1 2
**
2
1
15. SSLP/MICROSATELLITES
• Simple-sequence length polymorphism
• Most genomes contain repeats of three or four
nucleotides
• Length of repeat varies due to slippage in replication
• Use PCR with primers external to the repeat region
• On gel, see difference in length of amplified fragment
ATCCTACGACGACGACGATTGATGCT
12
18
1 2
2
1
ATCCTACGACGACGACGACGACGATTGATGCT
16. SNP
Single-nucleotide polymorphism
One-nucleotide difference in sequence of two
organisms
Found by sequencing
Example: Between any two humans, on average
one SNP every 1,000 base pairs
ATCGATTGCCATGAC
ATCGATGGCCATGAC2
1
SNP
17. PHYSICAL MAPPING
Determination of physical distance between two
points on chromosome
Distance in base pairs
Example: between physical marker and a gene
Need overlapping fragments of DNA
Requires vectors that accommodate large inserts
Examples: cosmids, YACs, and BACs
21. LARGE-INSERT VECTORS
Lambda phage and
cosmids
Inserts stable
But insert size too small
for large-scale
sequencing projects
YACs
Largest insert size
But difficult to work
with due to instability
22. BACS AND PACS
BACs and PACs
Most commonly used
vectors for large-scale
sequencing
Good compromise
between insert size and
ease of use
Growth and isolation
similar to that for
plasmids
23. CONTIGS
Contigs are groups of overlapping pieces of chromosomal
DNA
Make contiguous clones
For sequencing one wants to create “minimum tiling path”
Contig of smallest number of inserts that covers a
region of the chromosome
genomic DNA
contig
minimum
tiling path
24. CONTIGS FROM OVERLAPPING RESTRICTION
FRAGMENTS
Cut inserts with restriction
enzyme
Look for similar pattern of
restriction fragments
Known as “fingerprinting”
Line up overlapping
fragments
Continue until a contig is
built
25. RESTRICTION MAPPING APPLIED TO LARGE-
INSERT CLONES
Generates a large number of fragments
Requires high-resolution separation of fragments
Can be done with gel electrophoresis
26. ANALYSIS OF RESTRICTION FRAGMENTS
Computer programs perform automatic fragment-size
matching
Possibilities for errors
Fragments of similar size may in fact be different sequences
Repetitive elements give same sizes, but from different
chromosomal locations
29. BUILDING CONTIGS BY PROBING WITH END
FRAGMENTS
Isolate DNA from both
ends of insert and mix
Label and probe
genomic library
Identify hybridizing
clones
Repeat with ends of
overlapping clones
30. CHROMOSOME WALKING
Combines probing
with insert ends and
restriction mapping
First find hybridizing
clones
Then create a
restriction map
Identify the clone with
the shortest overlap
Make probe from its
end
Repeat process
probe
library
probe library
31. SEQUENCE SEPARATION
Terminated chains need
to be separated
Requires one-base-pair
resolution
See difference between
chain of X and X+1
base pairs
Gel electrophoresis
Very thin gel
High voltage
Works with radioactive
or fluorescent labels
A T C G
–
+
32. CAPILLARY ELECTROPHORESIS
Newer automated
sequencers use very
thin capillary tubes
Run all four
fluorescently tagged
reactions in same
capillary
Can have 96
capillaries running at
the same time
96–well plate
robotic arm and syringe
96 glass capillaries
load bar
33. SEQUENCE READING OF RADIOACTIVELY
LABELED REACTIONS
Radioactively labeled
reactions
Gel dried
Placed on X-ray film
Sequence read from
bottom up
Each lane is a different
base
–
+
C A G T C A G T
34. SEQUENCE READING OF FLUORESCENTLY
LABELED REACTIONS
Fluorescently labeled
reactions scanned by
laser as a particular point
is passed
Color picked up by
detector
Output sent directly to
computer
35. OPTICAL MAPPING
• Single-molecule technique
Individual DNA molecules attached to glass support
Restriction enzymes on glass are activated
When DNA is cut, microscope records length of
resulting fragments
Has potential to rapidly generate restriction maps
36. SUMMARY
Basics of mapping
Genetic mapping
Based on recombination frequencies
Physical mapping
Requires overlapping DNA fragments
Can use restriction enzymes
Probing with end fragments
Combination: chromosome walking
