In genetics, DNA marker is a gene or other fragment of DNA whose location in the genome is known. DNA markers are also known as molecular markers or genetic markers.It refers to any unique DNA sequence which can be used in DNA hybridization, PCR or restriction mapping to identify a particular sequence of DNA in a pool of unknown DNA.There are many types of genetic markers, each with particular weakness and strengths. Genetic markers there are divided into three different categories: First Generation Markers, Second Generation Markers, and New Generation Markers.These types of markers may also identify dominance and co-dominance within the genome. Codominant markers help identify heterozygotes from homozygotes within the organism. Thus codominant markers are more beneficial and more informative than the dominant markers
Types of Markers
• RFLP (or Restriction fragment length polymorphism)
RFLPs are genetic markers resulting from the variation in the length of DNA fragments produced by digestion of the DNA sample with restriction endonucleases.
• SSLP (or Simple sequence length polymorphism)
are used as genetic markers with Polymerase Chain Reaction (PCR). An SSLP is a type of polymorphism. SSLPs are repeated sequences over varying base lengths in intergenic regions of DNA. Polymorphism in the length of SSLPs can be used to understand genetic variation between two individuals in a certain species.
• AFLP (or Amplified fragment length polymorphism)
AFLP combines RFLP and PCR. It is based on the selective amplification of a subset of genomic restriction fragments using PCR.AFLP has higher reproducibility, resolution, and sensitivity compared to other techniques.
• RAPD (or Random amplification of polymorphic DNA)
Randomly Amplified Polymorphic DNA (RAPDs) are genetic markers resulting from PCR amplification of genomic DNA sequences recognized by ten-mer random primers of arbitrary nucleotide sequence RAPDs are dominant markers that require no prior knowledge of the DNA sequence, which makes them very suitable for investigation of species that are not well known
• VNTR (or Variable number tandem repeat)
It is a location in a genome where are short nucleotide sequences (20–100 bp) is organized as a repeat; in humans, these arrays are typically 1–5 kb long.
• SNP (or Single nucleotide polymorphism)is a DNA sequence variation occurring at a specific position in the genome between members of a species or paired chromosomes in an individual. A wide range of human diseases, e.g. sickle-cell anemia, β-thalassemia and cystic fibrosis result from SNPs
• SSR Microsatellite polymorphism, (or Simple sequence repeat)
• STR (or Short tandem repeat)
• SFP (or Single feature polymorphism)
• DArT (or Diversity Arrays Technology)
• RAD markers (or Restriction-site associated DNA markers)
Properties of DNA Marker:
An ideal DNA marker should have following characteristics.
i. Polymorphism: Markers should exhibit a high level of polymorphism. In other words, there should be variability in the markers. It should demonstrate measurable differences in expression between trait types and/or gene of interest.
ii. Co-Dominant: The marker should be co-dominant. It helps in identification of heterozygotes from homozygotes.
iii. Multi-Allelic: A DNA marker should be multi-allelic. It should be useful in getting more variability/ polymorphism for a character.
iv. No Epistasis: There should be absence of epistasis. It makes Identification of all phenotypes (homo- and heterozygotes) easy.
v. Neutral: The marker should be neutral. The substitution of alleles at the marker locus should not alter the phenotype of an individual. This property is found in almost all types of DNA markers.
vi. No Effect of Environment: Markers should be insensitive to the environment. This property is also found in almost all the DNA markers.
Advantages of DNA markers
• They are highly polymorphic.
• They have simple inheritance (often co-dominant).
• They are present abundantly throughout the genome.
• They allow easy and rapid detection
• They exhibit the minimum pleiotropic effect.
Applications of DNA Marker
i. DNA markers can be used to study the relationship between an inherited disease and its genetic cause
ii. DNA markers are useful in the assessment of genetic diversity in germplasm, cultivars and advanced breeding material.
iii. DNA markers are employed in genealogical DNA testing for genetic genealogy to determine genetic distance between individuals or populations and used for constructing genetic linkage maps.
iv. DNA markers are useful in identification of new useful alleles in the germplasm and wild species of crop plants.
v. DNA markers are used in the marker-assisted or marker-aided selection(MAS)
vi. DNA markers are useful in the study of crop evolution.
vii. DNA marker useful in Identification of QTL.