Gene, genome, allele, phenotype and genotype are several terms commonly used in the Genetics. In this article, we will explain each term and try to answer the question “what is a genotype, genotyping frequency and genotyping.”
What is a gene?
“A gene is the hereditary unit of an organism, inherits the characteristics from parents to their offsprings.” A gene is a long sequence of nucleotides codes for particular types of protein.
A gene which encodes for a protein contains exon, introns and non-coding promoters and enhancer sequences.
The exons are the coding parts of the gene which is interspersed by the non-coding introns. The introns are later deleted in the splicing process.
The promoters and enhancer sequences are present at the starting of the gene provides the binding sites for other proteins and enzymes which are involved in protein formation. Each gene has a unique promoter sequence recognised by the enzymes.
“An alternative form of the gene is called as an allele. More than two alleles may exist for one particular type of gene.”
What is a genotype?
“The genetic makeup/genetic constitution/genetic combination of an organism that determines or produces particular phenotype is a genotype.”
Remember, the genotype is not only the genetic composition, rather, we can say it is a genetic constitution which manufactures particular phenotype.
The phenotype is a characteristic of an organism produced by the interaction of genotype, environment and epigenetic factors.
Genotype, environment and epigenetic alterations are the three factors responsible for the production of a phenotype.
Histon modification, histone methylation, acetylation, RNA processing and methylation of the DNA sequence are some of the common types of epigenetic alterations.
Whereas, lifestyle, UV light, radiation, food and chemicals are some of the environmental factors responsible for the production of the phenotype.
In the year 1903, Wilhelm Johannsen a Danish botanist, geneticist and plant physiologist coined the term ‘genotype’. By doing experiments on plants (called as pure line experiments) he coined three different terms: gene, genotype and phenotype.
Let’s understand the term by taking an example,
Suppose, one gene codes for the eye colour (lets name is as Morgan gene). The Morgan gene has two different alleles, allele “M”, codes for a black eye and allele “m” codes for brown eye. Also, the allele “M” is dominant over the allele “m”.
As per the Mendelian law of inheritance, three black eyes and one brown eye coloured progenies will be produced. See the figure,
Here, due to the two different alleles “M” and “m” three different possible genotypes are manufactured, genotype MM, genotype Mm and genotype mm.
Therefore, two different alleles are responsible for the production of three different genotypes. So we can re-defined genotype as “a combination of two (same or different) alleles called as genotype.”
I think this definition which we are stated here, is more accurate than other definitions.
“The same genotype does not mean the same phenotype, likewise, the same phenotype does not mean the same genotype.”
The effect of genotype is based on population characteristics. A different population has a different environmental condition, growing conditions and lifestyle. So it is possible that, even though the genotypes are the same in two different population, the phenotype may different and vice verse.
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What is genotype frequency?
Genotype frequency and allelic frequency are two major parameters must involve in the population study. For a gene, a genotype and the alleles of that genotype are fixed in the population which gives us an idea about the phenotype of the population.
Let’s continue our previous example, the Morgan gene dominant allele “M” codes for the black eye and “m” codes for the brown eye. How can we find out how many individuals in the population has a black eye and how many individuals in the population has a brown eye?
We can calculate it by finding the genotyping frequencies of the population. Suppose if the population is in HW equilibrium than the Hardy-Weinberg’s law is,
p2 + 2pq + q2 = 1
Suppose in the population of the 100 individual, the 74 individuals have a black eye and 26 have a brown eye.
Among the 74 individuals, 40 have MM genotypes and 34 have Mm genotype. 26 individuals have mm genotype.
first, we have to find out the frequency of the allele M and m,
The frequency of the allele M = number of the copy of the allele M / total number of the alleles in the population
Genotype fraquency of MM = 40/ 100 = 0.4
Genotype frequency of Mm = 34/ 100 = 0.34
Genotyping frequency of mm = 26/ 100 = 0.26
The frequency of allele M is,
M = f (MM) + ½ f (Mm)
M = (0.4) + ½ (0.34)
The frequency of allele m is,
m = f (mm) + ½ f (Mm)
m = (0.26) + ½ (0.34)
m = 0.43
What is a genotyping? What are the different methods of genotyping?
“Determining the genotype with the help of different assay is called as a genotyping.” Actually, it is the process of determining which allele is present in a particular genome or organism. Majorly, three different types of DNA variation or alterations have occurred SNP, CNV and structural variation.
The SNP is the single nucleotide polymorphism occurred due to the variation in a single nucleotide.
Millions of SNPs are identified in the human genome. Based on that data different types of method used for the detection of SNP genotyping are,
- RFLP (Restriction Fragment Length Polymorphism)
- AFLP ( Amplified Fragments Length Polymorphism)
- ARMS PCR
- SNP microarray
- Single-stranded conformation polymorphism
- Oligonucleotide ligation assay
- Primer extension PCR method
- Molecular beacons
- High-performance chromatography
These techniques are used in SNP genotyping as well as copy number variation detection. For structural variations karyotyping and whole chromosomal microarray are used. We will discuss each method in another article.
Importantly, these techniques are used to encounter the known genotypes, for detection of new variations and genotypes, DNA sequencing is the only gold standard method.
Read more on DNA sequencing
In DNA sequencing, the nucleotides present into the entire strand of the DNA or a gene is read by the machines and compared it with the reference sequence for determining new variation or genotype.
Contrary, in the DNA microarray, millions of different known variations can be encountered. Here, short, single-stranded oligonucleotides are immobilised on the solid surface which hybridised with the sample DNA as well as control DNA.
A machine compares both DNA hybridization (control as well as a sample) and finds variation in the genotype.
Different types of genotyping methods are used for,
- Identification of disease-causing genotype
- Identification of mutant gene
- Microbial identification
- Identification of strains of bacteria as well as viruses.
- Investigation of genotypes of transgenics.
Recent advancement in genotyping
The most commonly used genotyping method is PCR based gel electrophoresis method.
Read more on,
The method is advance, accurate, rapid and cost-effective. The method is used for the identification of the different strains of the microbes.
Here, different Primers sets based on the variation in the DNA sequences of different strains of microbes, are designed which amplifies a specific type of strain. A single set of the primer can bind to one particular type of strain.
Detection of different types of the HPV strains is possible by HPV- PCR based genotyping method.
Also, different genotypes for the single gene disorder can be detected using the PCR based detection method. The best example is sickle cell anaemia. Generally, HBB genotype is present in normal individual whereas HBS mutant genotype is present in sickle cell anemia patient.
The detection of single mutation based on the genotype is possible with the help of the ARMS-PCR.
SNP genotyping or more specifically called as an SNP microarray is a popular method in recent time. Millions of SNP can be detected using a single chip contains millions of different SNP specific oligonucleotides.
We will cover an entire article on SNP genotyping.
More than one genotype is possible for one gene, the genotype may be helpful or harmful. Furthermore, it may be helpful in one population and harmful in another population. Which genotype will fix in the population depends on the phenomenon of natural selection.