Molecular Markers and its Applications | Online Biotech Notes

 

Online Biotech Notes

MOLECULAR MARKERS

A Molecular marker is a gene or DNA sequence with a known locations on a Chromosome and associated with a particular gene or trait. It can be described as a variation, which may arise due to mutation or alteration in the genomic loci that can be observed.
Sometimes the term Smart Breading is used to describe marker supported breeding strategies to select animals with superior genetic potential as parents for the next generation.
The molecular markers are based on the nucleotide sequence mutations within the individual's genome; they are the most reliable markers available. There are different types of molecular markers used to minimize the economic loss.

Restriction Fragment Length Polymorphism (RFLP)

The RELP is defined by the existence of alternative alleles associated with restriction fragments that differ in size from each other. The RELP is also one of the first methods used for genetic typing - also known as genetic fingerprinting, profiling or testing. Despite of having many Benefits, it is still a slow and more tedious process compared to some of the newer DNA analysis techniques. It also requires substanially larger sample size than forms of analysis.

Random Amplification of Polymorphic DNA (RAPD)

PCR based RAPD has been one of the most commonly used molecular techniques to develop DNA markers. The RAPD technology provides a quick and efficient screen for DNA sequences based polymorphism at a very large number of loci. The major advantages of RAPD is that, is does not require pre-sequencing of DNA but the polymorphisms are detected only as the presence or absence of a band with no information on heterozygosity besides being dominantly inherited, and show some problems with reproducibility of data.

Amplified Fragments Length Polymorphism ( AFLP)

AFLP method is used to generate hundreads of highly replicable markers from DNA; thus, allowing high-resolution genotyping of fingerprinting quality. The time and cost efficiency, reproducibility and resolution of AFLPs are superior or equal to those markers (RAPD, RFLP and microsatellite). However, AFLPs are dominant bi-allelic markers polymorphis, evaluate, and are unable to distinguish dominant homozygous from dominant heterozygous individuals. The molecular approach for population genetics and genome typing, consequently applied to detect genetics AFLP method is an ideal  molecular approach for approach for population genetics and genome typing, consequently applied to detect genetic polymorphisms, evaluate, and characterize animal genetic resources.

Microsatellites/SSR

Microsatellites or simple repeated (SSR) loci, which have been referred in the literature as variavle numver of tandem repeats (VNTRs) and simple sequence and to a lesser extent in prokaryotes. The sequence of di-, tri- and tetra nucleotide repeats are the most common chouces for molecular genetic studies. They are tandemly repeated (usually 5-20 times ) in the genome with a minimum repeat length of 12 base-pairs.

Single Nucleotide Polymorphism 

It refers to a sequences polymorphism caused by a single nucleotide mutation at a specific locus in the DNA sequence and instead that SNP to get a more accurate means of assessing overall genomic diversity in natural poulation. The SNP to get a more accurate means of assessing overall genomic diversity in natural populations. THe SNP markers have promising advantages over microsatellite  markers due to high-through put automated analysis, lower mutation rates and lower genotyping costs.