Comparison of General Features of Different Types of Molecular and their Use, Types of Polymorphism, Sequence Information Needed, Detection Methods

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DNA-Based Molecular Markers in Biotechnology DNA-Based Molecular Markers in Biotechnology Introduction Types of Molecular Markers/Principles Methods and Uses Hybridization Based Molecular Markers Restridization Fragment Length Polymorphisms (RFLPs) List Acronyms for Different DNA Markers along with References Dispersed Repetitive DNA (drDNA) for DNA Fingerprinting PCR based Molecular Markers PCR Methods Using a Single Primer PCR Methods Using a Pair of Primers Sequence-tagged Sites (STSs) and Sequence Characterized Amplified Regions (SCARs) Simple Sequence Repeats (SSRs) Expressed Sequence tags (ESTs) and their use for STSs,SSRs and SNPs Important Plant Genomes Available in dbEST Random Amplified Microsatellite Polymorphism (RAMP) and Retroposon-Micro-Satellite Amplified Polymorphism (REMAP)

Home >> Biotechnology and Genomics >> DNA-Based Molecular Markers in Biotechnology >>Comparison of General Features of Different Types of Molecular and their Use

Comparison of General Features of Different Types of Molecular and their Use

	RELPs	RAPDs	DAF
Principle	Endonuclease restriction Southern blot Hybridization	DNA amplification with random primers	DNA amplification with random primers
Types of polymorphism detected	Base changes (indel, subst.)	Base changes (indel, subst.)	Base changes (indel, subst.)
Sequence information needed	No	No	No
Detection method (radioisotope)	yes/no	no	yes/no
Reproducibility	High	Low	Low
No. of loci detected	1-5	1-10	20-30
Inheritance	Codominant	Dominant	Dominant
Technical difficulty	Medium	Low	Medium
Automation possible	-	-	-
Computation possible	+	+	+
Cost	Medium	Low	Medium
Use:	+	+	+
1. Varietal fingerprinting and genetic diversity
2. Qualitative gene tagging	+	+	+
3. ATL mapping	+	-	-
4. MAS	+	-/+	-
5. Comparative mapping	+	+	-

STS(CAPS)	SSRs	AFLPs	SAMPLs
May need endonuclease restriction PCR products	Amplification of simple sequence repeats using specific primers	Endonuclease restriction use of adapters selective primers	Same as AFLP except labelled primer is a compound SSR
Base changes (indel, subst.)	Variation in length of repeats	Base changes (indel, subst.)	Base changes (indel, subst.)
Yes	No	No	No
yes/no	yes/no	yes/no	yes/no
high	High	High	High
1-4	1-3	> 70	~50
Codominant	Codominant	Generally Dominant	Dominant Codominant
Low	Low	Medium/High	Medium/High
+	+	+	+
+	+++	+++	+++
Medium-High	High initially	High	High
+	+++	+++	+

+	+	+++	+++
+	+	+	+
+	+	+	+
+	+	+	+

REMAP/IRAP	SNPs
DNA amplification using both/one retrotranposon & one SSR primer	Sequence analysis
Variation in length	Single base changes
Yes	Yes
no	no
High	High
3-5	1 (biallelic)
Codominant	Dominant
Medium	Medium/High
+	+
+++	+++
Low	High
+	+

+	+
-	+
+	+
-	+

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Amplifed Fragment Length Polymorphism (AFLP) Single Strand Conformation Polymorphism (SSCP) Molecular Markers based on PCR Followed by Hybridization Oligonucleotide Fingerprinting Using RAPD/MP-PCR Framents Sequence based Molecular Markers Single Nucleotide Polymorphisms (SNPs) Gel-based Assays of PCR Products for SNP Detection Non-Gel based Assays of PCR Products for SNP Detection Taqman Assay Use of Molecular Beacon Oligonucleotide Ligation Assay (OLA) DNA Chip/Microarray Dynamic Allele-specific Hybridization Minisequencing Pyrosequencing for SNP Genotyping Temperature Modulated Heteroduplex Analysis TMHA Using DHPLC Wave^TM System A Non PCR Invasive Clevage Assay and Maldi TOF-MS for SNP Detection Comparison of Different Types of Molecular Markers High Throughput Approach in Molecular Marker Technology Comparison of General Features of Different types of Molecular and their use

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