A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or species. It can be described as a variation (which may arise due to mutation or alteration in the genomic loci) that can be observed. A genetic marker may be a short DNA sequence, such as a sequence surrounding a single base-pair change (single nucleotide polymorphism, SNP), or a long one, like minisatellites.
RAPD markers are decamer DNA fragments.
RAPD is a type of PCR reaction.
as the name suggest it is a fast method when compared to the traditional PCR medthod.
Molecular Marker and It's ApplicationsSuresh Antre
Molecular (DNA) markers are segments of DNA that can be detected through specific laboratory techniques. With the advent of marker-assisted selection (MAS), a new breeding tool is now available to make more accurate and useful selections in breeding populations.
RAPD markers are decamer DNA fragments.
RAPD is a type of PCR reaction.
as the name suggest it is a fast method when compared to the traditional PCR medthod.
Molecular Marker and It's ApplicationsSuresh Antre
Molecular (DNA) markers are segments of DNA that can be detected through specific laboratory techniques. With the advent of marker-assisted selection (MAS), a new breeding tool is now available to make more accurate and useful selections in breeding populations.
Morphological, Cytological and Biochemical MarkersJay Khaniya
I've put a lot of effort for create this presentation. This'll help to lot of biotechnology and agricultural students for there assignments and exam study.
A new era of genomics for plant science research has opened due the complete genome sequencing projects of Arabidopsis thaliana and rice. The sequence information available in public database has highlighted the need to develop genome scale reverse genetic strategies for functional analysis (Till et al., 2003). As most of the phenotypes are obscure, the forward genetics can hardly meet the demand of a high throughput and large-scale survey of gene functions. Targeting Induced Local Lesions in Genome TILLING is a general reverse genetic technique that combines chemical mutagenesis with PCR based screening to identity point mutations in regions of interest (McCallum et al., 2000). This strategy works with a mismatch-specific endonuclease to detect induced or natural DNA polymorphisms in genes of interest. A newly developed general reverse genetic strategy helps to locate an allelic series of induced point mutations in genes of interest. It allows the rapid and inexpensive detection of induced point mutations in populations of physically or chemically mutagenized individuals. To create an induced population with the use of physical/chemical mutagens is the first prerequisite for TILLING approach. Most of the plant species are compatible with this technique due to their self-fertilized nature and the seeds produced by these plants can be stored for long periods of time (Borevitz et al., 2003). The seeds are treated with mutagens and raised to harvest M1 plants, which are consequently, self-fertilized to raise the M2 population. DNA extracted from M2 plants is used in mutational screening (Colbert et al., 2001). To avoid mixing of the same mutation only one M2 plant from each M1 is used for DNA extraction (Till et al., 2007). The M3 seeds produce by selfing the M2 progeny can be well preserved for long term storage. Ethyl methane sulfonate (EMS) has been extensively used as a chemical mutagen in TILLING studies in plants to generate mutant populations, although other mutagens can be effective. EMS produces transitional mutations (G/C, A/T) by alkylating G residues which pairs with T instead of the conservative base pairing with C (Nagy et al., 2003). It is a constructive approach for users to attempt a range of chemical mutagens to assess the lethality and sterility on germinal tissue before creating large mutant populations.
Microsatellite are powerful DNA markers for quantifying genetic variations within & between populations of a species, also called as STR, SSR, VNTR. Tandemly repeated DNA sequences with the repeat/size of 1 – 6 bases repeated several times
Taxonomy is the branch of science concerned with the classification of organisms. A taxonomic designation is more than just a name. Ideally, it reflects evolutionary history and the relationship between organisms. Traditionally, taxonomic classification has relied upon morphological features and physiological characteristics. However, for bacterial taxonomy, phenotypic approaches have proven insufficient. Unrelated bacteria can exhibit identical traits, closely related bacteria can have divergent features, and methods for accurate identification may be too cumbersome for routine use. In contrast, molecular taxonomy approaches use data derived from hereditary material and provide a robust view of genetic relatedness. Advances in technology have been accompanied by improvements in the cost, speed, and availability of molecular methods. Here, we provide a brief history of approaches to prokaryotic classification and describe how molecular taxonomy is redefining our understanding of bacterial evolution and the tree of life.
Morphological, Cytological and Biochemical MarkersJay Khaniya
I've put a lot of effort for create this presentation. This'll help to lot of biotechnology and agricultural students for there assignments and exam study.
A new era of genomics for plant science research has opened due the complete genome sequencing projects of Arabidopsis thaliana and rice. The sequence information available in public database has highlighted the need to develop genome scale reverse genetic strategies for functional analysis (Till et al., 2003). As most of the phenotypes are obscure, the forward genetics can hardly meet the demand of a high throughput and large-scale survey of gene functions. Targeting Induced Local Lesions in Genome TILLING is a general reverse genetic technique that combines chemical mutagenesis with PCR based screening to identity point mutations in regions of interest (McCallum et al., 2000). This strategy works with a mismatch-specific endonuclease to detect induced or natural DNA polymorphisms in genes of interest. A newly developed general reverse genetic strategy helps to locate an allelic series of induced point mutations in genes of interest. It allows the rapid and inexpensive detection of induced point mutations in populations of physically or chemically mutagenized individuals. To create an induced population with the use of physical/chemical mutagens is the first prerequisite for TILLING approach. Most of the plant species are compatible with this technique due to their self-fertilized nature and the seeds produced by these plants can be stored for long periods of time (Borevitz et al., 2003). The seeds are treated with mutagens and raised to harvest M1 plants, which are consequently, self-fertilized to raise the M2 population. DNA extracted from M2 plants is used in mutational screening (Colbert et al., 2001). To avoid mixing of the same mutation only one M2 plant from each M1 is used for DNA extraction (Till et al., 2007). The M3 seeds produce by selfing the M2 progeny can be well preserved for long term storage. Ethyl methane sulfonate (EMS) has been extensively used as a chemical mutagen in TILLING studies in plants to generate mutant populations, although other mutagens can be effective. EMS produces transitional mutations (G/C, A/T) by alkylating G residues which pairs with T instead of the conservative base pairing with C (Nagy et al., 2003). It is a constructive approach for users to attempt a range of chemical mutagens to assess the lethality and sterility on germinal tissue before creating large mutant populations.
Microsatellite are powerful DNA markers for quantifying genetic variations within & between populations of a species, also called as STR, SSR, VNTR. Tandemly repeated DNA sequences with the repeat/size of 1 – 6 bases repeated several times
Taxonomy is the branch of science concerned with the classification of organisms. A taxonomic designation is more than just a name. Ideally, it reflects evolutionary history and the relationship between organisms. Traditionally, taxonomic classification has relied upon morphological features and physiological characteristics. However, for bacterial taxonomy, phenotypic approaches have proven insufficient. Unrelated bacteria can exhibit identical traits, closely related bacteria can have divergent features, and methods for accurate identification may be too cumbersome for routine use. In contrast, molecular taxonomy approaches use data derived from hereditary material and provide a robust view of genetic relatedness. Advances in technology have been accompanied by improvements in the cost, speed, and availability of molecular methods. Here, we provide a brief history of approaches to prokaryotic classification and describe how molecular taxonomy is redefining our understanding of bacterial evolution and the tree of life.
Dr. S. MANIKANDAN, M.Sc., Ph.D
Lecturer in Botany
Thiruvalluvar University Model Constituent College,
Tittagudi 606 106, Tamil Nadu, India.
Email id: drgsmanikandan@gmail.com
this is a presentation on molecular markers that include what is molecular marker, it's types, biochemical markets (alloenzyme), it's classification, data analysis and it's applications
An honest effort to present molecular marker in easiest way both informative and conceptual. Hybridization based (non-PCR) and PCR based markers are discussed to the point with suitable diagram.
TYPES OF MOLECULAR MARKERS,ITS ADVANTAGES AND DISADVANTAGESANFAS KT
Types of molecular markers (genetics)
ITS ADVANTAGES AND DISADVANTAGES
What is a genetic marker?
RFLP: Restriction fragment length polymorphism
AFLP: Amplified fragment length polymorphism
RAPD: Random amplification of polymorphic DNA
ISSR: Inter simple sequence repeat
STR: Short tandem repeats
SCAR: Sequence characterized amplified region
SNP: Single nucleotide polymorphism
SSR: Simple sequence repeat
Restriction fragment length polymorphism (abbreviated RFLP) refers to differences (or variations) among people in their DNA sequences at sites recognized by restriction enzymes. Such variation results in different sized (or length) DNA fragments produced by digesting the DNA with a restriction enzyme.
TYPES OF MOLECULAR MARKERS,ITS ADVANTAGES AND DISADVANTAGESANFAS KT
Types of molecular markers (genetics)
ITS ADVANTAGES AND DISADVANTAGES
What is a genetic marker?
RFLP: Restriction fragment length polymorphism
AFLP: Amplified fragment length polymorphism
RAPD: Random amplification of polymorphic DNA
ISSR: Inter simple sequence repeat
STR: Short tandem repeats
SCAR: Sequence characterized amplified region
SNP: Single nucleotide polymorphism
SSR: Simple sequence repeat
Molecular markers for measuring genetic diversity Zohaib HUSSAIN
Molecular markers for measuring genetic diversity
Introduction:
The molecular basis of the essential biological phenomena in plants is crucial for the effective conservation, management, and efficient utilization of plant genetic resources (PGR).
Determining genetic diversity can be based on morphological, biochemical, and molecular types of information. However, molecular markers have advantages over other kinds, where they show genetic differences on a more detailed level without interferences from environmental factors, and where they involve techniques that provide fast results detailing genetic diversity
Comparison of different methods
Morphological characterization does not require expensive technology but large tracts of land are often required for these experiments, making it possibly more expensive than molecular assessment. These traits are often susceptible to phenotypic plasticity; conversely, this allows assessment of diversity in the presence of environmental variation.
Biochemical analysis is based on the separation of proteins into specific banding patterns. It is a fast method which requires only small amounts of biological material. However, only a limited number of enzymes are available and thus, the resolution of diversity is limited.
Molecular analyses comprise a large variety of DNA molecular markers, which can be employed for analysis of variation. Different markers have different genetic qualities (they can be dominant or co-dominant, can amplify anonymous or characterized loci, can contain expressed or non-expressed sequences, etc.).
Genetic marker
The concept of genetic markers is not a new one; in the nineteenth century, Gregor Mendel employed phenotype-based genetic markers in his experiments. Later, phenotype-based genetic markers for Drosophila melanogaster led to the founding of the theory of genetic linkage. A genetic marker is an easily identifiable piece of genetic material, usually DNA that can be used in the laboratory to tell apart cells, individuals, populations, or species. The use of genetic markers begins with extracting proteins or chemicals (for biochemical markers) or DNA (for molecular markers) from tissues of the plant (for example, seeds, foliage, pollen, sometimes woody tissues).
Molecular markers In genetics, a molecular marker (identified as genetic marker) is a fragment of DNA that is associated with a certain location within the genome. Molecular markers which detect variation at the DNA level such as nucleotide changes: deletion, duplication, inversion and/or insertion. Markers can exhibit two modes of inheritance, i.e. dominant/recessive or co-dominant. If the genetic pattern of homozygotes can be distinguished from that of heterozygotes, then a marker is said to be co-dominant. Generally co-dominant markers are more informative than the
Molecular marker and its application in breed improvement and conservation.docxTrilokMandal2
Molecular markers have revolutionized the field of genetics and genomics by providing valuable tools for studying genetic diversity, identifying individuals, and characterizing traits of interest. This review paper aims to explore the applications of molecular markers in breed improvement and conservation. We discuss the various types of molecular markers commonly used, such as microsatellites, single nucleotide polymorphisms (SNPs), amplified fragment length polymorphisms (AFLPs), and many more. Additionally, we examine their applications in genetic diversity assessment, parentage analysis, marker-assisted selection (MAS), and conservation efforts. The paper highlights the importance of molecular markers in accelerating breed improvement programs and enhancing conservation strategies for maintaining genetic diversity within a population.Molecular markers have had a significant impact on breed development and conservation efforts, transforming genetics and offering vital insights into genetic diversity, lineage tracing, and genotype characterization. The importance of molecular markers in improving genetic gains, facilitating breeding programs, and preserving genetic diversity for the long-term sustainability of the animal population has been underlined in this review paper. Emerging advancements in molecular marker technology show enormous potential for improving and conserving breeds. Deeper insights into the genetic basis of complex traits will be provided through GWAS, CRISPR/Cas9, gene editing technologies, and sequencing technologies, resulting in faster genetic gains. Breeders and conservationists will be able to make more informed judgments thanks to these technologies. In conclusion, molecular markers have had a significant impact on breed conservation and enhancement. Their innovations have changed the industry and given both conservationists and breeders vital knowledge. We can pave the road for more effective and sustainable genetic improvement and the preservation of biodiversity for future generations by combining the power of molecular markers with conventional breeding and conservation techniques.
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1. Presented by :
Ankit Tiwari
M.Sc. (MBT)
Final year
Pt. J.N.M. Medical College, Raipur
Department of Biochemistry
Session:2018-19
1
2. Introduction
Genetic Markers
Dominant and Codominant Marker
Restriction Fragment Length Polymorphism (RFLP)
Random Amplified Polymorphic DNA (RAPD)
Amplified Fragment Length Polymorphism (AFLP)
Microsatellites
Applications
References
2
3. What are markers ?
In 1980, scientists studying human genetics observed that variation
in the pattern of DNA fragments generated by restriction enzyme
digestion of genomic DNA could be used as Genetic Marker.
Markers are genetically linked with the gene of interest.
If the gene of interest in not known, markers linked to the gene of
interest can still be used to select for individuals with desirable
alleles of the gene of interest.
3
4. Genetic marker is a gene or DNA
sequence with known location on
chromosome that can be used to
identify individuals or species.
Generally they do not
represent the target genes
themselves but act as signs or
flags.
Fig. 1 : Genetic Makers
Source : http://usda-ars-beaumont.tamu.edu/dblhelix.jpg
All genetic markers occupy
specific genomic position within
the chromosome called ‘loci’.
4
5. Dominant Marker :
Dominant marker can't differentiate the homozygous and
heterozygous.
Indicate difference on the basis of present and absent.
Examples : RAPD, AFLP.
Codominant Marker :
Codominant marker can differentiate the homozygous and
heterozygous.
Indicate differences in size.
Examples : RFLP, Microsatellites.
5
6. RFLPs were the first type of DNA marker to be studied.
Restriction Fragment Length Polymorphism (RFLP) is a difference in
homologous DNA sequences that can be detected by the presence of
fragments of different lengths after digestion of the DNA samples with
specific restriction endonucleases.
Fig.2 A Restriction Fragment Length Polymorphism
Source: Genomes, Brown TA ;2002.
6
7. Fig.3 Workflow of RFLP
Source:
https://www.slideshare.net/search/slideshow?searchfrom=header&q=Gentic+marker+&
ud=any&ft=all&lang=**&sort= 7
8. PCR based technology.
RAPD is a DNA polymorphism assay based on the amplification of
random DNA segments with single primers of arbitory nucleotide
sequence.
It do not require any specific knowledge of DNA sequence of target
organism.
The primers will or will not amplify a segment of DNA depending
on positions that are complementary to the primers sequence.
Therefore, if a mutation has occurred in template DNA at site
that was previously complementary to primer, a PCR product will
not be produced. This results in different pattern of amplified
DNA segments on gel.
8
11. AFLP is based on the selectively amplifying the subset of restriction
fragments from a complex of DNA fragments obtained after the
digestion of genomic DNA with restriction endonucleases.
This is the combination of RFLP and RAPD.
Typically, two different restriction enzymes are used to cut the
genomic DNA to produce large number of fragments.
Restricted fragments are ligated with adapters (25-30 bp long).
Primers are used to amplify the restricted fragments. These primers
are complementary to adapters.
11
12. Fig.8 Workflow of AFLP
Source: https://www.researchgate.net/figure/Schematic-representation-
of-AFLP-workflow_fig2_298971868
12
13. Microsatellites are also known as short tandem repeats.
Microsatellites, or short tandem repeats/simple sequence repeats
are polymorphic loci present in DNA that consist of repeating units
of one to six base pairs in length.
The repeated sequence is often simple, consisting of two, three or
four nucleotides (di-, tri-, and tetra-nucleotide repeats) and can be
repeated many times.
Microsatellites can be amplified for identification by PCR using the
unique sequences of flanking regions as primers.
13
14. 14
Fig.9 Variation in microsatellite alleles can be detected by analyzing polymerase chain
reaction (PCR) products using agarose gel electrophoresis.
Source : Genetic Linkage and Recombination through Mapping with Molecular
Markers, Lisa M McDonnell and Jennifer Klenz,2014.
15. RFLPs have been widely used in gene mapping studies because of
their high genomic abundance due to ample availability of different
restriction enzymes and random distribution throughout the
genome.
RAPDs have been used for many purpose, ranging from studies at
the individual level (e.g. Genetic identity) to studies involving closely
related species.
The AFLP technology has the capability to detect various
polymorphism in different genomic regions simultaneously.
Microsatellites are very informative markers that can be used for
many population genetics studies, ranging from the individual level
to that of closely related species.
15
16. 16
Genetic Maker Dominant(D) or
Codominant (C)
Advantages Disadvantages
Restriction
Fragment length
polymorphism
(RFLP)
C Robust,
Reliable.
Transferable across
populations
Time consuming,
laborious and
expensive
Large amount of
DNA required
Random Amplified
Polymorphic DNA
(RAPD)
D Quick and simples,
Inexpensive
Generally not
transferable
Simple Sequence
Repeats (SSR) or
microsatellites
C Technically simple,
Reliable
Large amount of
time and labour
required
Amplified Fragment
length
polymorphism
(AFLP)
D Multiple loci,
High level of polymorphism
generated
Large amount of
DNA required
Complicated
17. Satyanarayana U. Biotechnology. Book and allied (p) Ltd; 2013.
4:649-52.
Lewin Benjamin. Genes VIII. Pearson Education International; 2004.
54-55.
Brown TA. Genomes.Oxford: Wiiley-Liss; 2002 ISBN-10: 0-471-
25046-5
Lodish H, Berk A, Matsudaira P et al. Molecular cell biology; 2004. 5:
396-97.
Pierce BA. Genetics: a conceptual approach. WH.Freeman and
company; 2012. 4:186.
Collard BCY, Jahufer Z and Kyong Pang EC. An introduction to
markers, quantitative trait loci (QTL) mapping and marker- assisted
selection for crop improvement: the basic concepts. Euphytica; 2005.
142: 169-196.
17
18. I would like to express my sincere gratitude to Dr. Abhigyan
Nath sir and Dr. Khushboo Bhange Ma’am for their guidance
and help in preparation of this presentation. I would also like
to thanks Dr. G.K. Sahu sir, Dr. Abhigyan Nath sir and Dr.
Khushboo Bhange Ma’am for providing me the opportunity to
present a seminar at this level.
This power point presentation has been prepared from
various text books (Biochemistry by U. Satyanarayan, Genes
VIII by Lewin, Genetics by Benjamin A. Pierce etc.) and review
articles.
I am also thankful to my classmates for their support in
completion of the assignment.
18
