UNIVERSITY OF AGRICULTURE FSD (CABB)
APPLICATONS OF BIOINFORMATICS IN
AGRICULTURE
MUDASSAR HUSSAIN
2010-ag-3545
Sub to: yadish bukhari
Bioinformatics and Its
Applications in Plant
Biology
Bioinformatics is a new field of science but it is making progress in every field of
biotechnology very rapidly. As it has its application in the medicine by providing
the genome information of various organisms, similarly the field of agriculture
has also taken advantage of this field because microorganisms play an important
role in agriculture and bioinformatics provides full genomic information of these
organisms.
Tools of bioinformatics are playing significant role in providing the information
about the genes present in the genome of theses species. These tools have also
made it possible to predict the function of different genes and factors affecting
these genes. The information provided about the genes by the tools makes the
scientists to produce enhanced species of plants which have drought, herbicide,
and pesticide resistance in them. Similarly specific genes can be modified to
improve the production of meat and milk
When the evolutionary changes occurred in the plants, their genome remained
conserved and did not provided much information. Since the arrival of
bioinformatics tools, it is possible to extract the required information from the
genome of specific plants. There are two species of food plants, the genome of
which has been mapped completely for example Arabidopsis thaliana and Oryza
sativa. These two species of plants have their names in English as water cress
and rice respectively.
Water cress is a small plant which is found on the rocks. Researchers took
interest in its genome because of its smaller genomic size and studied the plant
developmental processes. Its genome consists of 5 chromosomes on which 100
Mbp DNA is distributed. It reproduces in 5 weeks and makes new generation.
The understanding about its genes and their expressions provides information
about the other plants' proteins and their expressions. There are many uses of
knowing the genome of A. thaliana but the major use is that the yield of the
plants can be increased.
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Many plants have been made insect resistant by incorporating the desired genes.
Bacillus thuringiensis is bacterial specie which increases the soil fertility and
protects the plants against pests. When the researchers mapped its genome,
they used its genes to incorporate into the plant to make it resistant against
insects. For example, corn, cotton and potatoes have been made insect resistant
so far. By having the genes of bacteria in the plants genome, when insects eat
the plants, the bacteria enter in their bloodstream and make them starved,
ultimately they die. Bt corn is one specie of food plants which have been
modified by inserting bacterial genes in it. It is effective against insects by
developing resistance against them. The use of Bt genes in the plants genome
has made the agriculturists to use the insecticides in very little amount. As a
result the productivity and nutritional value of plants will also increase and will
be beneficent for human health.
When the changes are made in the genome of the plants, the nutritional value of
plants also increases. For example some genes are inserted in the rice genome
to increase the Vitamin A level in the crop. Vitamin A is an important component
for the eyes and if the Vitamin A deficiency occurs in the body, it may result in
blindness. This work has allowed the scientists to reduce the rate of blindness
from the world by giving genetically modified rice to the people.
Some varieties of cereals are developed which have the ability to grow in poor
soils and are drought resistant. Due to this method, those areas can also be
used which have less soil fertility.
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Applications of Bioinformatics in Agricultural Research
The science of bioinformatics has many beneficial uses in the modern day world. Main application of bioinformatics can
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Single gene analysis
Biochemical pathways
Molecular techniques
1.Single gene analysis
Comparative studies:
Comparative studies involves analyzing and comparing the genetic material of different species, studying the func
tions of genes, mechanisms of inherited diseases and species evolution. Various Bioinformatics tools are used to make
comparisons between the number of genes, their locations and their biochemical functions in different organisms.
Comparative studies can be done using Bioinformatics.
Sequence alignment:
Sequence alignment in of two types: pair wise alignment and multiple alignment. The pairwise alignment can be
either global alignment or local alignment. BLAST and FASTA- the most widely used tools are examples of local
alignment.
2. Biochemical pathways
KEGG- Kyoto Encyclopedia of Genes and Genomes is a suite of databases and associated software, integrating our
current knowledge on molecular interaction networks, information about the genes and proteins, information about the
chemical compounds and reactions.
3. Molecular techniques
There are several online tools devoted to serving molecular biologist design effective PCR primers. There are a
numerous web-based resources for PCR and primer design which are freely available. Some of them include: Primer
premier, Vector [VecScreen], Gene prediction [Genscan], Restriction analysis and Probe design [Primose]
Current status and future trends:
 To encourage the submission of all sequence data into the public domain, through repositories
 To provide rational annotation of genes, proteins and phenotypes
 To elaborate relationships both within the plants’ data and between plants and other organisms.
 EST sequences aided research
 Conserving plant data using Biodiversity Informatics
 Using plant genes as Phylogenetic markers
Other areas of applications of Bioinformatics in Agriculture are in:
 Plant systematics
 Plant breeding
 Biopharmaceuticals and edible vaccines
 Biodiversity informatics
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Biological sequence such as DNA, RNA, and
protein sequence is the most fundamental
object for a biological system at the molecular
level. Several genomes have been sequenced
to a high quality in plants, including Arabidopsis
Advances in sequencing technologies provide
opportunities in bioinformatics for manag ing, processing, and analyzing the sequences.
Shotgun sequencing is currently the most common method in genome sequencing:
pieces of DNA are sheared randomly, cloned,
and sequenced in parallel. Software has been
developed to piece together the random overlapping segments that are sequenced separately into a
coherent and accurate continuous seq.
The exponential growth of genomics is due to
computational challenges of systematically collecting,
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storing, organizing, manipulating visualizing and
analyzing large amounts of biological information come
from the experiments carried out by the biologists.. Thus,
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bioinformatics, in its broad sense, can be seen as
providing both the infrastructure and the scientific
framework in which biologists take information and use
computers to help convert it into knowledge .Apart
from the fact that bioinformatics is a newly recognized
discipline; there is an impressive diversity o bioinformatics resources currently available. Though a
wide array of commercial resources exist, some of which
are ideally suited to specific tasks, and freely available.
Many of the databases and analysis tools we describe
here are hosted by government or academic research
centers and can be accessed via user-friendly web
interfaces
The term "sequence analysis" in biology implies
subjecting a DNA or peptide sequence to sequence
alignment, sequence databases, repeated sequence
searches, or other bioinformatics methods on a
computer. In bioinformatics, a sequence alignment is a
way of arranging the sequences of DNA, RNA, or protein
to identify regions of similarity that may be a consequence of functional, structural, or evolutionary
relationships between the sequences. Sequence
analysis can be used to assign function to genes and
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proteins by the study of the similarities between the
compared sequences. Nowadays there are many
tools and techniques that provide the sequence
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comparisons (sequence alignment) and analyze the
alignment product to understand the biology
In protein functional studies we compare the protein
sequence to the secondary (or derived) protein
databases that contain information on motifs, signatures
and protein domains. Highly significant hits against these
different pattern databases allow us to approximate the
biochemical function of our query protein [38, 39]. Motif
finding, also known as profile analysis, constructs global
multiple sequence alignments that attempt to align short
conserved sequence motifs among the sequences in the
query set. This is usually done by first constructing a
general global multiple sequence alignment, after which
the highly conserved regions are isolated and used to
construct a set of profile matrices. The profile matrix for
each conserved region is arranged like a scoring matrix
but its frequency counts for each amino acid or
nucleotide at each position are derived from the
conserved region's character distribution rather than from
a more general empirical distribution
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Comparing sequences provides a foundation
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for many bioinformatics tools and may al low inference of the function, structure, and
evolution of genes and genomes. For ex ample, sequence comparison provides a ba sis for building a
consensus gene model like
UniGene ). Also, many computational
methods have been developed for homology
identification .Although sequence com parison is highly useful, it should be noted
that it is based on sequence similarity between
two strings of text, which may not correspond
to homology (relatedness to a common an cestor in evolution), especially when the confidence level of a comparison result is low.
Also, homology may not mean conservation in
function
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