New genetic markers are increasingly being discovered that help to identify and therefore better prevent multiple diseases.

These markers are used to link certain genetic mutations to the risk of occurrence and development of numerous inherited disorders. The use of new techniques for sequencing the genome will be essential in advancing knowledge of this type of disease and many others.

In this article we explain what a genetic marker is, what types of markers exist, how the different genetic variants are detected and what are the main techniques used in genomic sequencing.

What is a genetic marker?

Genetic markers are segments of DNA located at a known position (a locus) on a particular chromosome. These markers are usually associated with specific disease phenotypes and are very useful in identifying different genetic variations in specific individuals and populations.

DNA-based genetic marker technology has revolutionized the world of genetics, making it possible to detect polymorphisms (responsible for the great variability among individuals within a species) between different genotypes or alleles of a gene for a given DNA sequence in a group of genes.

Those markers that confer a high probability of a disease occurring are most useful as diagnostic tools . A marker may have functional consequences, such as altering the expression or function of a gene that contributes directly to the development of a disease; and conversely, it may have no functional consequences, but may be located near a functional variant so that both the marker and the variant tend to be inherited together in the general population.

DNA variations are classified as “neutral” when they produce no change in metabolic or phenotypic traits (the observable traits), and when they are not subject to any evolutionary pressure (either positive, negative, or balancing); otherwise, the variations are called functional.

Mutations in the key nucleotides of a DNA sequence can change the amino acid composition of a protein and lead to new functional variants. Such variants may have a higher or lower metabolic efficiency compared to the original sequence; they may lose their functionality completely or even incorporate a new one.

Polymorphism detection methods

Polymorphisms are defined as genetic variants in the DNA sequence between individuals of the same species . They can have consequences on the phenotype if they are found in coding regions of the DNA.

There are two main methods for detecting these polymorphisms: the Southern method, a nucleic acid hybridization technique; and the PCR polymerase chain reaction technique, which allows small specific regions of DNA material to be amplified.

Using these two methods, genetic variations in DNA samples and polymorphisms in a specific region of the DNA sequence can be identified. However, studies show that for more complex diseases it is more difficult to identify these genetic markers, as they are often polygenic, i.e. caused by defects in multiple genes.

Types of genetic markers

There are two main types of molecular markers s: those of post-transcription-translation, which are performed by an indirect analysis of the DNA; and those of pre-transcription-translation type, which allow the detection of polymorphisms directly at the DNA level and which we will discuss next.

1. RFLP markers

The genetic markers RFLP (Restriction Fragment Length Polymorphism) are obtained after the extraction and fragmentation of DNA, by cutting an endonuclease by restriction enzymes .

The restriction fragments obtained are then analyzed using gel electrophoresis. They are a fundamental tool for genomic mapping and in the analysis of polygenic diseases.

2. AFLP Markers

These markers are bi-allelic and dominant . Variations at many loci (denomination of various locus) can be ordered simultaneously to detect single nucleotide variations of unknown genomic regions, where a given mutation may often be present in undetermined functional genes.

3. Microsatellites

Microsatellites are the most popular genetic markers in genetic characterization studies . Their high mutation rate and their co-dominant nature allow the estimation of genetic diversity within and between different races, and the genetic mix between races, even if they are closely related.

4. Mitochondrial DNA markers

These markers provide a quick way to detect hybridization between species or subspecies .

Polymorphisms in certain sequences or in the mitochondrial DNA control region have contributed greatly to the identification of the parents of domestic species, the establishment of geographical patterns of genetic diversity and the understanding of domestication behaviours.

5. RAPD markers

These markers are based on the polymerase chain reaction or PCR technique. The fragments obtained by RAPD are amplified in different random regions.

Its usefulness lies in the fact that it is a technique that is easy to use and allows many polymorphisms to be distinguished quickly and simultaneously. It has been used in the analysis of genetic diversity and the improvement and differentiation of clonal lines.

Genome sequencing techniques

Many of the diseases that exist have a genetic basis. The cause is usually determined by the appearance of one or more mutations that cause the disease, or at least increase the risk of developing it.

One of the most common techniques to detect these mutations and which has been used until recently is the genetic association study , which involves the sequencing of the DNA of one or a group of genes suspected of being involved in a certain disease.

Genetic association studies study the DNA sequences in the genes of carriers and healthy people in order to find the gene(s) responsible. These studies have sought to include members of the same family to increase the likelihood of detecting mutations. However, this type of study can only identify mutations linked to a single gene, with the limitations that this entails.

In recent years, new sequencing techniques have been discovered that have made it possible to overcome these limitations, known as new generation sequencing techniques (NGS). These allow the genome to be sequenced with less time (and less money). As a result, so-called genome-wide association studies (GWAS) are now being carried out.

Genomic sequencing using GWAS allows all the mutations present in the genome to be explored , exponentially increasing the probability of finding the genes responsible for a given disease. This has led to the creation of international consortiums with researchers from all over the world sharing chromosome maps with the risk variants of many diseases.

However, GWASs are not without limitations, such as their inability to fully explain genetic and familial risk of common diseases, the difficulties in assessing rare genetic variants, or the small effect size obtained in most studies. These are undoubtedly problematic aspects that will have to be improved in the years to come.

Bibliographic references:

  • Korte, A., & Farlow, A. (2013). The advantages and limitations of trait analysis with GWAS: a review. Plant methods, 9(1), 29.

  • Pritchard, J. K., & Rosenberg, N. A. (1999). Use of unlinked genetic markers to detect population stratification in association studies. The American Journal of Human Genetics, 65(1), 220-228.

  • Williams, J. G., Kubelik, A. R., Livak, K. J., Rafalski, J. A., & Tingey, S. V. (1990). DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic acids research, 18(22), 6531-6535.