APPLICATIONS OF BIOINFORMATICS IN AGRICULTURE

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 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.

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 scientist to produce enhanced
species of plants which have drought, herbicide and pesticide resistant in them. Similarly
specific genes can be modified to improve the production of meat and milk. Certain changes
can be made in their genome to make them disease resistant.

Genomics in Agriculture
The sequencing of the genomes of plants and animals will provide enormous
benefits for the agricultural community. Bioinformatics tools can be used to search for the
genes within those genomes that are useful for the agricultural community and to elucidate
their functions. This specific genetic knowledge could then be used to produce stronger, more
drought, disease and insect resistant crops and improve the quality of livestock making them
healthier, more disease resistant and more productive.

Comparative genetics of the plant genomes has shown that the

organization of genes has remained more conserved over evolutionary time than was
previously believed. These findings suggest that information obtained from the model crop
systems can be used to suggest improvements to other food crops. Arabidopsis thaliana
(water cress) Oryza sativa (rice), Triticum aestivum (wheat) and Zea mays (Maize) are
examples of available complete land plant genomes.

CROP IMPROVEMENT:

When evolutionary changes occurred on the plants, their genome remained

conserved and did not provide much information. Since the arrival of bioinformatics tools, it
is possible to extract the required information from the genome of specific plant. There are
two species of food plants, the genomes of which has been mapped completely, for example
Arabidopsis thaliana(water cress) and Oryza sativa(rice).
 Water cress is a small plant which is found on the rocks. Researchers took
interest in its genome because of its smaller genome size and study the plant development
processes. Its genome consist of 5 chromosomes on which 100 Mbp of DNA are distributed.
The understanding about its genes and their expression provides information about the other
plants’proteins and their expression. There are many uses knowing the genome of A.thaliana,
but the major use is that the yield of plants can be increased.

Insect Resistance:

• Genes from Bacillus thuringiensis that can control a number of serious pests have
been successfully transferred to cotton, maize and potatoes.

• This new ability of the plants to resist insect attack means that the amount of
insecticides being used can be reduced and hence the nutritional quality of the crops is
increased.

• By having the genes of bacteria in plant genome, when insects the plant the bacteria
enter into their blood stream and make them starved, ultimately they die.

• The use of Bt genes in the plant genome has made the agriculturist to use insecticides
in a very little amount.

• As a result the productivity and nutritional value of plants will also increase and also
be beneficient to human health.
Improve nutritional quality and growth in poorer soils:
Gene-Diet-Disease interaction of Nutritional genomics aims to study the
susceptible genes and provide dietary interventions for individuals at risk of such diseases.
Scientists have recently succeeded in transferring genes into rice to increase levels of Vitamin
A, iron and other micronutrients. This work could have a profound impact in reducing
occurrences of blindness and anaemia caused by deficiencies in Vitamin A and iron
respectively.

Scientists have inserted a gene from yeast into the tomato, and the result is a plant
whose fruit stays longer on the vine and has an extended shelf life. Bioinformatics play an
important role to detect the metal from Metagenomic sequencing obtains from contaminated
soil. Soil arguably houses the most complex microbial communities because of its ancient
history, complex sets of interrelating gradients, and protective, isolating and relatively
resource poor and stable physical structure. This results in an incredibly diverse set of gene
sequences; at least at the scale soils are normally sampled.

The challenge is no longer sequence yield, but the analysis of those sequences, and
especially so due to the short sequence products of current sequencing technologies. Progress
has been made in developing cereal varieties that have a greater tolerance for soil alkalinity,
free aluminum and iron toxicities.

Transgenic oilseed
Nutritionally improved oils are the goal of transgenic research in canola. Canola is a major
oilseed crop. Transgenic research has focused on improving the
nutritional quality of canola oil by enhancing the Vitamin E content or by modifying the
balance of fatty acids.

Coffee and Tea:

Decaffeinated coffee is now made by coffee bean treatment with organic solvents. These
methods reduce flavour. Genes for caffeine production in coffee beans and Tea leaves
identified. Research is going on to “turn off” these genes. So naturally decaffeinated coffee
and tea with full flavour and aroma can be developed.

Tobacco:
Nicotine-free tobacco is now being grown for introduction of nicotine-free cigarettes.
Previous attempts removed some of the flavor along with nicotine. Genetically engineered
nicotine-free tobacco does not synthesize nicotine in leaf.
Improvement for plant resistance against biotic and abiotic stresses
Application of insect genomics helps in the identification of resistance
mechanisms and finding the novel target sites. Genes from Bacillus thuringiensis that can
control a number of serious pests have been successfully transferred to cotton, maize and
potato. This new ability of the plants to resist insect attack means that the amount of
insecticides being used can be reduced.

A plant’s first line of defense against abiotic stress is in its roots. If the soil
holding the plant is healthy and biologically diverse, the plant will have a higher chance of
surviving stressful conditions. Plants are extremely sensitive to the changes, and do not
generally adapt quickly. Plants also adapt very differently from one another, even from a
plant living in the same area. When a group of different plant species was prompted by a
variety of different stress signals, such as drought or cold, each plant responded uniquely.
Hardly any of the responses were similar, even though the plants had become accustomed to
exactly the same home environment. So, species are more likely to become population
threatened, endangered, and even extinct, when and where abiotic stress is especially harsh.
By using in silico genomics technology researcher can identify defense/ disease resistance
gene-enzyme with their promoter region and transcription factor which help to enhance the
immunity and defence mechanism.

Sequence Analysis:
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 proteins by the
study of the similarities between the compared sequences. Nowadays there are many tools
and techniques that provide the sequence comparisons (sequence alignment) and analyze the
alignment product to understand the biology.

The most commonly used similarity search method is the Basic Local Alignment
Search Tool [BLAST; 30]. BLAST is a heuristic modification of the Smith–Waterman (1981)
algorithm and in practice it is widely used. In BLAST, statistical methods are used to
determine the likelihood of a particular alignment between sequences or sequence regions
arising by chance given the size and composition of the database being searched.

The most popular online interface to BLAST is available at NCBI, where a standalone
version is also available for downloading. There are several parameters controlling the
behaviour of the BLAST algorithm, and these need to be carefully considered. The set of
tools allows us to carry out further, more detailed analysis on our query sequence including
evolutionary analysis, identification of mutations, hydropathy regions, CpG islands and
compositional biases. Sequence alignments are useful in bioinformatics for identifying
sequence similarity, producing phylogenetic trees and developing homology models of
protein structures.

Intelligent technologies in Agriculture

Artificial intelligence (AI) is a branch of computer science and engineering that deals
with intelligent behavior, learning, and adaptation in machines. Intelligent technology is a
kind of artificial simulation, which simulates a human being’s activity of thinking. It is fast
becoming active technique in agro informatics. The term AI was first used by John McCarthy

Eg. of IT are

1. Experts system techniques,

2. Computing intelligence,

3. Machine learning,

The agriculture production system is a giant complex system. It is influenced by soil,

species, climate and many other factors. The application in agriculture domain has broad
prospects

Application of IT
 Irrigation
 Fertilization
 Planting
 Diagnosis and prevention of diseases and insect pests
 Aquaculture
 Machine learning and
 knowledge discover

Robotic Weeding
The vision of the Robotic Weeding project is to develop new weeding measures that can
reduce the manual weeding effort in organic vegetables and beets by 50-100% and reduce
herbicide use in conventional grown row crops by 75-100%, by developing a hybrid system,
which integrates, high-precision seed mapping Computer vision for plant recognition
Advanced tools for weed removal/control

The activities are split in two:

 Development and demonstration of a robot that will establish, care for, survey and/or
harvest the crops according to conventional as well as organic site specific weeding.
 Development of IT-systems for central planning and follow-up on crop related tasks,
as well as IT-systems, that can be used for coordination and optimisation of the
cooperation between manned and unmanned vehicles.
 One way of decreasing labour costs is robotic weed control.
  The machine is adapted from a commercial lawn mower and it is designed to follow a
predefined route and to cut the weeds by means of a rotary cutter that can be moved in
between the trees in the row area.
 Lukas can recognize the difference between crops and weeds and remove
automatically the weeds. It could be used for all vegetables that are grown in rows,
like lettuce, cauliflower, and carrots, or sugar beets, for which it has originally been
designed. This robot is not ready yet to enter the market, but it should greatly benefit
ecological growers by reducing costs and by eliminating the need to find people
willing to do this work.
 The robot functions with the aid of computerized image processing. An infrared
camera is installed on the robot to read the rows. The images are processed using a
specially developed computer program that in turn steers the robot’s wheels and
weeding tool.
 Within the rows, the robot distinguishes between crop and weeds with the aid of
another camera, which takes color images, and a program that analyzes the color and
form of the plants. This method works extremely well under certain conditions, but
the system is susceptible to differences in the appearance of crops. The appearance
can differ considerably within a field and can be influenced by factors such as rain,
wind, and diseases.

Virtual insect modelling system

This project will construct a generic system for expressing models of insect behaviour on and
around plants. It will draw on ideas from the areas of virtual reality, artificial life, robotics,
and individual-based modelling to develop simulation techniques for insect behaviour in an
environment expressed using L-system models of plants and microclimate prediction routines
being developed Major applications will include analysis of fundamental questions
regarding the movement of insects on plants (rigid behaviour versus flexible responses to
plant defences, predators and micro-climate) and how population level phenomena in insects
emerge from the behaviour of individuals.

A virtual plant is NOT just a computer-generated image. Such an image is "a" model in the
sense of being a representation of a plant at particular instant but it is not "the" virtual plant
model which generates a sequence of developmental stages over time.

Milking Robots
The robotic milking machine is an air-hydraulic device equipped with a laser scanner. Once it
detects that a cow has entered the stall, the laser scanner directs the milking cups to the cowís
teats and hydraulically pushes them into place.

The system monitors milk production, then releases when it detects that the cow has
delivered all her milk. The system is linked to a PC and automatically logs in the amount of
milk produced by each cow. It can also be programmed to distinguish between different milk
formulas, such as milk with or without antibiotics, and can separate that milk into different
holding tanks.

While the robotic system operates on a 24 hour-a-day basis, there are about 21 hours of actual
milking time. Three hours are needed for two wash cycles and occasional unscheduled
downtime, for cleaning a dirty laser eye or replacing a hose.

Fruit Picker:
The robot can distinguish between fruit and leaves by using video image capturing. The
camera is mounted on the robot arm, and the colours detected are compared with properties
stored in memory. If a match is obtained, the fruit is picked. If fruit is hidden by leaves, an air
jet can be used to blow leaves out the way so a clearer view and access can be obtained

Robotic mushroom picker: the robot uses a charged coupled camera to spot and select only
mushrooms of the exact size required for picking achieving levels of accuracy far in excess of
human labour.

Sensory response to food texture:

Intelligent technologies for measuring human sensory response to food texture have been
undertaken to study relation between physiological and sensory testing of perception. The
technological mimic of main functions of human olfaction became possible through
Intelligent technology. The original idea pursuing the fabrication of electronic tongue was
found.

Research was focused on the development of quantity and quality automatic conformity
control instruments, method and algorithms at testing and accounting of the agricultural
products.

The electronic tongue or e-nose gives either simple answer like recognizd, ‘good’ or ‘bad’ or
a more sophisticated response such as odour intensity or a molecule concentration. Sensors
are immersed directly into the liquid or into other mediums. In the most generic sense, quality
refers to the combination of characteristics that are critical in establishing a product
consumers acceptability. In the food industry this is usually an integrated measure of taste,
purity, flavour, texture, colour, appearance and workmanship.

“Chernoff faces”, a geometrical deviation analysis method for quality control of agricultural
products also developed for referring standards of indentity.

Therefore many patented technical decisions were developed, measuring methods and
algorithms, also measuring and error correction method for quality conformity assessing of
agricultural products, raw materials and goods.