The explanation of genotype and phenotype

What is Genetics?- Definition, History, Applications and Branches 

“Genetics is a field of science that includes the study of inheritance and genetic variations by investigating the DNA, genes, genome, chromosome and other components of it.”


 In a broader sense, we can say, that the study of genes, genomes & chromosomes and the inheritance of traits is referred to as genetics. The phenomenon of inheritance was first explained by Gregor Johann Mendel during the late 18’s.

As per Mendel’s finding, “the traits inherited from parents to their offsprings.” Some traits are physical while some are biological. What he called a trait are now known as genes; genes pass down to consecutive generations. Before going ahead in the topic, we first need to understand, genes, DNA, mutation and chromosomes.

Genes are the sequence of DNA, encoding a specific protein. A specific combination makes it possible, which is our “genotype”. Contrary, physical and visible characteristics such as the color of the eye, skin color, height, and hair color are known as “phenotype”.

The biochemical traits are those, involved in the regulation of biological reactions of ours which aren’t visible. For example, the reaction of lipid metabolism, the reaction of purine synthesis.

Change that occurs in a gene creates mutations that can be either helpful or harmful to us. Unfortunately, most are harmful. We can define mutation as any alteration in the sequence of a gene that possibly alters the phenotype is known as mutation. Read the article on it: Genetic Mutations- Definition, Types, Causes and Examples

When a mutation occurs, it stabilizes in the genome, causes genetic disease and thereby transmits to the next generations. Gene- a sequence of DNA, is located on chromosomes. It’s a complex network of DNA and protein that helps DNA to settle, the process of DNA packaging makes it possible.

A total of 46 chromosomes in 23 pairs are present in our cells. Among 23 pairs, 22 are knowns as autosomes while a pair of XX or XY chromosomes are knowns as sex-chromosomes. XX and XY are present in females and males, respectively.

The overview of how DNA arranged in the cell.

Notedly, a change in the number of chromosomes also causes mutation, known as aneuploidy. Down syndrome is the classic example of this condition in which additional chromosome 21 is present along with the pair. The condition is known as trisomy. Another example is the Turner syndrome in which only a single X chromosome is present in a female.

In addition, another kind of chromosomal abnormality also exists, known as structural chromosomal alteration. In this, structural changes cause varying degrees of abnormalities, some examples are chromosomal deletions, duplications, translocations and inversions.

Cytogenetics studies chromosomal alterations such as structural or numerical chromosomal changes while molecular genetics studies DNA, gene and interaction of proteins to investigate genetic defects. This article is going to be a simple basic article, comprises information regarding “genetics”, definition, branches and several common applications.

It may help newbies to understand the topic. The content of the article is,

  • Definition of genetics
  • Applications of genetics
  • History of genetics 
  • Branches of genetics
    • Molecular genetics 
    • Cytogenetics 
    • human genetics
    • Preimplantation genetics 
    • Clinical genetics
    • Plant genetics
    • Microbial genetics
    • Metagenomics
    • Population genetics 
    • Epigenetics
    • Biochemical genetics
    • Physiological genetics
    • Quantitative genetics 
    • Conservative genetics 
    • Behavioral genetics 
  • Tools used in genetics
  • Conclusion

Definition of genetics:

“The branch of biology dealing with the study of ‘heredity’ and ‘variation’ in genes and genotypes is called genetics. “

or

“The study of structure and function of DNA, genes, chromosomes and related alterations is known as genetics.”

The term “Genetics” was coined by William Bateson in 1905.

The term “genetics” was derived from the Greek word “genetikos” and “genesis”. Genetikos: generative and genesis: origin.

Related article: Definition Of Genetics And Related Terminologies.

In detail, we can define genetics as,

“Genetic contains the study of DNA, genes, chromosomes, inheritance, genotypes, phenotype, genetic abnormalities and epigenetics using techniques like PCR, DNA sequencing, microarray, karyotyping and FISH.”

Common terminologies used in the present article: 

Terminology Definition 
DNA Inheritance unit of an organism. 
Gene A sequence of DNA that encodes a protein. 
Genotype A genotype is a heritable portion of a genome that produces a specific phenotype. 
Phenotype A set of the observable characteristics of an organism. 

Several applications of genetics are given below,

Applications of genetic studies: 

  • Characterization and diagnosis of genetic disease
  • Identification of pathogenic mutations
  • Preserving biodiversity 
  • Identification and characterization of microbes
  • Studying inheritance pattern 
  •  Creating advanced plant species 
  • Creating genetically modified organisms 
  • DNA fingerprinting 
  • Antibiotic resistance study and drug discovery 
  • Genetic/DNA medicines 
  • Genetic engineering 
  • Crop improvement 
  • Animal and Plant Breeding program 
  • Infectious disease diagnosis
  • Screening, prognosis, and diagnosis of cancer

Related article: 50 Powerful Applications Of PCR.


History of Genetics:

Mendel was the pioneer in experimenting and establishing the basis of genetics and henceforth Gregor Johann Mendel is known as the father of genetics. During the period of 1856 to 1865, he experimented on pea plants and discovered the phenomenon of “inheritance of traits”.

Traits are heritable and now known as genes that can transmit to offspring. In 1866, Mendel published his research paper describing the law of inheritance and independent assortment.

Some of the milestone discoveries in genetics are enlisted below, 

1842: Wilhelm von Nageli, a Swiss botanist, observed the plant cell.

1866: Mendel’s research work was published under the title of “experiments on plant hybridization.”

 1869: Friedrich Miescher discovered nucleic acid.

1888: Waldeyer identified the chromosome present in the cell.

1889: Richard Altmann purified DNA from the protein.

1905: William Bateson coined the term “genetics”.

1908: discovery of Hardy-Weinberg’s law.

1910: Morgan T, explained that the genes are located on the chromosomes. Also, they experimented on Drosophila Melanogaster and determined the nature of sex-linked traits.

1923: Griffith F, experimented on bacteria and postulated that DNA is the genetic material.

1953: Watson and Crick given the structure of DNA.

Read more on DNA: DNA story: The structure and function of DNA.

Branches of genetics: 

The branches of genetics

Molecular genetics: 

Molecular genetics is an interdisciplinary sub-branch of genetics dealing with the study of the structure and function of DNA as well as genes (at a molecular level) using techniques such as Polymerase chain reaction and DNA sequencing. 

Using molecular genetics techniques one can detect pathogenic mutations, SNPs (single nucleotide polymorphism), minor deletion or duplication at a DNA level. Furthermore, those techniques can study gene expressions too. 

A state-of-the-art technique- DNA sequencing is powerful enough to find new variations or mutations. Polymerase chain reaction, gene cloning, DNA sequencing, and DNA quantification are some of the techniques used in molecular genetic analysis. 

Any of the molecular genetic experiments are divided into the 4 sub-steps: 

  1. Separation of molecule 
  2. Purification of molecules 
  3. Processing of molecule
  4. Detection of molecule

Separation is the process of extracting molecules like DNA or mRNA from other cell debris. We have covered so many articles on DNA extraction. Some of the DNA extraction methods are enlisted here: 

  1. Phenol chloroform DNA extraction method
  2. Proteinase K DNA extraction method

After that, DNA is purified using the ready-to-use kit or using alcohol. Following purification, DNA has been processed for downstream applications.  

PCR: 

The polymerase chain reaction is a process in which we can amplify millions of copies of a DNA segment of our interest in vitro. The process is temperature-dependent, divided into three steps,

Denaturation: the double-stranded DNA denatured into a single-stranded one.

Annealing: the Sequence-specific DNA primer binds/anneal to its complementary sequence on single-stranded DNA.

Extention: the Taq DNA polymerase amplifies the DNA using the 3′ end of the primer.

A comprehensive handbook of long-range PCR

Read more on PCR: Polymerase Chain Reaction (PCR)- Definition, Principle, Steps, Procedure, Protocol, Applications and Types.

DNA cloning: 

DNA cloning is a traditional method for the synthesis of DNA. Using a cloning vector our sequence of interest can be synthesized by using a bacterial artificial chromosome. The method is time-consuming and not so accurate. It includes tedious steps like cell culture and isolation. 

DNA sequencing: 

DNA sequencing is the process of reading the sequence of DNA using a computational tool. The denatured sequence can be read using the fluorescence-labeled dNTPs when anneal. It detects new mutations.

Cytogenetics: 

Cytogenetics is a sub-branch of genetics including the study of inheritance through chromosomal analysis utilizing techniques such as karyotyping, chromosomal staining and chromosomal banding, and FISH. Structural and numerical chromosomal abnormalities can be screened using cytogenetic techniques.

However, copy number variations more than 10Kb can only be detected using FISH or DNA microarray. Some of the structural and numerical anomalies are enlisted in the table below,

Disease Abnormality Cytogenetic indication 
Down syndrome Numerical Trisomy 21
Klinefelter syndrome Numerical One extra X chromosome in males (XXY).
Philadelphia syndrome Structural Translocation between chromosome 9 and 22 
Turner syndrome Numerical monosomy in female, single X chromosome.
Neuroblastoma Structural Chromosome 1p deletion 

We have already covered a beautiful article on cytogenetics, you can read it here: A Brief Introduction To Cytogenetics.

Human genetics: 

The branch of genetics comprises the study of genetic alterations and its role in the development of disease especially in humans is referred to as human genetics.

Using the cytogenetic, molecular genetics, phylogenetic, population genetics, and clinical genetic methods, any mutation can be characterized which are involved in the development of the disease. 

We can study,

  • The inheritance pattern of disease.
  • The severity of the disease. 
  • Possibility of inheritance in the consecutive generation

Furthermore, more recently, genetic techniques are also used in the screening, prognosis, and diagnosis of cancer. So many oncogenes are now known due to the advancement in genetic.

Preimplantation genetics: 

Characterizing or profiling the genetic composition of the embryo before implantation, the branch of genetics is known as preimplantation genetics. 

Preimplantation genetic techniques are powerful enough to screen the genetic profile of oocyte or sperm cells before fertilization. The major application of preimplantation genetic is to screen high-risk pregnancies. A couple having a previous history of any genetic disorder can be suggested for preimplantation genetic screening. 

It is advantageous in preventing selective abortions because we are screening cells before implantation. The process includes steps like isolation of cells from the pre-embryonic stage, cell culture and genetic analysis. All procedures are performed in a lab, cultured cells can be employed for molecular genetic or cytogenetic analysis. The figure below explains the whole procedure.

The outline of preimplantation genetic diagnosis process

We can say, genetic alterations and abnormalities can be ruled out before implantation but despite having promising applications, PIGD studies are still under the pre-clinical phase.

Clinical genetics: 

Clinical genetics involves the study of disease, finding the root of the disease, its adverse effects, and its inheritance pattern. We already have discussed all the points above. 

Plant genetics: 

The branch of genetics deals with the study of genetic variations and chromosomal abnormalities in plants studied in plant genetics. We know, that the mechanism of inheritance was developed from experimenting with plant species. Mendel, the father of genetics experimented on pea plants and established a mechanism that is the basis of genetics.

It includes the study of plant genomes and genetically modified plant species using the techniques such as karyotyping, PCR, and DNA sequencing. Genetically modified plant species have tremendous economical value. The native plant genome is modified in such as way that increases the yield, disease resistance, nutritional values and stress resistance. 

BT-cotton and BT- brinjal is the best example of genetically modified plant species. 

Standard karyotyping technique studies ploidy level in plants (either polyploidy or aneuploidy) whilst techniques like PCR or sequencing studies mutations at the gene level. In addition to this, genetic tools also study species and speciation in plants.

Nicotiana benthamiana, Arabidopsis thaliana and Brachypodium distachyon are some of the model organisms used in plant genetic studies. 

Techniques like gene editing and gene manipulations are helpful in inducing new variations in the plant genome. One of the traditional gene-editing methods is Agrobacterium-mediated gene transfer. In this method, mainly the genome of the dicot plants is edited by introducing the gene in the T-plasmid of Agrobacterium. 

Modern methods like gene guns, particle bombardment, and viral vector-mediated gene transfer are more accurate & advanced and used in plant genomic research. 

Microbial genetics: 

The microbial genetics is an applied branch of genetics includes the study of the genes, genotypes ad gene expression of microorganism for various genetic engineering applications. The study includes genetic analysis of bacteria, viruses, archaea, protozoa and some fungi. 

Excluding the RNA viruses, DNA is the genetic material in both prokaryotes as well as in eukaryotes, in addition to this, the hereditary and genotypic processes in microbes are similar to eukaryotes (to some extend) hence the microbes can be used as a model organism for studying the genetic traits. 

For instance, the operon model has provided information regarding gene expression and the role of different enzymes involved in the metabolism of biomolecules such as lactose. lac and trp operon are two of the most commonly studied bacterial operons.

Some microbes infect us badly. By studying those microorganisms, infectious diseases can be prevented. Furthermore, vaccines and antibiotics against any microbes can be developed by studying their genetic profile. Genetic tools detect new antibiotic-resistant species and distinguish them from the native ones. 

The Novel coronavirus COVID-19 infecting people in recent times and causing respiratory problems is detected accurately using the RT-PCR technique. You can read this article to know more: What is the Ct value of SARS-CoV-2 (COVID-19) RT-PCR? 

Apart from all these, microbial genetic study helps in genetic engineering practices such as the development of therapeutic drugs and therapeutic proteins. All these studies can be possible because of the genetic tools used for microbial genetic analysis.

Related article: Microbial genetics: A rapid advancement in microbiology.

Metagenomics: 

Meta: Vast or huge, Genomics: a study of genetics or inheritance

The branch of genetics that deals with the study and identification of different microorganisms by processing the environmental samples using modern genetics techniques is called metagenomic studies. 

The present method is rapid and accurate, lacking tedious cell culturing and cultivation techniques. researcher uses genetic tools to screen, study and identify various microorganisms from the recovered environmental samples.

Traditional microbiology techniques such as culturing or cultivation may not help in the identification of all organisms present in any biological/ environmental sample. A majority of microbial diversity is missing out, contaminated or not cultured properly which creates a loophole in the study. 

Using genetic tools such as DNA sequencing or polymerase chain reaction, one can identify microbial diversity in any biological sample. Shotgun sequencing and PCR direct sequencing are commonly used for metagenomic analysis. 

By extracting DNA from any biological sample, one can identify and characterize any microorganism present in that sample using the species-specific and sequence-specific primers and bioinformatic tools. A powerful sequencing tool can even identify any unknown organism or new microbe or strains of microorganisms. 

The outline of metagenomics analysis

Population genetics: 

An interdisciplinary branch of genetics includes the study of genetic differences within and between the population or individual is known as population genetics. 

By doing mathematical calculations, statistical analysis, fieldwork and genetic analysis one can calculate the genetic frequency, allelic frequency, and other factors with respect to the population. 

We can also determine how natural selection, mutation, genetic drift, and gene flow can influence the phenotype and genotype in the population. The Hardy-Weinberg’s equation is the basis of the population genetics, H-D equation: P2 + 2pq + q2 = 1 

Epigenetics:

Put simply, epigenetics is the study of gene expression. 

The branch of genetics investigates gene expression profiles but not gene mutations, known as epigenetics.

Gene expressions are tissue-specific. What we eat, how we sleep, how we exercise and stress has a major impact on our epigenetic profile. Methylation, ubiquitination, and histone modifications are several mechanisms that altered the epigenetic profile of an organism. 

When any of the mechanisms changes or behave unnaturally it activates oncogenes and causes cancer. You can read this article to learn more: What is epigenetic?

Besides these major genetic branches, several others are biochemical genetics, physiological genetics, quantitative genetics, conservative genetics and behavior genetics.

Biochemical genetics: 

The branch of genetics studying the chemistry of DNA, gene, chromosome, RNA and related biomolecules is called biochemical genetics. 

Physiological genetics: 

Physiological genetics deals with the study of physiological characteristics such as sex differentiation and sex determination, blood group factor and sickle cell anemia like physiological conditions. 

Quantitative genetics: 

It is actually a branch of population genetics that studies the continuously varying phenotypes. The correlation between phenotype and related genotype is the basis for quantitative genetics.  

Conservation genetics: 

Again, conservative genetics is a subfield of population genetics in which, using the genetic tools and by understanding the dynamics of genes and their expression profile, researchers study the endangered species of plants, animals and other organisms. 

Behavioral genetics:

Studying the behavioral phenotypes of an organism at the genetic level is conducted in behavioral genetics. The behavior of an organism is influenced by the interaction between the environment and genetic composition.

Some of the behaviors of ours are governed by inherited genetic factors. Read our article on it: Behavioural Genetics: Science behind the behavior

Tools used in genetics: 

Using the tool listed below, any genetic abnormality like SNP, copy number variation, structural and numerical chromosomal abnormality, gene expression and any new variation can be studied. 

Conclusion:

In a broader sense, genetics is a study of genotype, its related phenotype, and alterations in the genome. Using genetic tools, nowadays, the diagnosis of inherited diseases is a common medical practice.

The Human Genome Project was completed in the year 2013. Now we have the entire genomic sequence of humans. We can use this data for the identification of new mutations and alterations. Furthermore, scientists now can use genetic data of different microbes for the identification and characterization of strains.

Summary
Article Name
What is Genetics?- Definition, History, Applications And Branches 
Description
Genetics is a field of science that includes the study of inheritance and genetic variations by investigating the DNA, genes, genome, chromosome and other components of it."
Author
Publisher Name
Genetic Education Inc.

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