Expressed Sequence Tags ESTs and Their use for Developing STSs, SSRs and SNPs, Analysis of Gene Expression, Utilizing Opportunities, Sequencing Reaction

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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 >> Expressed Sequence Tags ESTs and Their use for Developing STSs, SSRs and SNPs

Your Ad Here	(c) Expressed sequence tags (ESTs) and their use for developing STSs, SSRs and SNPs. An EST is a DNA sequence from a cDNA clone that corresponds to a mRNA or a part thereof. It has been shown that ESTs, 150 to 400 bp in length, are useful for search of similarity and for mapping by workers in different laboratories. High throughput approaches have also been used for producing ESTs. One such method is SAGE (serial analysis of gene expression), which generates a number of ESTs (10-14 base pairs long) through the same sequencing reaction. Utilizing these opportunities, ESTs are being generated in several mammals and in a variety of plant systems.
In humans, cDNA libraries derived from mRNA have been utilized for generation of more than five million ESTs. In plants also a large number of ESTs have been generated and some of them have also been mapped. For instance in wheat, through the efforts of an International EST Triticeae Co-operative (IETC), at the end of the year 2002, more than 200,000 ESTs had already become available in the public domain (another more than 200,000 ESTs in wheat were available at this time with the private sector) and a target of 300.000 public ESTs was fixed each for wheat and barley.
Sever.11 companies also possess large private EST databases for various crop plants (e.g., wheat, maize and soybean), the access to which can he negotiated on a case-by-case-basis. In any organism, EST databases can also be used for the preparation of cDNA microarrays for a study of the functions of all specific gene sequences and their expression in time and space (for microarrays, consult). These microarrays can be used for hybridization leading to the preparation of expression profiles of genes in different organs of a plant system. Using nucleotides sequence database (GenBank) and protein sequence database (PIR), ESTs can also be matched with existing sequences and assigned to specific genes with the help of available softwares.	Your Ad Here
It has been shown that more than one half of the total set of Arabidopsis genes are likely to be represented in EST database, and a massive project described as "The 2010 Project" has been initiated in USA, to decipher the functions of all 25,000 genes in this genome. The large-scale cDNA analysis of rice is also in progress with an aim at cataloguing all the expressed genes of this cereal including tissue-specific, developmental stage specific, and stress-specific genes. EST databases have thus proven to be a tremendous resource for finding genes and for interspecies sequence comparison. They have also provided markers for genetic/physical mapping, as well as clones for expression analyses. However, a recent analysis of collinearity between Arabidopsis and cereal genomes has shown that collinearity with genomes like that of Arabidopsis may not always be sufficient to allow cross-species gene prediction and isolation in crops like rice and other cereals.
	ESTs, which are accumulating in large number at a fast speed due to current emphasis on functional genomics, can be converted into STSs and tested for polymorphism, so that polymorphic STS markers can be developed from EST databases. EST derived SSRs and SNPs (see later) have also been identified recently in humans and also in several crops to facilitate mapping of ESTs, a task which is otherwise difficult due to the conserved nature of cDNA sequences. Although, the relative frequency of these EST derived SSRs may be low, their usefulness lies in their expected transferability, since they are based on the conserved coding region of the genome.

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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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