Genetic Markers - An Overview

Introduction:

Any alteration in the sequence of genes can be readily detected and can help in identifying the population or individual which is involved in the inherited disorder. These altered sequences of DNA (deoxyribonucleic acid) which has a specific location on a chromosome are called genetic markers. Genetic markers are genetic polymorphisms that can differ from the length of the sequence of DNA or the alteration of nucleotide bases on a chromosome. Some common types of genetic markers are single polymorphism nucleotides, restriction fragment length polymorphisms, and indels. PCR (polymerase chain reaction) is a technique to produce a copy of DNA and is also used to detect polymorphisms.

What Is a Genetic Marker?

A genetic marker is a sequence of DNA that has a specific location on the chromosome, and those genetic markers that are nearby are inherited together. They help in linking a responsible gene with a particular disease and tracking the inheritance of nearby genes which are unknown. Genetics markers are usually polymorphisms, which include such as single polymorphism nucleotides (SNPs), variable number of tandem repeats (VNTRs), restriction fragment length polymorphisms (RFLPs), copy number variants (CNVs), microsatellites and indels (insertion-deletion mutations in DNA).

What Are the Types of Genetic Markers?

The different types of genetic markers are:

• Single Polymorphism Nucleotides (SNPs): This affects only one nucleotide base, which are adenine (A), thymine (T), guanine (G), and cytosine (C). For example in a nucleotide sequence ACCTG, in some individuals, it can be ACGTGA instead, and the third position is SNP. These can predict drug response in an individual, and the risk of developing the disorder. SNPs are associated with Alzheimer's disease (a type of brain disorder, which slowly causes memory loss, and destroys thinking skills including simple tasks), diabetes, cancer, migraine, and schizophrenia (a mental disorder that affects the person’s ability to interpret reality).

• Short Tandem Repeats (STR): These are also called microsatellites, simple sequence length polymorphisms (SSLPs), sequence tagged microsatellites (STMS), or a variable number of tandem repeats (VNTRs), a type of marker in which a part of a sequence is repeated multiple times (one to six) in a row and the repeats can vary across individuals. These are found in non-coding regions of DNA. They can help track the inheritance of disorders in families, gene mapping, and DNA fingerprinting. Based on repeat structure, they are classified as:

  • Perfect repeats (simple repeats), which contain only one repetitive unit.

  • Imperfect repeats (compound repeats), contain different types of repeats.

Examples of these repeats are:

1. Myotonic dystrophy (an inherited disorder where there is a decrease in muscle size and weakness) has CTG repeats.

2. Friedreich ataxia (a degenerative disorder that damages the peripheral nerves, spinal cord, and the cerebellum portion of the brain, due to nerve injury it causes uncontrolled movements and loss of sensation) has GAA repeats.

3. Fragile X syndrome (causes intellectual disability, and learning disabilities, and affects memory and thinking abilities) has CGG repeats.

• Indels: A type of marker in which a piece of DNA, there can be an insertion of an allele or deletion of an allele. For example, DNA insertions in the FMR1 gene’s promoter regions can cause Fragile X syndrome.

• Restriction Fragment Length Polymorphisms (RFLPs): It is a type of marker, which refers to the differences among people in their DNA sequence due to restriction enzymes. The different lengths of DNA fragments are due to the digestion of DNA by restriction enzymes. These genetic markers are locus-specific and are used in identifying inheritance patterns running in the family, carrier of disorder, forensic science (use of scientific methods to investigate crime), genetic fingerprinting, and gene mapping. But this technique requires a large DNA sample.

• Copy Number Variants (CNVs): It is a type of genetic marker that refers to the genetic trait involving a particular gene that has many copies of a particular gene in the genome (the entire set of DNA) of an individual. Variations that can include such as deletions, duplications, or insertions of DNA segments, collectively are called copy number variants.

• Random Amplified Polymorphic DNA (RAPD): It is a PCR (polymerase chain reaction, a technique to produce a copy of DNA) based genetic marker. This procedure uses 8 to 12 base pair primer to amplify the DNA and the fragments which are obtained by using this technique are analyzed using agarose gel electrophoresis (a technique to separate RNA, DNA, and protein molecules). In case of mutation in the primer region, no PCR products will be formed, and amplified DNA segments will be distinct.

• Amplified Fragment Length Polymorphism (AFLP): It is a PCR technique, in which the DNA fragment is amplified, restriction enzymes are used in the digestion of DNA and the fragments are analyzed using gel electrophoresis. This technique does not require prior sequencing of DNA and requires small fragments. These markers are used in crop improvement programs and genomic interpretation of different crops.

• Inter Simple Sequence Repeat (ISSR) Markers: It is a PCR-based technique in which a primer containing microsatellite core regions is used to amplify segments of DNA of 2 similar microsatellite repeat regions. It is used in analyzing genetic diversity, somaclonal variations in plants (variations in plants that are produced by plant tissue culture), and phylogenetic analysis (study of the evolution of species through changes in genetics).

• Cleaved Amplified Polymorphic Sequence (CAPS): It is also referred to as PCR-RFLP, in which the amplified DNA fragments are digested by a restriction endonuclease, and the products are screened for differential migration rate. These markers are locus-specific and used in gene mapping.

• Expressed Sequence Tags (ESTs): These markers are developed by partial sequencing of random cDNA (copy DNA) clones and by sequencing the nucleotides to form two types of EST. sequencing the 3′ end of cDNA gives rise to 3′ EST, which is a non-coding region, and sequencing the 5’ end of cDNA gives rise to 5′ EST, which is the coding region for proteins. This marker is used in whole genome sequencing, cloning gene, and gene mapping.

What Are the Uses of Genetic Markers?

The uses of genetic markers are:

• It helps in gene mapping by recognizing the linked gene’s position in the chromosome which is inherited together.

• It helps in the identification of variations in genetics.

• Genetic markers like RAPD are used in studying polymorphisms.

• It helps in identifying any alterations in the genes which are usually involved in genetic disorders.

• It helps in distinguishing between individuals by determining variable characters in the gene.

Conclusion:

As mentioned above, genetic markers are useful in many ways such as studying the polymorphisms in humans, gene mapping, DNA fingerprinting, and in forensic science. Research is still on in this field and other areas are being explored such as population genetics, and conservation genetics.