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A molecular marker (identified as genetic marker) is a fragment
of DNA that is associated with a certain location within the genome.
Molecular markers are used in molecular biology and biotechnology to
identify a particular sequence of DNA in a pool of unknown DNA.
DNA based Molecular markers
What is an ideal DNA marker?
1) Highly polymorphic nature: It must be polymorphic as it is polymorphism that is
measured for genetic diversity studies.
2) Codominant inheritance: determination of homozygous and heterozygous states
of diploid organisms.
3) Frequent occurrence in genome: A marker should be evenly and frequently
distributed throughout the genome.
4) Easy access (availability): It should be easy, fast and cheap to detect.
5) Easy and fast assay
6) High reproducibility
7) Easy exchange of data between laboratories
8) Gene based molecular markers
IGNTU-eContent-328712472244-M.Sc-EnvironmentalScience-2-ManojkumarRai-Environmentalmicrobiologyandbiotechnology-3 (1).pdf
IGNTU-eContent-328712472244-M.Sc-EnvironmentalScience-2-ManojkumarRai-Environmentalmicrobiologyandbiotechnology-3 (1).pdf
IGNTU-eContent-328712472244-M.Sc-EnvironmentalScience-2-ManojkumarRai-Environmentalmicrobiologyandbiotechnology-3 (1).pdf
IGNTU-eContent-328712472244-M.Sc-EnvironmentalScience-2-ManojkumarRai-Environmentalmicrobiologyandbiotechnology-3 (1).pdf
IGNTU-eContent-328712472244-M.Sc-EnvironmentalScience-2-ManojkumarRai-Environmentalmicrobiologyandbiotechnology-3 (1).pdf
IGNTU-eContent-328712472244-M.Sc-EnvironmentalScience-2-ManojkumarRai-Environmentalmicrobiologyandbiotechnology-3 (1).pdf
IGNTU-eContent-328712472244-M.Sc-EnvironmentalScience-2-ManojkumarRai-Environmentalmicrobiologyandbiotechnology-3 (1).pdf
IGNTU-eContent-328712472244-M.Sc-EnvironmentalScience-2-ManojkumarRai-Environmentalmicrobiologyandbiotechnology-3 (1).pdf
IGNTU-eContent-328712472244-M.Sc-EnvironmentalScience-2-ManojkumarRai-Environmentalmicrobiologyandbiotechnology-3 (1).pdf
IGNTU-eContent-328712472244-M.Sc-EnvironmentalScience-2-ManojkumarRai-Environmentalmicrobiologyandbiotechnology-3 (1).pdf
IGNTU-eContent-328712472244-M.Sc-EnvironmentalScience-2-ManojkumarRai-Environmentalmicrobiologyandbiotechnology-3 (1).pdf
IGNTU-eContent-328712472244-M.Sc-EnvironmentalScience-2-ManojkumarRai-Environmentalmicrobiologyandbiotechnology-3 (1).pdf
IGNTU-eContent-328712472244-M.Sc-EnvironmentalScience-2-ManojkumarRai-Environmentalmicrobiologyandbiotechnology-3 (1).pdf
IGNTU-eContent-328712472244-M.Sc-EnvironmentalScience-2-ManojkumarRai-Environmentalmicrobiologyandbiotechnology-3 (1).pdf
IGNTU-eContent-328712472244-M.Sc-EnvironmentalScience-2-ManojkumarRai-Environmentalmicrobiologyandbiotechnology-3 (1).pdf
Application of SSRs
• Genetic diversity analysis (measurement of genetic similarity or
differences among plant species)
• Cultivar identification
• Phylogenetic relationships
• Gene mapping and identification of quantitative trait loci (QTLs) which
can lead to the identification of candidate genes for the trait of interest
• Marker-assisted selection (MAS)
• sex determination of dioecious plants
An expressed sequence tag (EST) is a short sub sequence of a cDNA
sequence
Expressed sequence tags (ESTs), obtained by partial random sequencing
of cDNA libraries, are 300–500 nucleotide long mRNA sequences from
many of the genes expressed in a sample from an organism
SSRs present in EST region is known as ESR-SSRs or genic
microsatellites.
EST-SSR
IGNTU-eContent-328712472244-M.Sc-EnvironmentalScience-2-ManojkumarRai-Environmentalmicrobiologyandbiotechnology-3 (1).pdf
Start Codon Targeted Polymorphism (SCoT)
PCR based technique developed by Collard and Mackill in 2009.
Simple and novel DNA marker technique, uses 18-mer single primer
in PCR and an annealing of 50 ºC.
PCR products are resolved using standard agarose gel
electrophoresis.
SCoT based on the short conserved region flanking the start codon
(ATG) in plant genes.
This technique has been demonstrated high polymorphic and
efficient, and successfully utilized in a number of plant species for
cultivar identification and genetic diversity analysis
IGNTU-eContent-328712472244-M.Sc-EnvironmentalScience-2-ManojkumarRai-Environmentalmicrobiologyandbiotechnology-3 (1).pdf
Advantages and applications of SCoT
• Technically simple
• SCoT employs longer primers (18-mer) producing high polymorphism
which is reproducible
• There is requires no prior sequence information and the polymorphism
is correlated to functional genes and their corresponding traits
• It could be used directly in marker-assisted breeding programmes.
• Point mutations affecting the primer binding region generate
polymorphism with SCoT primers
• It has been used to evaluate genetic relationships and genetic diversity
analysis in plants.
• Since, it is a gene targeted marker, therefore it is useful in
QTLidentification and gene mapping.
IGNTU-eContent-328712472244-M.Sc-EnvironmentalScience-2-ManojkumarRai-Environmentalmicrobiologyandbiotechnology-3 (1).pdf
IGNTU-eContent-328712472244-M.Sc-EnvironmentalScience-2-ManojkumarRai-Environmentalmicrobiologyandbiotechnology-3 (1).pdf
Single-nucleotide polymorphism (SNP)
A single-nucleotide polymorphism (SNP) is a substitution of a
single nucleotide that occurs at a specific position in the genome
Single-nucleotide polymorphisms may fall within coding sequences
of genes, non-coding regions of genes, or in the intergenic regions
(regions between genes).
It determines genetic variation in an organism which is associated
with a disease or trait.
Point mutation: major cause of SNP
A point mutation or substitution is a genetic mutation where a single
nucleotide base is changed, inserted or deleted from a sequence of DNA
or RNA
Transitions are replacement of a purine base with another purine or
replacement of a pyrimidine with another pyrimidine.
Transversions are replacement of a purine with a pyrimidine or vice versa.
Transition mutations are about ten times more common than transversions.
Transitions (Alpha) and transversions
(Beta)
In human beings, 99.9 percent bases are same.
Remaining 0.1 percent makes a person unique. – Different attributes /
characteristics / traits
These variations can be
Harmless (change in phenotype)
(The severity of illness and the way the body responds to treatments
are also manifestations of genetic variations. For example, a single-
base mutation in the APOE (apolipoprotein E) gene is associated with
a lower risk for Alzheimer's disease.)
Harmful
(diabetes, cancer, heart disease, Huntington's disease, and
hemophilia )
(SNPs pinpoint differences in our susceptibility to a wide range of
diseases (e.g. sickle-cell anemia, β-thalassemia and cystic fibrosis
result from SNPs)
• SNPs occur with a very high frequency – about 1 in 1000 bases to
1 in 100 to 300 bases.
• SNPs close to particular gene acts as a marker for that gene.
• SNPs in coding regions may alter the protein structure made by
that coding region.
• In many organisms most polymorphisms result from changes in a
single nucleotide position (point mutations), has led to the
development of techniques to study single nucleotide
polymorphisms (SNPs).
• SNPs and flanking sequences can be found by sequencing or
through the screening of readily available sequence databases.
• Once the location of SNPs is identified and appropriate primers
designed for cultivar discrimination in crops where it is difficult to
find polymorphisms.
IGNTU-eContent-328712472244-M.Sc-EnvironmentalScience-2-ManojkumarRai-Environmentalmicrobiologyandbiotechnology-3 (1).pdf
IGNTU-eContent-328712472244-M.Sc-EnvironmentalScience-2-ManojkumarRai-Environmentalmicrobiologyandbiotechnology-3 (1).pdf
IGNTU-eContent-328712472244-M.Sc-EnvironmentalScience-2-ManojkumarRai-Environmentalmicrobiologyandbiotechnology-3 (1).pdf
IGNTU-eContent-328712472244-M.Sc-EnvironmentalScience-2-ManojkumarRai-Environmentalmicrobiologyandbiotechnology-3 (1).pdf
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IGNTU-eContent-328712472244-M.Sc-EnvironmentalScience-2-ManojkumarRai-Environmentalmicrobiologyandbiotechnology-3 (1).pdf

  • 1. A molecular marker (identified as genetic marker) is a fragment of DNA that is associated with a certain location within the genome. Molecular markers are used in molecular biology and biotechnology to identify a particular sequence of DNA in a pool of unknown DNA. DNA based Molecular markers
  • 2. What is an ideal DNA marker? 1) Highly polymorphic nature: It must be polymorphic as it is polymorphism that is measured for genetic diversity studies. 2) Codominant inheritance: determination of homozygous and heterozygous states of diploid organisms. 3) Frequent occurrence in genome: A marker should be evenly and frequently distributed throughout the genome. 4) Easy access (availability): It should be easy, fast and cheap to detect. 5) Easy and fast assay 6) High reproducibility 7) Easy exchange of data between laboratories 8) Gene based molecular markers
  • 18. Application of SSRs • Genetic diversity analysis (measurement of genetic similarity or differences among plant species) • Cultivar identification • Phylogenetic relationships • Gene mapping and identification of quantitative trait loci (QTLs) which can lead to the identification of candidate genes for the trait of interest • Marker-assisted selection (MAS) • sex determination of dioecious plants
  • 19. An expressed sequence tag (EST) is a short sub sequence of a cDNA sequence Expressed sequence tags (ESTs), obtained by partial random sequencing of cDNA libraries, are 300–500 nucleotide long mRNA sequences from many of the genes expressed in a sample from an organism SSRs present in EST region is known as ESR-SSRs or genic microsatellites. EST-SSR
  • 21. Start Codon Targeted Polymorphism (SCoT) PCR based technique developed by Collard and Mackill in 2009. Simple and novel DNA marker technique, uses 18-mer single primer in PCR and an annealing of 50 ºC. PCR products are resolved using standard agarose gel electrophoresis. SCoT based on the short conserved region flanking the start codon (ATG) in plant genes. This technique has been demonstrated high polymorphic and efficient, and successfully utilized in a number of plant species for cultivar identification and genetic diversity analysis
  • 23. Advantages and applications of SCoT • Technically simple • SCoT employs longer primers (18-mer) producing high polymorphism which is reproducible • There is requires no prior sequence information and the polymorphism is correlated to functional genes and their corresponding traits • It could be used directly in marker-assisted breeding programmes. • Point mutations affecting the primer binding region generate polymorphism with SCoT primers • It has been used to evaluate genetic relationships and genetic diversity analysis in plants. • Since, it is a gene targeted marker, therefore it is useful in QTLidentification and gene mapping.
  • 26. Single-nucleotide polymorphism (SNP) A single-nucleotide polymorphism (SNP) is a substitution of a single nucleotide that occurs at a specific position in the genome Single-nucleotide polymorphisms may fall within coding sequences of genes, non-coding regions of genes, or in the intergenic regions (regions between genes). It determines genetic variation in an organism which is associated with a disease or trait.
  • 27. Point mutation: major cause of SNP A point mutation or substitution is a genetic mutation where a single nucleotide base is changed, inserted or deleted from a sequence of DNA or RNA Transitions are replacement of a purine base with another purine or replacement of a pyrimidine with another pyrimidine. Transversions are replacement of a purine with a pyrimidine or vice versa. Transition mutations are about ten times more common than transversions. Transitions (Alpha) and transversions (Beta)
  • 28. In human beings, 99.9 percent bases are same. Remaining 0.1 percent makes a person unique. – Different attributes / characteristics / traits These variations can be Harmless (change in phenotype) (The severity of illness and the way the body responds to treatments are also manifestations of genetic variations. For example, a single- base mutation in the APOE (apolipoprotein E) gene is associated with a lower risk for Alzheimer's disease.) Harmful (diabetes, cancer, heart disease, Huntington's disease, and hemophilia ) (SNPs pinpoint differences in our susceptibility to a wide range of diseases (e.g. sickle-cell anemia, β-thalassemia and cystic fibrosis result from SNPs)
  • 29. • SNPs occur with a very high frequency – about 1 in 1000 bases to 1 in 100 to 300 bases. • SNPs close to particular gene acts as a marker for that gene. • SNPs in coding regions may alter the protein structure made by that coding region. • In many organisms most polymorphisms result from changes in a single nucleotide position (point mutations), has led to the development of techniques to study single nucleotide polymorphisms (SNPs). • SNPs and flanking sequences can be found by sequencing or through the screening of readily available sequence databases. • Once the location of SNPs is identified and appropriate primers designed for cultivar discrimination in crops where it is difficult to find polymorphisms.