Single Nucleotide Polymophisms SNPs, Necessary Comsuming, Emphasis is Shifting, Development of the SNPs, Oligonucleotide Arrays, Permitting Easier Automatiion

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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 >>Single Nucleotide Polymorphisms SNPs

Your Ad Here	Single Nucleotide Polymorphisms (SNPs) RFLPs, RAPDs and SSRs, earlier described in this chapter, were the markers of choice during the last two decades of the 20th century (1980-2000), but none of them is as frequent as single nucleotide polymorphisms (SNPs) that were discovered later. These SNPs involve either gel-based assays or non-gel based assays, while for all other markers discussed earlier, gel-based assay are necessary that are time consuming and expensive. In view of this, in the early years of the 21st century, emphasis is shifting towards the development of these single nucleotide polymorphisms (SNPs; often pronounced as snips), which represent sites, where DNA sequence differs by a single base (some workers prefer to call them 'simple nucleotide polymorphisms' to include in this class indels and other sequence variations due to few bases; indels = insetions + deletions).
In human genome, this polymorphism has been shown to be the most abundant with an estimated average frequency of one SNP per kilobase pairs, so that there should be approximately 3,000,000 SNPs in the entire human genome. The development of these SNPs involving non-gel based' assays has recently been also facilitated by the availability of genome-wide sequences and EST data. The high density oligonucleotide arrays on DNA chips, the use of MALDI-TOF MS, and pyrosequencing that recently became available, also allow genotyping at large number of these biallelic loci in parallel, since it requires only plus/minus assay, permitting easier automation.
The approach used for this purpose, relies on the capacity to distinguish a perfect match from a single base mismatch. Although, SNPs also suffer with some disadvantages, being biallelic as against polyallelic SSRs, their abundance makes them more attractive. For instance, at least in some parts of the human genome, the frequency of SNPs has been shown to be an order of magnitude higher than that of SSRs. There is also some evidence that the stability of SNPs and, therefore, the relative fidelity of their inheritance is higher than other marker systems like SSRs and AFLPs.	Your Ad Here
These advantages led to rapid development of a number of methods for SNP detection, leading to construction of a human SNP genetic map, that is being expanded. In future similar maps will certainly be prepared and used extensively in many plant systems. Recently (2000-2003), in crops like barley, wheat and maize also, SNPs have been discovered in large number.

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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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