Genetic Marker: Key Concepts, Types, and Applications

A genetic marker is a gene or DNA sequence that is used to identify individuals or species and has a known position on a chromosome. It can be defined as an observable variation, which may develop as a result of a mutation or modification in the genetic locus. A genetic marker can be a short DNA sequence, such as one encircling a single base-pair alteration, such as a single nucleotide polymorphism, or a long one, such as minisatellites.

Characteristics of Genetic Marker

For many years, gene mapping technology was restricted to the use of phenotype markers to identify species. Genes encoding visible features such as blood types or seed shapes were included. The quantity of these features in various organisms was minimal, limiting the mapping attempts. This spurred the creation of gene markers, which can detect genetic traits that aren't visible in organisms, such as protein variations. These molecular markers are used to construct further variations as well as in scientific experiments and in finding out their impact on the functioning of their end products. 

Types of Genetic Markers

Commonly, used different types of molecular markers and more specific genetic markers are:

• RFLP: Restriction fragment length polymorphism (RFLP) is a molecular biology approach that uses polymorphisms in homologous DNA sequences to classify individuals, populations, or species or to locate the positions of genes within a sequence. The phrase may refer to the polymorphism itself, as found by differences in restriction enzyme site positions, or to a related laboratory approach that must have demonstrated such changes. In RFLP analysis, one or more restriction enzymes digest a DNA sample into fragments, and the resulting restriction fragments are subsequently sorted by gel electrophoresis according to their size. RFLP analysis was the first DNA profiling approach that was affordable enough to see the broad application, despite the fact that it is now obsolete due to the introduction of inexpensive DNA sequencing technology. These RFLP types of molecular markers are used to construct analysis which was a crucial early method for genome mapping, gene localisation for genetic diseases, illness risk assessment, and paternity testing.

• SSlP: With polymerase chain reaction, simple sequence length polymorphisms (SSLPs) are commonly utilised as genetic markers (PCR). A polymorphism is a difference in DNA sequence between individuals. An SSLP is a sort of polymorphism. SSLPs are known to be repetitive sequences in deoxyribonucleic acid intergenic regions with changing base lengths (DNA). The SSLP length variation is commonly used to understand genetic diversity between two individuals in the same species.

• AFLP: AFLP-PCR, also known as AFLP, is a PCR-based method that is used in genetics research, DNA fingerprinting, and genetic engineering. AFLP, which was invented by Keygene in the early 1990s, works by digesting genomic DNA with restriction enzymes and then ligating adaptors to the sticky ends of the restriction fragments. After that, a subset of the restriction fragments is chosen for amplification. Primers complementary to the adaptor sequence, the restriction site sequence, and a few nucleotides inside the restriction site fragments are typically used to achieve this selection (as described in detail below). The amplified fragments are separated and seen on agarose gel electrophoresis, either by autoradiography or fluorescence or by automated capillary sequencing devices.

• RAPD: Random amplification of polymorphic DNA (RAPD), pronounced "rapid," is a form of polymerase chain reaction (PCR) that amplifies random regions of DNA. The RAPD scientist creates multiple arbitrary, short primers (8–12 nucleotides), then performs PCR on a large template of genomic DNA in the hopes of amplifying fragments. The RAPD response molecular markers are used to construct semi-unique profiles by resolving the ensuing patterns.

• VNTR: A variable number tandem repeat (or VNTR) is a region of the genome where a short nucleotide sequence is arranged as a tandem repeat. These can be present on a variety of chromosomes and can vary in length (number of repetitions) between individuals. Each variant functions as an inherited allele, allowing them to be used to identify individuals or parents. Genetics and biology research, forensics, and DNA fingerprinting all benefit from their findings.

• SSR: A microsatellite is a piece of repetitive DNA that repeats particular DNA motifs 5–50 times, ranging in length from one to six base pairs. Microsatellites can be found in hundreds of places across an organism's genome. They have a higher mutation rate than other parts of the genome, resulting in a lot of genetic variation. Forensic geneticists and genetic genealogy experts refer to microsatellites as short tandem repeats (STRs), whereas plant geneticists refer to them as simple sequence repeats (SSRs).

• SNP: A single-nucleotide polymorphism (SNP) is a single nucleotide substitution at a specific location in the genome that occurs in the germline. Many publications do not apply such a frequency requirement, despite the fact that many definitions need the substitution to be present in a high proportion of the population (e.g. 1 percent or more).

• DArT: Diversity arrays technology (DArT) is a molecular genetics technique for developing sequence markers for genotyping and other genetic analysis procedures. Microarray hybridisations are used in DArT to determine the presence or absence of particular fragments in genomic representations. To boost the probability of detection, DArT uses a randomised library of fragments to screen. These molecular markers in plant breeding are used in the examination of polyploid plants, and this approach provides substantial benefits over conventional array-based single-nucleotide polymorphism detection tools.

• RAD: RAD markers are a form of genetic marker that can be used for association mapping, QTL mapping, population genetics, ecological genetics, and evolutionary genetics. RAD mapping is a process in which one uses RAD markers for the mapping of genes. In this method, RAD tags are isolated, which are DNA sequences that immediately flank each instance of a restriction site of a restriction enzyme present throughout the genome. They are the key features of RAD markers and mapping. RAD tags can be used to identify and genotype DNA sequence polymorphisms in the form of single nucleotide polymorphisms once they've been isolated (SNPs). RAD markers are polymorphisms that can be detected and genotyped by isolating and analysing RAD tags.

There are two types of molecular genetic markers:

1. Biochemical indicators detect variation in gene products like proteins and amino acids.

2. Molecular markers that detect variation in DNA like nucleotide alterations like deletion, duplication, inversion, and/or insertion. 

Markers can be Inherited in one of two ways: dominant/recessive or codominant. A marker is considered to be co-dominant if the genetic pattern of homo-zygotes can be separated from that of hetero-zygotes. Co-dominant markers are generally more informative than dominant markers. Most of these different types of genetic markers are measured based on some form of score matrix, and while doing experimentations, the scorable markers provide us with the information wanted from the genetic markers meaning, a score achieved by a marker on a profile while doing analysis gives the information both about quantitative and qualitative nature of these markers.

Uses of Genetic Markers

The association between an inherited disease and its genetic cause can be studied using genetic markers (for example, a particular mutation of a gene that results in a defective protein). It is well known that DNA fragments that are close together on a chromosome are more likely to be inherited together. This trait allows for the employment of a marker, which may then be used to establish the exact inheritance pattern of a gene that has yet to be precisely localised.

In genealogical DNA testing for genetic genealogy, genetic markers are used to assess the genetic distance between people or communities. For determining maternal or paternal lineages, uniparental markers (on mitochondrial or Y chromosomal DNA) are investigated. For all ancestries, autosomal markers are used.

Because homozygotes provide no information, genetic markers must be identifiable, linked to a specific locus, and polymorphic. The marker can be detected directly using RNA sequencing or indirectly utilising allozymes. RFLP, AFLP, RAPD, and SSR are some of the tools used to analyse the genome or phylogenetics. They can be used to make genomic maps of any creature under investigation.

The transmissible agent of CTVT (canine transmissible venereal tumour) was a point of contention. Many researchers speculated that virus-like particles were responsible for the cell's transformation, while others speculated that the cell might infect other dogs as an allograft. Researchers were able to give strong evidence that the malignant tumour cell developed into a transmissible parasite using genetic markers. Molecular genetic markers were also employed to determine natural transmission, breed of origin (phylogenetics), and the age of the canine tumour.

In livestock, genetic markers have also been employed to assess the genomic response to selection. The genetic makeup of the cell changes as a result of natural and artificial selection. The presence of distinct alleles due to skewed segregation at genetic markers distinguishes selected from non-selected livestock.