Bioinformatics equity. Every person involved in the food system—growers,

Bioinformatics in
Agriculture

ROLE OF BIOINFORMATICS IN AGRICULTURE AND SUSTAINABLE DEVELOPMENT

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Abstract

Bioinformatics is an interdisciplinary area of the science composed of
biology, mathematics and computer science. Bioinformatics is the application of
information technology to manage biological data that helps in decoding plant
genomes. During the last two decades enormous data has been generated in
biological science, firstly, with the onset of sequencing the genomes of model
organisms and, secondly, rapid application of high throughput experimental
techniques in laboratory research. Biological research that earlier used to
start in laboratories, fields and plant clinics is now starts at the
computational level using computers (In-silico) for analysis of the
data, experiment planning and hypothesis development.

Bioinformatics develops algorithms and suitable data analysis tools to
infer the information and make discoveries. Application of various
bioinformatics tools in biological research enables storage, retrieval,
analysis, annotation and visualization of results and promotes better
understanding of biological system in fullness. This will help in plant health
care based disease diagnosis to improve the quality of Plant.

 

 

Introduction

What is sustainable
agriculture?

The goal of sustainable agriculture is
to meet society’s food and textile needs in the present without compromising
the ability of future generations to meet their own needs. Practitioners of
sustainable agriculture seek to integrate three main objectives into their
work: a healthy environment, economic profitability, and social and economic
equity. Every person involved in the food system—growers, food processors,
distributors, retailers, consumers, and waste managers—can play a role in
ensuring a sustainable agricultural system.

 There are many
practices commonly used by people working in sustainable agriculture and
sustainable food systems. Growers may use methods to promote soil
health, minimize water
use, and
lower pollution
levels on the farm. Consumers and retailers concerned with
sustainability can look for “values-based” foods
that are grown using methods promoting farm
worker wellbeing, that are environmentally
friendly, or that strengthen the local economy. And researchers
in sustainable agriculture
often cross disciplinary lines with their work: combining biology, economics,
engineering, chemistry, community development, and many others.
However, sustainable agriculture is more than a collection of practices.
It is also process of negotiation: a push and pull between the sometimes
competing interests of an individual farmer or of people in a community as they
work to solve complex problems about how we grow our food and fiber.

 

 

 

 

 

Sustainable agriculture integrates three
main goals — environmental
health, economicprofitability,
and social and economic equity.

 

 

 

Potential Costs of Modern Agricultural Techniques

Topsoil
Depletion

Groundwater
Contamination

Degradation
of
Rural Communities

Lowered
Conditions
For Farmworkers 

Increased
Production
Costs

 

Why is bioinformatics important?

 

The greatest challenge facing the
molecular biology community today is to make sense of the wealth of data that
has been produced by the genome sequencing projects. Traditionally, molecular
biology research was carried out entirely at the experimental laboratory bench but
the huge increase in the scale of data being produced in this genomic era has
realized a need to incorporate computers into the research process. With the
advent of new tools and databases in molecular biology we are now enable to
carry out the research not only at genome level but also at proteome,
transcriptome and metabalome levels. The challenges faced by the bioinformatics
community today are the intelligent and efficient storage of huge amount of
data generated, and to provide easy and reliable access to this data. Therefore,
incisive computer tools must be developed to allow the extraction of meaningful
biological information.

 

 

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

.

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 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), Triticumaestivum
(wheat) and Zea mays (Maize) are examples of available complete land plant
genomes

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 12. 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.

 

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 .

 

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 .

 

Similarity Searching Tools

 

The exponential growth of genomics is due to computational
challenges of systematically collecting, storing, organizing,
manipulating visualizing and analyzing large amounts of biological
information come from the experiments carried out by the biologists..
Thus, 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 of 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.

 

Soil
Fertilization       

Farmers
can use biochar to make highly effective fertilizer to increase their yields
without purchased chemical fertilizers, saving money and protecting the
environment. Applied to fields, biochar increases soil porosity and water
retention, raises pH, encourages soil life, and improves soil fertility. It
also protects crops against disease, fungi, and insects. Warm Heart field tests
demonstrate that biochar soil amendments outperform synthetic fertilizers in
rice paddies by more than 10% and outperform synthetics by far larger margins
in steep corn fields with highly degraded soils.

 

Improve
Public Health

The
production and use of biochar have major public health benefits. Much attention
is given to the problem of urban air particulate pollution, but little to the
often extreme levels of PM 10 and PM 2.5 air pollution in rural areas, which
actually exceed levels found in urban areas. These particulates result largely
from field burning and most can be eliminated with extensive biochar
production. Poor farmers and agricultural laborers also suffer agro- and
industrial chemical poisoning from pesticide use or farming contaminated land.
(Blood tests of 2,000 people in North Thailand reveal that 100% of rural
residents are at extreme risk – the highest risk level – from pesticide
poisoning.)

The
large-scale use in soil can reduce the bioavailability of poisons,
decontaminate water flows, and help to remove toxins from the food chain.

 

Crop
Rotation

Rule
one of successful sustainable farming: ROTATE YOUR CROPS EVERY SEASON!

Why rotate your crops?

1.     
Because you are smarter than
the bugs! If you change the menu every season, last year’s bugs will always
starve this year while your new crops grow.

2.     
Because different plants
need different nutrients. If you grow the same crops every year, you will
exhaust your soil.

 

So
rotate your crops every planting season. This means, every season, choose a
crop from different family than the crop you planted this season. Never plant
from the same family in the same field one season to the next. Ideally, leave
three seasons between crops from the same family in the same field. You may
download this chart for your personal reference at the bottom of the page.

Families of Common Crops for Rotation

Grass family (Gramineae):

Rice, corn, sugar cane, oats, wheat, and
other cereal crops.

Cabbage family (Cruciferae):

Bok choy, Chinese cabbage and other Asian
greens, broccoli, Brussels sprouts, cabbage, cauliflower, collard, kale,
kohlrabi, mustard, radish, turnip.

Legume family (Leguminosae):

All beans, pulses and peas (long bean,
mung bean), peanuts
Cover
crops such as kudzo, Brazil nut, alfalfa, clovers, and vetch.
Perennials
legume shrubs–rensonii, flemingia. Trees- kha farang, phak krathin, flame
tree.

Allium family (Alliaceae):

Garlic, leeks, onion, shallots

Daisy family (Compositae):

Chamomile, chicory, dandelion, endive,
globe artichoke, Jerusalem artichoke, lettuce, salsify, sunflowers

Carrot or Parsley family (Umbelliferae):

Carrots, celery, celeriac, coriander,
caraway, dill, fennel, parsley, parsnips

Beet family (Chenopodiaceae):

Beet, spinach, Swiss chard, lamb’s
quarters

Gourd family (Cucurbitaceae):

Cantaloupe, cucumber, gourd, calabash,
honeydew, luffa, pumpkin, squash, watermelon

Potato family (Solanaceae):

Potatoes, Tomatoes, Aubergines, Peppers.

 

What Is Sustainable Agriculture?

If
you had to choose, which would you prefer to eat: food that is grown more
naturally or food that is enhanced by spraying it with pesticides or applying
chemical fertilizers Most people would prefer the natural food that is free of
chemicals and artificial enhancements. Unfortunately, the majority of food we
consume is produced using industrialized agriculture, which is a type of
agriculture where large quantities of crops and livestock are produced through
industrial techniques for the purpose of sale. This type of agriculture relies
heavily on a variety of chemicals and artificial enhancements, such as
pesticides, fertilizers, and genetically modified organisms. This type of agriculture
also uses a large amount of fossil fuels and large machines to manage the farm
land. Although industrialized agriculture has made it possible to produce large
quantities of food, due to the negative aspects of this technique, there has
been a shift towards sustainable agriculture.

Sustainable
agriculture is a type of agriculture that focuses on producing long-term
crops and livestock while having minimal effects on the environment. This type
of agriculture tries to find a good balance between the need for food
production and the preservation of the ecological system within the
environment. In addition to producing food, there are several overall goals
associated with sustainable agriculture, including conserving water, reducing
the use of fertilizers and pesticides, and promoting biodiversity in crops
grown and the ecosystem. Sustainable agriculture also focuses on maintaining
economic stability of farms and helping farmers improve their techniques and
quality of life.

There
are many farming strategies that are used that help make agriculture more
sustainable. Some of the most common techniques include growing plants that can
create their own nutrients to reduce the use of fertilizers and rotating crops
in fields, which minimizes pesticide use because the crops are changing
frequently. Another common technique is mixing crops, which reduces the risk of
a disease destroying a whole crop and decreases the need for pesticides and
herbicides. Sustainable farmers also utilize water management systems, such as
drip irrigation, that waste less water.

Benefits of Sustainable Agriculture

There
are many benefits of sustainable agriculture, and overall, they can be divided
into human health benefits and environmental benefits. In terms of human
health, crops grown through sustainable agriculture are better for people. Due
to the lack of chemical pesticides and fertilizers, people are not being
exposed to or consuming synthetic materials. This limits the risk of people
becoming ill from exposure to these chemicals.

 

 

 

 

 

 

 

 

 

 

 

 

References:

1
Untergasser A., Nijveen H., Rao X., Bisseling T., Geurts R. and Leunissen
J.A.M. (2007) Nucleic Acids Research, 35, W71-W74.

 

2
Kumari N., Singh V.K., Narayan O.P., Rai L.C. (2011) Online Journal of
Bioinformatics, 12, 289-303.

 

3
Mahalakshmi V. and Ortiz R. (2001) Electronic Journal of Biotechnology,
3.

 

4
Matthews D.E., Carollo V.L., Lazo G.R. and Anderson O.D. (2003). Nucleic
Acids Research, 31, 183-186.

5
Caetano-Anolles. (2005) Crop Science, 45, 1809-1816.

 

 

 

 

 

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