Simple Sequence Repeats SSRs, Tandem Repeats, Microsatellites, Ubiquitous in Eukaryotic Genomes, Across Related Genera, Flanking sequences

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Your Ad Here	Simple sequence repeats (SSRs). SSRs, also known as short tandem repeats (STRs) or microsatellites (1-6 bases long), are ubiquitous in eukaryotic genomes and can be analysed through PCR technology. The sequences flanking specific microsatellite loci in a genome are believed to be conserved within a particular species, across species within a genus and rarely even across related genera.
These flanking sequences, therefore, have been used to design primers for individual microsatellite loci (for details, see later) and the technique is described as sequence tagged micro satellite site (STMS) analysis or as simple sequence length polymorphism (SSLP). The STMS or SSR markers reveal polymorphisms due to variation in the lengths of microsatellites at specific individual loci; they are, therefore, poly allelic and co-dominant in nature, thus proving to be very useful. Consequently, they have been used extensively not only for mapping SSR loci in human, mouse and many crop plants, but also for tagging genes in a variety of organisms.
Since development of SSR markers requires cloning and sequencing, initially it is very costly and labour-intensive, but once the locus specific primers become available, the approach becomes cost-effective. STMS primers, based on sequences flanking individual microsatellites, can be developed either through a search for microsatellites in the DNA sequence databases (including genomic sequences and cDNA sequences or ESTs) or through sequencing of restriction fragments or clones carrying microsatellites. Using the above methods, STMS primers have now become available not only in human and mouse but also in several crops including rice and bread wheat.	Your Ad Here
However, more recently emphasis has also been laid on EST-derived SSRs, since they represent the transcribed part of the genome and therefore may have higher level of transferability (see later for ESTs). In SSR analysis, high resolution, even without applying radioactivity, can be achieved through the use of polyacrylamide gels in combination with either ethidium bromide staining or silver staining.
	The time needed for SSR analysis may be reduced by using one or more of the following approaches: (i) high throughput approaches of DNA extraction (since high quality DNA is not needed for PCR), (ii) multiplexing facilitated either by size differences in the amplified products or through the use of fluorescent primers, (iii) multiple loading in a series of tiers on the same slab gel, (iv) laser detection through the use of automated DNA sequencers, and (v) use of capillary electrophoresis (CE) in place of conventional slab gel electrophoresis.

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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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