An introduction on sequence tagged site mapping

The slides gives total introduction on sts mapping and its working process.

1. Genetic mapping or genome mapping describes the methods used to identify the location of a gene on a chromosome and the distances between genes. Types of genetic map – Conventional mapping Restriction mapping (fingerprint mapping) Flurescent in situ hybridization (FISH) mapping Sequence tagged site (STS) mapping.

2. Sequence tagged site (STS) mapping Sequence-tagged site (STS) mapping is a technique used to identify the location of genes on chromosomes. A short, unique sequence of DNA (200-500 base pairs) Located at a known position on a chromosome . Can be easily detected by the polymerase chain Reaction using specific primers

3. History Of STS Mapping The STS concept was introduced by Olson et al (1989). In assessing the likely impact of the Polymerase Chain Reaction (PCR) on human genome research, they recognized that single-copy DNA sequences of known map location could serve as markers for genetic and physical mapping of genes along the chromosome.

4. Why STSs are used in genetic mapping ? STSs are used to create genetic and physical maps of chromosomes. Genetic maps show the relative positions of genes on a chromosome. Physical maps show the actual distance between genes on a chromosome. By analyzing the inheritance of STSs along with genes of interest, researchers can determine the location of those genes on the chromosome.

5. Constructing a STS map involves a series of steps The genome is broken down into large DNA fragments. These fragments are then cloned into vectors, which are carrier molecules that allow the DNA to replicate within bacteria. The bacteria are grown in cultures, and the DNA is extracted from the clones. PCR is used to screen the DNA for the presence of STS markers. Finally, the identified STS markers are mapped onto a chromosome map, establishing their relative positions

6. Types of STS Marker STS include such markers as -microsatellites (SSRs, STMS or SSRPs) -SCARS -CAPS, and -ISSRS

7. Microsatellites Polymorphic loci present in nuclear DNA and organellar DNA that consist of repeating units of 1-10 base pairs, most typically, 2-3 bp in length, also called Simple Sequence Repeats (SSR), Sequence-Tagged Microsatellite Sites (STMS) or Simple Sequence Repeats Polymorphisms (SSRP). SSRs are highly variable and evenly distributed throughout the genome.This type of repeated DNA is common in eukaryotes.

8. Sequence Characterized Amplifie Region (SCAR) DNA fragments amplified by the Polymerase Chain Reaction (PCR) using specific 15-30 bp primers, designed from nucleotide sequences established in cloned RAPD (Random Amplified Polymorphic DNA) fragments linked to a trait of interest.By using longer PCR primers, SCARS do not face the problem of low reproducibility generally encountered with RAPDs.

9. Cleaved Amplified Polymorphi Sequences (CAPS) Cleaved Amplified Polymorphi Sequences (CAPS)Cleaved Amplified Polymorphic Sequences (CAPS) polymorphisms are differences in restriction fragment lengths caused by SNPs or INDELs that create ог abolish restriction endonuclease recognition sites. in PCR amplicons produced by locus-specific oligonucleotide primers.

10. Inter-simple Sequence Repeats (ISSRS) ISSRs are amplified by PCR using microsatellite core sequences as primers with a few selective nucleotides as anchors into the non-repeat adjacent regions (16-18 bp )

11. Applications Of STS STSs are very helpful for: Detecting microdeletions in some genes. For example, some STSs can be used in screening by PCR to detect microdeletions in Azoospermia (AZF) genes in infertile men. Identification of genes in elephants could provide additional information for evolutionary studies and for evaluating genetic diversity in existing elephant populations

12. Advantages of STS gene mapping Highly specific: STSs target unique sequences of DNA, making them very specific. Codominant inheritance: STSs can distinguish between homozygotes and heterozygotes. Reproducible: STS assays are highly reproducible, meaning that anyone who wishes to make copies of the marker would simply look up the STS in the database, synthesize the specified primers, and run the PCR under specified conditions to amplify the STS from genomic DNA.

13. Thank you