Bioinformatics in
Agriculture
Sajid Ali
BS VIII
Registration
no: 2012-kiu-094
Course facilitator: Sir Tika-khan
Date of submission: 9/10/ 2015
Department of Biological Sciences
Introduction
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. The genome sequencing of the plants and animals
has also provided benefits to agriculture.
Bioinformatics
has grown into a large topic, but still one of the most widely used tools in
bioinformatics is that for searching a sequence database for all sequences
similar to a given query sequence (Waterman, 2000). There are three main
bioinformatics problems:
1. Connection with “Dogma”: sequence, structure
and function.
2. Connection with data: keeping, access and
analysis.
3. Biological process simulation.
Tools of bioinformatics are playing significant role in providing the information about the genes present in the genome of the 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. Certain changes can be made in their genome to make them disease resistant. Declining costs have enabled geneticists to move towards genome-wide genotyping arrays and Genotyping-by-sequencing (GBS). Data analysis, storage and management are the most essential elements of these technologies. A computer system for genetic studies in agriculture has certain requirements in common, regardless of the technology used and the species. These requirements can be broken into two major categories, data management and data analysis. Data management requires storage and backup systems of the raw data, a large memory workspace to process data, methods to extract relevant variables for analysis, and sufficient bandwidth to transfer data among different sites, servers, and researchers. Data analysis usually is performed with specialized software and, depending on the analysis, may require parallel and high performance computing (HPC).These requirements have become a significant barrier to progress in genomics, particularly in agriculture. We introduce a web application specifically tailored for agriculture genetics studies that addresses these problems. The system is comprised of a relational database and a software application for managing and analyzing genotypes, traits, and annotations. The system reduces programming and computing overhead while providing a flexible and scalable framework for new genotyping technologies and accumulating samples and variables. The system uses a centralized database, allowing researchers concurrent access to study data and the ability to share results in real time. In the next section, we give an overview of the software design and describe the database, web application, and interfaces to external software.
In a
recent report by the Food and Agriculture Organization of the United Nations
(FAO), it is estimated that by
the year 2050 the population
of the world will increase by 34%. This increase will demand a
70% increase in food production. Presently there exists a tightly balanced
supply and demand in food production. A single shock to the system (e.g., a
natural disaster or disease) may create a food shortage. Technology
can be used
to alleviate this sensitivity, one
of which is
in the field
of genetics. DNA
genotyping and sequencing technologies are
being used to
uncovering the genetic
component of important
traits and diseases in plants and animals. Desirable traits such
as high yield and higher nutritional content are cultivated and preserved while
undesirable traits such as genetic susceptibility to disease are removed.
Most trait mapping studies
use genetic variants
called single-nucleotide polymorphisms (SNP) due to their abundance
and relatively even distribution
throughout the genome.
Bioinformatics
has aided in genome sequencing, and has shown its
success in locating
the genes, in
phylogenetic comparison and
in the These tools
range from image
the processing techniques
that read out
the data, to the visualization tools that provide a first-sight hint to
the biologists; from preprocessing techniques
(Durbin et al.,
2002) that remove
the systematic noise in
the data to
the clustering methods (Eisen
et al., 1998; Sheng
et al., 2003)
that reveal genes
that behave similarly
under different experimental
conditions. In proteomics, bioinformatics helps in the study of protein structures
and the discovery of sequence sites
where protein-protein interactions
take place. To help
understanding biology at
the system level, bioinformatics begins
to show promise
in unraveling genetic
networks (Segal et
al., 2003). Bioinformatics is used to
study the dynamics
in a cell,
and thus to
simulate the cellular interactions (978 Jian Xue et al.)
Application of Bioinformatics in Agriculture
Plant
life plays important and diverse roles in our society, our economy, and our global
environment. Especially crop is the most important plants to us. Feeding the
increasing world population is a challenge for modern plant biotechnology. Crop
yields have increased during the
last century and will continue to
improve as agronomy
re-assorting the enhanced
breeding and develop new
biotechnological-engineered strategies.
The onset
of genomics is providing massive information to improve crop phenotypes. The accumulation of
sequence data allows
detailed genome analysis
by using friendly database
access and information
retrieval. Genetic and molecular genome co
linearity allows efficient
transfer of data
revealing extensive conservation
of genome organization between species. The goals of genome research are the
identification of the sequenced genes and the deduction of their functions
by metabolic analysis and
reverses genetic screens
of gene knockouts. Over 20% of
the predicted genes occur as cluster of related genes generating a considerable
proportion of gene families. Multiple alignments provides a method to estimate
the number of genes in gene families allowing the identification of previously
undescribed genes. This information enables new strategies to study gene expression
patterns in plants. Available information
from news technologies, as the database stored DNA microarray expression data,
will help plant biology functional genomics.
Expressed sequence tags (ESTs) also give the opportunity to perform
“digital northern” comparison of gene
expression levels providing
initial clues toward unknown regulatory
phenomena.
Crops: -
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.
Insect Resistance: -
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 species 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.
Improve nutritional Quality: -
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.
Poorer soils and Drought Resistant: -
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.
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.
Insect Resistance: -
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 species 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.
Improve nutritional Quality: -
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.
Poorer soils and Drought Resistant: -
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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