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WHAT IS A MARKER?
Any stable and inherited variation, detectable or measurable by suitable method and which can be used to detect the presence of specific genotype or phenotype that otherwise is not measurable or difficult to detect. The markers could be: MORPHOLOGICAL MARKER: Classical markers CYTOGENETIC MARKERS: Chromosomal aberrations
MORPHOLOGICAL MARKERS
Morphological markers generally correspond to the qualitative traits that can be scored visually. They have been found in nature or as the result of mutagenesis experiments. Morphological markers are usually dominant or recessive
They cause such large effects on phenotype that they are undesirable in breeding programs They mask the effects of linked minor gene(s) They are highly influenced by the environment.
BIOCHEMICAL MARKERS
Isozymes have been used very successfully as biochemical markers in certain plant breeding experiments. Biochemical markers are proteins produced by gene expression . These proteins can be isolated and identified by electrophoresis. They are the products of various alleles of one or several genes.
Low polymorphism Requires expression of trait / gene Dominance effect Expression sex limited Expressed late in life
A molecular marker is a DNA sequence that is readily detected and whose inheritance can easily be monitored . The DNA markers to be utilized may be fragments produced by restriction digestion (like RFLP) or through PCR amplification. Thus they may be hybridization based or PCR based.
All molecular genetic markers fall under three basic categories: Insertion-Deletion Length Polymorphisms Single Nucleotide Polymorphisms Simple Sequence Repeat Length Polymorphisms (Miniand Micro-Sattellites) Direct Sequencing: The Gold Standard The gold standard in DNA polymorphism analysis is direct sequencing. Direct sequencing uncovers all of the polymorphisms in a DNA target. Because direct sequencing of individuals is obviously impractical on a large scale, numerous methods have been invented to assay for DNA polymorphisms.
RFLP
In 1980 Botstein et al. described the first polymorphic assay. RF stands for Restriction Fragments - fragments of DNA that are cut by restriction enzymes. L stands for Length of the restriction fragments. P stands for Polymorphism (many shapes). The lengths of some of the restriction fragments differ greatly between individuals, thus there are many lengths of DNA possible
Restriction enzymes
Restriction enzymes are isolated from a wide variety of bacterial genera These enzymes are named by using the first letter of the genus, the first two letters of the species, and the order of discovery Restriction endonucleases are enzymes that cleave DNA molecules at specific nucleotide sequences depending on the particular enzyme used. Enzyme recognition sites are usually 4 to 6 base pairs in length. Generally, the shorter the recognition sequence, the greater the number of fragments generated If molecules differ in nucleotide sequence, fragments of different sizes may be generated. The fragments can be separated by gel electrophoresis.
Restriction site 5..GAATTC..3 3..CTTAA,G..5 5..GTTAAC..3 3..CAAT,TG..5 5..CC GG..3 3..GG C,C..3
Sal I
Streptomycets albus
RFLP is a sequence of DNA that has a restriction site on each end with a "target" sequence in between for particular RE For example: RE -EcoRI
PCR-RFLP
PCR RFLP
PCR: Exponential amplification of desired segment of DNA in vitro i.e. DNA xeroxing Karry Mullis et al (1986) DNA segment bracketed by two primers amplified by polymerase enzyme using dNTPs in cyclic manner
Method
Usually, DNA from an individual specimen is first extracted and purified. Sepatated segment of DNA amplified by PCR.
The DNA is then chopped into restriction fragments by endonucleases which only cut where there are specific DNA sequences recognized by the enzymes. The restriction fragments are then separated according to length by agarose gel electrophoresis
PCR-RFLP Protocol
Reaction mixture for PCR
a. b. c. d. e. f. g. h.
Buffer (10X) MgCl2 (50mM) dNTP (10mM) Primer 1(8pmol) Primer 2(8pmol) DNA template(30ng) Distilled water (sterile) Total
Cycle conditions
1) 2) 3) 4) 5) 6) Initial denaturation 940 C 5min Denaturation 940 C 1min Annealing 55-650 C 1min Extension 720 C 1min Repeat steps 24-29 times Final extension 10min
Buffer(10X) PCR product REs(10Units/ul) Dist. Water Reaction volume Incubate at 370C for 1 hr
PCR-RFLP 1.Particular segment of DNA 2.Primer is used for amplification of particular DNA 3.RE enzymes used after separating particular DNA segment 4.Southern bloting is not req. 5.Radioactive probe is not req.
APPLICATIONS
PCR-RFLPs have provided valuable information in many areas of biology, including: Can be used in paternity cases or criminal cases to determine the source of a DNA sample Can be used determine the disease status of an individual. Can be used to construct genetic map Typing of Microbial Organisms Species identification in meat products using mitochondrial DNA Species determination using PCR RFLP of ancient DNA from Prehistoric Skeletal Remains
Williams etal. (1990) developed Random Amplified Polymorphic DNA (RAPD) a technique using very short 10 base primers to generate random fragments from template DNAs Extensively used for genetic characterization in organisms (Bacteria to Mammals) DNA sequences which are relatively variable between different individuals or species. These variable stretches of DNA within a genome among individuals will be useful for analytical method to distinguish individuals from one-another
fragment of DNA to be amplified 4. dNTPs 5. Taq DNA Polymerase (or another thermally stable DNA polymerase)
1. 2.
3.
Annealing temperatures are generally very low, around 37oC - This allows very short primers to anneal to template DNA A singe 10-mer primer is used instead of a pair of bracketing primers in the conventional/ classical PCR More thermal cycles are used, typically 45 - This compensates for the inefficiency which results from using such short primers.
RAPD
Template DNA
RAPD
Template DNA
RAPD
Template DNA
RAPD
Template DNA
Template DNA
2 3 4
9 10
Which variable has the greatest impact on fragment patterns? Lowering Magnesium ion concentration results in loss of the largest fragment visible in lanes 2-7
RAPD protocol
Reaction mixture Buffer (10x) MgCl2 (50mM) dNTPs(10mM) Primers(8pmol/ul) DNA template(30ng/ul) Distilled water (sterile) 2.5ul 0.75ul 0.5ul 1.0ul 3.0ul 17.25ul
Cycle conditions
Pre denaturation 940C 4min Denaturation 940C 1min Annealing 370C 1min Extension 720C 2min Repeat steps 2-4 for 35-45 times Final extension 720C 5min
Electrophoresis
Electrophoresis conditions required are Matrix:1.5-2% Agarose Buffer:1x TBE Voltage:80volts for 30 min, Visualize under UV light
ADVANTAGES 1) The level of detectable polymorphisms very high 2) In comparison to RFLP, It is less expensive, faster, requires smaller amount of DNA, requires less skill 3) Does not involve use of radioisotopes
DISADVANTAGES 1) Lack of reproducibility 2) PCR results are very sensitive to amplification conditions and consequently variable between laboratories and even between assays
AFLP
METHODOLOGY
1) Digestion of total cellular DNA with one or more restriction enzymes and ligation of restriction half-site specific adaptors to all restriction fragments. 2) Selective amplification of some of these fragments with two PCR primers that have corresponding adaptor and restriction site specific sequences. 3) Electrophoretic separation of amplicons on a gel matrix, followed by visualisation of the band pattern.
Digestion
Digestion
Adaptor
Adaptor-Ligation
Digestion
Adaptor-Ligation
PCR-Amplification
ADVANTAGES
Extremely sensitive, oligonucleotides used as adaptors and primers. High reproducibility with exactly the same banding patterns being detected over a million-fold difference in initial cDNA concentration. Discriminates heterozygotes from homozygotes when gel scanner used. Allow specific co-amplification of a high number of restriction fragments (50-100in each AFLP reaction) resulting in large number of loci scored per reaction. AFLP are quantitative, in that heterozygote and homozygote genotypes can be differentiated by the intensity of the amplified bands. Choosing the different base number and composition of nucleotides in the adaptors can control the number of DNA fragments that are amplified.
DISADVANTAGES
Highly expensive and requires more DNA than is needed in RAPD (1 mg per reaction). Technically more demanding than RAPDs, as it requires experience of sequencing gels. Relatively complex and requires high-quality DNA; However new software programmes are available to automate scanning and analysis of gels.
APPLICATIONS
Used to distinguish strains. These fingerprints may be used as a tool for determining the identity of a specific DNA samples or to assess the relatedness between samples. Fingerprints are also used as the source for genetic markers to generate linkage maps or to identify molecular markers linked to phenotypic traits and/or genetic loci. AFLP have potentiality in statutory testing for distinguishing new cultivars.
MICROSATELLITES
MICROSATELLITES
Another class of hyper variable loci consisting of short tendem repeats of 2-6 bp.
Repeat units of Microsatellite markers are flanked by unique sequence. Hence, can be amplified by PCR
Highly polymorphic
PCR based technique: Easy to detect radio active or non radio active
Also called as Simple sequence repeats (SSR) OR Short tandem repeats (STR) For example, AAAAAAAAAAA would be referred to as (A)11 GTGTGTGTGTGT would be referred to as (GT)6 CTGCTGCTGCTG would be referred to as (CTG)4 ACTCACTCACTCACTC would be referred to as (ACTC)4
Feature Origin
SSR Anonymous
RAPD Anonymous
AFLP Anonymous
Isozymes Genic
Limited by the number of enzyme genes and histochemical enzyme assays available (3050)
Limited by the size of genome and number of simple repeats in a genome (tens of thousands)
Codominant
Codominant
Dominant
Dominant
Within species
Medium to high
Low to medium
Very high
2-10 mg DNA
10-20 ng DNA
2-10 ng DNA
0.2-1 g DNA
Moderate to difficult Possible Very good Very limited
Several mg of tissue
Ease of assay Automation / multiplexing Genome and QTL mapping potential Comparative mapping potential Candidate gene mapping potential Potential for studying adaptive genetic variation
Difficult
Difficult Good
Good
Limited
Very limited
Excellent
Limited
Useless
Useless
Useless
Limited
Limited
Limited
Limited
Limited
Good