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Chapter 12
Bioinformatics: Concepts and Applications

Sonam1 and Shailesh Kumar Singh2*

1
Ph.D. Student, Department of Horticulture, Lovely Professional University, Punjab,
144411
2
Associate Professor, Department of Horticulture, Lovely Professional University,
Punjab, 144411`
*Corresponding Author: [email protected]

Abstract: Bioinformatics is an approach which includes creation of database, development

of algorithm or software and data handling for analysis and interpretation. The plant
bioinformatics has potential to bring magnificent change in crop productivity specially
when genetic engineering is used in conjugation with omics approaches. Genome
sequencing of voluminous plant species has resulted creation of giant databases which can
be used for genetic modification and reorganisation for development of noble products.
This has further opened the concepts of genomics, proteomics and metabolomics which are
the current field of study and are being progressively explored and applied. Thus,
bioinformatics can provide greater scope for crop improvement and agricultural
sustainability.
Keywords: Agriculture, Bioinformatics, Crop improvement, Genome, Genomics,
Proteomics.

Introduction
Bioinformatics is an interdisciplinary approach integrating information technology
with biological sciences. Bioinformatics is considered as a tool for interpretation of
biological data by using information technology and computer science (Raza, 2012). Plant
Bioinformatics deals with application of computational study in various aspects of plant
species. Bioinformatics is being used for various aspects of crop improvement in
agriculture which can be varietal information system, plant genetic resources data base,
studies on genomics, studies on proteomics, studies on metabolomics, studies on plant
modelling, pedigree analysis, biometrical analysis, forecasting models etc. The application
of bioinformatics and its components are illustrated in Figure-1. In field of agriculture,
bioinformatics is useful tool for identification of gene of importance, study of metabolic
pathways of various biological processes to understand the molecular movement, gene
transfer for creating trait specific varieties, understanding mode of actions of pathogen and
chemicals, identifying suitable techniques for plant protection measures, climate resilience
agriculture, variable rate application of agricultural inputs, phylogeny prediction,
germplasm characterization and conservation, many more and ultimately the crop
productivity. Although, exploitation of bioinformatics and its branches for crop
improvement is very low its application in allied sciences like physical, chemical,
biological and medical sciences confirms the possible scope in agriculture as well.

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Fig. 1: Applications of bioinformatics in crop improvement

Applications of Bioinformatics in Crop Improvement

There are number of applications of bioinformatics viz. sequence analysis and
alignment, molecular modelling, docking, annotation and dynamic simulation to accelerate
the biotechnological research (Khan, 2018). It covers many areas of biological sciences
especially of modern biology viz. genomics, transcriptomics, proteomics, genetics,
evolution genomics, cheminformatics, climate change studies, drug discovery and
development, waste clean-up, bioenergy, crop improvement, veterinary sciences, forensic
sciences and biodefense. Some important applications of bioinformatics in improvement of
horticulture are described below:
Varietal Information System: Bioinformatics has useful applications in developing
varietal information system. Variety refers to a genotype which has been released for
commercial cultivation. State Variety Release Committee or Central Variety Release
Committee and notified by the Government of India. Various types of varieties are used in
plant breeding. All such terms are defined below: The detailed information about various
type of varieties can be developed using highly heritable characters. Such information can
be used in various ways as given below:
(i) In DUS testing for varietal identification
(ii) In grouping of varieties on the basis of various highly heritable characters.
(iii) In sorting out of cultivars for use in Pre-breeding and traditional breeding. The
information can be stored in the computer memory and be retrieved as and when required.

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PGR Data Base: Genetic material of plant which is used as resource by people of different
generations is considered as plant genetic resource. It is also known as gene pool, genetic
stock and germplasm. The germplasm is evaluated for several characters such as highly
heritable morphological and other characters as given below:
➢ Highly heritable morphological traits
➢ Yield contributing traits
➢ Quality characters
➢ Resistance to biotic and abiotic stresses
➢ Characters of agronomic value.
International Plant Genetic Resources Institute (IPGRI), Rome, Italy has developed
descriptors and descriptor states for various crop plants. Such descriptors help in uniform
recording of observations on germplasm of crop plants throughout the world. Thus, huge
data is collected on crop germplasm for several years. Bioinformatics plays an important
role in systematic management of this huge data. Bioinformatics is useful in handling of
such data in several ways as follows:
➢ It maintains the data of several locations and several years in a systematic way.
➢ It permits addition, deletion and updating of information.
➢ It helps in storage and retrieval of data.
➢ It also helps in classification of PGR based on various criteria.
➢ It helps m retrieval of data belonging to specific group such as early maturity,
late maturity, dwarf types, tall types, resistant to biotic stresses, resistant to
abiotic stresses, genotypes with superior quality, genotypes with marker genes,
etc.
All such data can be easily managed by computer aided programmes and can be
manipulated to get meaningful results.
Genomics: Genomics aims at the collective characterization and quantification of genes
and includes the sequencing, mapping, editing and analysis of genomes to understand
mechanism and path of evolution of an individual species, to assemble and analyse the
structure and function of entire set of genomes, and to decipher mechanism of gene
expression (Culver and Labow, 2002).
The intragenomic phenomena such as epistasis, pleiotropy, heterosis and other
interactions between loci and alleles within the genome (Pevsner, 2009). The term
genomics was coined by Tom Roderick in 1986 (Yadav, 2007). Plenty of data are generated
during gene sequencing, analysis of structure and function of entire genomes which cannot
be managed through simple statistical analysis so use of computational algorithms will be
helpful to manage this vast enormous data. Thus, progressive genome sequencing of new
organism the database is being increased which are helpful to provide both conceptual bases
and practical approaches for detecting systemic functional behaviours of the cell and the
organism (Nakagami et al., 2010; Greene et al., 2014).
The study of structure and function of entire genome of an organism is referred to
as genomics. Thus, genomics consists of two groups, viz: (i) Structural genomics and (ii)
Functional genomics. Bioinformatics plays a vital role in both of the areas, structural
genomics and functional genomics. In structural genomics, the genetic structure of each
chromosome of the genome or 3-dimensional structure of all macromolecular represented

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in a genome (Jennifer, 2000) while functional genomics refers to transcription of RNAs

from a genome and encoding of proteins by a genome.
Structural genomics emphasizes high throughput determination of 3D protein
structures (Goldsmith‐Fischman and Honig, 2003), determining RNA structures (Jennifer,
2000) and gene mapping (Cheema and Dicks, 2009). The structural database obtained from
structural genomics is having potential to be useful for deciphering biological functions of
these macromolecules which is referred as functional genomics (Jennifer, 2000).
Studies on Proteomics: Proteomics refers to the study of structures and functions of all
proteins in an individual. In other words, it deals with the study of entire protein expression
in an organism. Advanced techniques in biology led to accumulate enormous data of
protein-protein interactions, protein profiles, protein activity pattern and organelles
compositions. This vast data can be managed and access easily by using bioinformatics
tools, software and databases. Till now, a bulk of algorithms in the field of proteomics viz.
image analysis of 2D gels, peptide mass fingerprinting and peptide fragmentation
fingerprinting have been developed (Gholizadeh and Kohnehrouz, 2010; Gholizadeh,
2011; Gholizadeh and Kohnehrouz, 2013).
Proteomics is of two types, viz: (i) Structural proteomics and (ii) Functional
proteomics. The Structural Proteomics refers to the study of the structures of all proteins
found in a living organism. The Functional Proteomics deals with functions of all proteins
found in a living organism. In fact, proteomics is a new sub-discipline of functional
genomics. It is the study of proteomes which refer to complete set of proteins encoded by
a genome. A variety of techniques are used for the study of proteomics. Now computer
aided programmes are available for the study of proteomics.
Studies on Metabolomics: Metabolomics refers to the study of all metabolic pathways in
a living organism. In other words, it is the computer aided information of all metabolic
pathways of a living organism. Main points related to metabolomics are listed below:
➢ It deals with the study of all metabolic pathways in a living organism.
➢ It is computer-based information about metabolic pathways in a living
organism.
➢ It helps in identification and correction of metabolic disorders in an organism.
➢ It helps in selection of individuals with normal metabolic pathways.
➢ It helps early detection of genetic disorders associated with metabolic
pathways.
Modelling of Plants: Bioinformatics plays an important role in modelling of crop plants.
Such computer aided studies have already been made in field pea and several other field
crops. First the plant model is conceptualized using various plant traits and then efforts are
made to develop such model by using appropriate breeding procedures.
First donor sources for these traits are identified from the available germplasm. Then efforts
are made to combine these traits in one genotype particularly in a popular variety. Such
computer-based studies help in developing plant ideotype suitable for machine picking and
used in multiple cropping system.
Pedigree Analysis: Computer aided studies are useful in pedigree analysis of various
cultivars and hybrids. Information about the parentage of cultivars and hybrids is entered
into the computer memory which can be retrieved any time. The list of parents that are

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common in the pedigree of various cultivars and hybrids can be sorted out easily. It helps
in the pedigree analysis which in turn can be used in planning plant breeding programmes
especially in the selection of parents for use in hybridization programmes. Through study
of protein structures, it helps in pedigree analysis.
Biometrical Analysis: In plant breeding and genetics, various types of biometrical
analyses such as correlation, path coefficient, discriminant function, diallel, partial diallel,
triallel, quadriallel, generation means, line x tester, triple test cross, stability parameters, D
statistics, metroglypth etc. are carried out. Computer aided programmes are very much
useful in carrying out such biometrical analyses. The information obtained from such
biometrical analysis is used in better planning of plant breeding programmes for achieving
specific goal.
Forecasting Models: Computer aided programmes have wide applications in developing
various types of forecasting models especially useful for predicting crop production and
productivity and in forecasting incidence of insects and diseases in crop plants. Weather
parameters are used in making such predictions. Computer aided remote sensing techniques
are used for such predictions.
Other Applications: Besides agricultural applications, bioinformatics has several other
useful applications. Such applications include use of bioinformatics in: (i) Medical science,
(ii) Forensic science, (iii) Pharmaceutical and biotech industry.
In medical science, computer aided studies are useful in detection of genetic diseases at an
early stage of life. It can help in cure of genetic diseases in some cases. The pedigree
analysis helps in advising future parents to prevent certain genetic diseases. In forensic
science, bioinformatics is useful in settling disputed cases of children and detecting
criminal cases. In pharmaceutical industry, computer aided programmes help in detecting
various metabolic pathways involved in the production of a medicine. Thus, it can help in
mass production of such chemicals.
Drug Discovery: Bioinformatics is playing an important role in drug discovery, drug
assessment and drug development through its utility for prediction, analysis and
interpretation in clinical and preclinical findings (Livak and Schmittgen, 2001).
Tradition approach of drug discovery was time consuming and cumbersome practice
while the bioinformatics-based approach i.e. computer-aided drug design (CADD)
has made the task rapid, cost effective and easier to handle the increasing and
voluminous demand of drugs with low risk. Bioinformatics provides a range of drug-
related databases and algorithms which are used for drug designing and drug
development (Rabbani et al., 2003).
Transcriptomics: The study of sets of all messenger RNA molecules in the cell is
called as transcriptomics. This can also be called as Expression Profiling where DNA
microarray is used to determine the expression level of mRNA in a given cell
population. The microarray technique generates vast amount of data, single run
generates thousands of data value and one experiment requires hundreds of runs.
Analysis of such vast data is done by numerous software packages. In this way,
bioinformatics is used for transcriptome analysis where mRNA expression levels can
be determined (Gholizadeh, 2014). RNA sequencing (RNAseq) also has been
included under transcriptomics. It is carried out using next generation sequencing to

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determine the presence and quantity of RNA in a sample at a given time. It is used to
analyze the continuously changing cellular transcriptome.
Cheminformatics: Cheminformatics (chemical informatics) focuses on storing,
indexing, searching, retrieving, and applying information about chemical
compounds. It involves organization of chemical data in a logical form to facilitate
the retrieval of chemical properties, structures and their relationships. Using
bioinformatics, it is possible through computer algorithm to identify and structurally
modify a natural product, to design a compound with the desired properties and to
assess its therapeutic effects, theoretically. Cheminformatics analysis includes
analyses such as similarity searching, clustering, QSAR modelling, virtual screening,
etc. (Ausubel et al., 1999).
Evolutionary Studies/Phylogenetics: The study of evolutionary relationship among
individuals or group of organisms is defined as phylogenetics. Taxonomists find the
evolutionary relationship using various anatomical methods that takes too much time.
Using Bioinformatics, phylogenetic trees are constructed based on the sequence
alignment using various methods. Various algorithmic methods are developed for the
construction of phylogenetic tree that are used depending on the various evolutionary
lineages (Shinozaki et al., 2003).
Crop Improvement: Sustainability in agricultural production in response to global
climate change and population pressure is the issue which needs to be addressed on
urgent basis. The integrated ‘omics’ approach is helpful to clarify the molecular
system of the plant which are applied to improve the crop productivity. The
application of comparative genomics improves the understanding the structure,
biological properties and functioning of genes. The available databases are applied
for design and development of new techniques and experiments for ensuring plant
production (Shinozaki and Yamaguchi, 2007).
Veterinary Science: Food production from livestock can meet demand of human
population for food. For better bio-economy, there is a need of efficient animal
production and reproduction. This is achieved with better understanding of livestock
species. Current and new methods in livestock species using data from experimental
or field studies with bioinformatics are helping in understanding the systems genetics
of complex traits and provide biologically meaningful and accurate predictions.
Finally, almost all of the next generations-omics tools and methods that are used in
other fields of biological sciences, can also be used in veterinary sciences
(Yamaguchi and Shinozaki, 2005; Bartels et al., 2005).
Forensic Science: Forensic science includes the study regarding identification and
relatedness of individuals. It is inherently interdisciplinary with bioinformatics as
both are dependent on computer science and statistics. This field is based on the
molecular data and many databases are being developed to store the DNA profiles of
known offenders. This field is being pushed due to technological and statistical
advances in microarray, Bayesian networks, machine learning algorithms, TFT
biosensors and others. This provides the effective way of evidence organization and
inference (Seki et al., 2001).

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Biodefense: Biodefense includes measures to restore biosecurity to a group of

organisms who are subjected to biological threats or infectious diseases. Although,
there is significant development in bioinformatics application in various field but its
application in forensic studies, medical intelligence and mitigation of biothreats
needs special attention to develop advanced algorithms for better interoperability
(Schimid et al., 2005; Valdivia-Granda, 2010).
Waste Clean-up: Today, the major concern all over the Globe is environmental
pollutants. The main concern of the environmentalists is waste generated from the
industries. These pollutants progressively deteriorate the environment which in turn
affects human health. There are few microorganisms that are considered to remediate
the pollutants into the natural biogeochemical cycle. Bioremediation is the recent
technology which explores the microbial potentiality for biodegradation. This
technology can be further improved by using bioinformatics. Genomic and
bioinformatics data provide a wealth of information that would be greatly enhanced
by structural characterisation of some protein. Bioinformatics provides data of
microbial genomics, proteomics, systems biology, computational biology, and
bioinformatics tools for understanding of the mechanisms of biodegradative
pathways (Raza, 2012; Valdivia-Granda, 2010).
Climate Change Studies: Another Global concern is the Climate change because of
loss of sea ice, accelerated sea level rise and longer and more intense heat waves. To
solve this issue, bioinformatics may help by way of sequencing microbial genome
which can reduce levels of carbon dioxide and other greenhouse gases. This plays an
important role in stabilizing the global climate change. Not much work has been done
in this area in bioinformatics domain, and more region-specific work must be
conducted considering microbes of that region and their capability in CO2 reduction
(Khan, 2018).
Bioenergy/Biofuels: Biofuels has greater potential to serve as alternative and
renewable energy source. Bioinformatics is important in understanding and analysis
of biofuel producing pathways. Recent progress in algal genomics, in association
with various “omics” approaches, has enabled the identification of metabolic
pathways and genes for development of genetically modified micro-algal strains for
optimum lipid production (National Human Genome Research Institute, 2010).
Advantages of Bioinformatics
Bioinformatics has several practical applications in genetics and plant breeding as
discussed above. Its main advantages in crop improvement are given below:
1. It provides systematic information about genomics, proteomics and metabolomics
of living organisms. This information is useful in planning various breeding and
genetical programmes.
2. It helps in finding evolutionary relationship between two species. Studies of
nucleotide and protein sequences help in such matter. The closely related organisms
have similar sequences and distantly related organisms have dissimilar sequence.
The time of divergence between two species can also be estimated from such
studies. Thus, bioinformatics helps in the study of evolutionary biology. It helps in
drawing phylogenic trees (trees of relatedness).

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3. Rapid Method. Is a rapid method of gene mapping and sequencing. Earlier methods
of gene mapping were time consuming and pains taking. Bioinformatics has made
this task very simple. Now gene hunting has become faster, cheaper and systematic.
4. Identification of similar genes. Computer aided studies help in identification of
similar genes in two species. For example, genes similar for biotic and abiotic
stresses in two species can be easily detected.
5. High Accuracy. The computer-based information has very high level of accuracy
and is highly reliable.
6. Bioinformatics has led to advances in understanding basic biological processes
which in turn have helped in diagnosis, treatment and prevention of many genetic
diseases:
7. It has become possible to reconstruct genes from Expressed Sequence Tags (EST).
The EST is nothing but short pieces of genes which can express.
8. Computer aided programmes have made it possible to group proteins into families
based on their relatedness.
9. Computer aided programmes are useful in designing primers for PCR. Such primers
can be designed with little efforts. Such primers are used to sequence unknown
genes or genes of interest.
10. In life science, computer aided programmes are useful in storing, organizing and
indexing huge databases.
Limitations of Bioinformatics:
Computer based programmes have helped in better understanding of various
processes of life science. However, there are some limitations of bioinformatics which are
listed below:
1. Bioinformatics requires sophisticated laboratory of molecular biology for in depth
study of biomolecules. Establishment of such laboratories requires lot of funds.
2. Computer based study of life science requires some training about various computer
programmes applicable for the study of different processes of life science. Thus,
special training is required for handling of computer based biological data.
3. There should be uninterrupted electricity (power) supply for computer aided
biological investigations. Interruption of power may sometimes lead to loss of huge
data from the computer memory.
4. There should be regular checking of computer viruses because viruses may pose
several problems such as deletion of data and corruption of the programmes.
5. The maintenance and up keeping of molecular laboratories involve lot of
expenditure which sometimes becomes a limiting factor for computer based
molecular studies.
Conclusion
The increasing population questions about the food and nutritional security,
increasing pollution questions for environmental security, biodiversity degradation
questions for conservational security and growing database questions for database security
but the answer is single i.e. Bioinformatics.

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