Biodiversity?

The term biodiversity (from “biological diversity”) refers to the variety of life on Earth at all its
levels, from genes to ecosystems, and can encompass the evolutionary, ecological, and cultural
processes that sustain life. Biodiversity includes not only species we consider rare, threatened, or
endangered but also every living thing—from humans to organisms we know little about, such as
microbes, fungi, and invertebrates.

Biodiversity refers to the various life forms that exist on Earth, including animals,
plants, microorganisms, and the entire ecosystem they live in. It manifests as biological
resources, including genes, species, organisms, and ecosystems.

Thus, the four main levels of biodiversity;

 Species biodiversity
 Genetic biodiversity
 Ecosystem biodiversity
 Global biodiversity

Because of these characteristics, biodiversity plays a fundamental role in maintaining the

aesthetic value and the integrity of the natural environment and helps promote the overall well-
being of all plant and animal life.

1. Genetic Diversity

Genetic diversity encompasses the range of genetic information found in animals,

microorganisms, and plants. A single species of organisms with diverse genetic diversity
portray more adaptability and survival mechanism against adverse environmental conditions
than organisms of a single species with the same genetic makeup.

2. Species Diversity

Species diversity refers to the variety of organisms in the environment. They can be further
subdivided into:

 Species richness is the total number of species in a given region or locality. It is

measured using the Menhink and Mangalet indices.
 Species abundance: This is the sum total of organisms from a given species within a
given area. (the number of individuals per species). When species have equal
abundance, their variation becomes high, which also makes the diversity to be high. A
low diversity scenario is noted when the number of one species is 98 and the other
species 1.
  Taxonomic diversity (Phylogenetic). Taxonomic diversity (TD) is the genetic
relationship between various species groups. This diversity is represented using a
hierarchical classification based on the phylogenetic evolution of different species of
organisms.
 3. Ecosystem Diversity
 It is relatively similar to species diversity except for the fact that it deals with the
variations in ecosystems within a geographical location. From one region or country to
another, there are different ecosystems or biomes, with examples such as alpine
meadows, taigas, wetlands, grasslands, mangroves, and deserts, among others.
 4. Global Diversity
 Global diversity refers to the range of differences that depict the composition of a
group of two or more species in a global context. According to the International Union
for Conservation of Nature (IUCN), there are approximately 1. 5 million
different species of plants and animals spread across the world. 70% represent
animal species, while 22% represent plants.

Importance of Biodiversity
Biodiversity is important to most aspects of our lives. We value biodiversity for many reasons,
some utilitarian, some intrinsic. This means we value biodiversity both for what it provides to
humans, and for the value it has in its own right. Utilitarian values include the many basic needs
humans obtain from biodiversity such as food, fuel, shelter, and medicine. Further, ecosystems
provide crucial services such as pollination, seed dispersal, climate regulation, water purification,
nutrient cycling, and control of agricultural pests. Biodiversity also holds value for potential
benefits not yet recognized, such as new medicines and other possible unknown services.
Biodiversity has cultural value to humans as well, for spiritual or religious reasons for instance.
The intrinsic value of biodiversity refers to its inherent worth, which is independent of its value
to anyone or anything else. This is more of a philosophical concept, which can be thought of as
the inalienable right to exist. Finally, the value of biodiversity can also be understood through the
lens of the relationships we form and strive for with each other and the rest of nature. We may
value biodiversity because of how it shapes who we are, our relationships to each other, and
social norms. These relational values are part of peoples’ individual or collective sense of
wellbeing, responsibility for, and connection with the environment. The different values placed
on biodiversity are important because they can influence the conservation decisions people make
every day.

Threats to Biodiversity
Over the last century, humans have come to dominate the planet, causing rapid ecosystem
change and massive loss of biodiversity across the planet. This has led some people to refer to
the time we now live in as the “anthropocene.” While the Earth has always experienced changes
and extinctions, today they are occurring at an unprecedented rate. Major direct threats to
biodiversity include habitat loss and fragmentation, unsustainable resource use, invasive species,
pollution, and global climate change. The underlying causes of biodiversity loss, such as a
growing human population and overconsumption are often complex and stem from many
interrelated factors.

Development in Biodiversity

The good news is that it is within our power to change our actions to help ensure the survival of
species and the health and integrity of ecological systems. By understanding threats to
biodiversity, and how they play out in context, we can be best prepared to manage conservation
challenges. The conservation efforts of the last decades have made a significant difference in the
state of biodiversity today. Over 100,000 protected areas—including national parks, wildlife
refuges, game reserves, and marine protected areas, managed both by governments and local
communities—provide habitat for wildlife, and help keep deforestation in check. When
protecting habitat is not enough, other types of conservation actions such as restoration,
reintroduction, and the control of invasive species, have had positive impacts. And these efforts
have been bolstered by continuous efforts to improve environmental policies at local, regional,
and global scales. Finally, the lifestyle choices of individuals and communities can have a large
effect on their impacts on biodiversity and the environment. While we might not be able to
prevent all negative human impacts on biodiversity, with knowledge we can work to change the
direction and shape of our effects on the rest of life on Earth.

The Conservation and Biodiversity program amplifies and accelerates transformative societal
change to restore and protect biodiversity. In a future committed to protecting both wildlife and
humanity, this preservation of biodiversity is one of the many solutions to the climate crisis.

All living things have an intrinsic value, and each plays a unique role in the complex web of life.
The rate of extinction can still be slowed. Many of our declining, threatened and endangered
species can still recover if we work together now to build a united global movement of
consumers, voters, educators, faith leaders and scientists to demand immediate action.

The Conservation and Biodiversity program educates and raises awareness about the accelerating
rate of extinction of millions of species and the causes and consequences of this phenomenon.
The program seeks to build a global movement that embraces nature and its values and
encourage individual actions such as adopting plant based diets and stopping pesticide and
herbicide use.

One way the program achieves its goals is through a diverse network of partners. Targeting
boots-on-the-ground activism, the program guides organizations to increase ambition and grow
public participation in species and biodiversity conservation in their respective regions.
Climate change threatens the stability of ecosystems around the world. Nature’s gifts to our
planet are the millions of species that we know and love, and many more that remain to be
discovered. The Conservation and Biodiversity program allows people to explore and connect
with nature around them and helps establish a care ethic to make positive decisions for the
environment.

Biodiversity conservation
Biodiversity conservation relates to the preservation, protection and management of
biodiversity. It is about how resources can be obtained from Sustainable Development. To
demonstrate this, it is crucial to conserve the three primary levels of biodiversity - genetic,
species and ecosystem. Conserving these biodiversity elements can preserve genetic diversity
and utilise species and ecosystems more sustainably.

Human impact on biodiversity

Human impact on biodiversity is significant. Some examples include:

 Deforestation: Cutting down large areas of trees for agriculture and expansion of cities,
along with others.
 Global warming: Greenhouse gases released into the environment cause climate
warming. This occurs due to our use of fossil fuels, agriculture and others.
 Poor waste management: Producing lots of waste which ends up in landfills.
 Water Pollution: Discharge of substances into streams and rivers, which can Lead to
eutrophication (body of water enriched with organic substances).

Importance of Biodiversity Conservation

Definitely, biodiversity conservation comes with numerous benefits. Let’s take a close look at
some of them:

1. Biodiversity Conservation Is Important for Economic Growth and Poverty

Reduction

This argument is based on the numerous direct economic benefits that humans derive from
natural environments, such as food, construction material, fiber, firewood, industrial products,
and medicinal value.

As an example, approximately 25,000 plant species are used by native people to extract
traditional medicine. More than 25% of drugs sold worldwide are derived from plants.
And according to the UN, most of the world’s poor people live in rural areas and depend upon
wetlands, forests, pastures, and water for their livelihoods.

Billions of people worldwide also depend on timber products for income and subsistence. The
national parks and sanctuaries are a source of tourism that amazes people as a source of natural
beauty.

2. Supports the Continuity of Various Ecosystems Globally

Biodiversity plays an essential role in ecosystem rejuvenation and protection. The Amazon
forest, for example, can produce approximately 20% of the total oxygen on Earth through
photosynthesis.

There are also thousands of pollinators, such as insects and birds, and other numerous biological
activities that take place in the forest. If the biodiversity of the forest is conserved, it means the
entire ecosystem that relies on the Amazon forest is equally protected and allowed to rejuvenate.

Other ecosystems like coral reefs, tundra, rivers and streams, and grasslands can also be
supported and protected through biodiversity conservation.

3. Aesthetic Value

The natural environment provides great pleasure to human beings with its shape, structure,
senses, and color, which enriches people’s culture. Activities such as visits to animal parks, bird
watching, nature art, and cultural heritage as ways of enjoying and appreciating nature are only
made possible through biodiversity conservation.

4. Ecological Balance

The integrity of the ecology – the harmonious coexistence of organisms and their environment is
preserved by biodiversity.

Some of the main aspects can be explained through:

 Carbon dioxide and oxygen balance (which helps in addressing the effects of climate
change). The sequential balance between atmospheric carbon dioxide and oxygen is
maintained through biodiversity. Failure to conserve biodiversity leads to the
accumulation of carbon dioxide, resulting in a greenhouse effect and the gradual
depletion of ozone. The results are global warming and natural calamities.
 Biochemical cycles. An example is a hydrological cycle. The availability of biological
resources such as forests and wetlands is vital for biochemical cycles. Lack of these
resources would lead to incomplete cycles and increased incidences of natural calamities
like desertification and species extinction.
 Decomposition. Biodiversity conservation protects decomposers – organisms that aid in
the breakdown of waste organic matter. Decomposition is thus an essential part of the
 food chain as it transforms the waste of dead organic matter, which is then converted into
other biochemicals that are availed for primary producers.
 Climate. The maintenance of the micro, local, or regional climate is determined and
regulated by biodiversity. Biodiversity achieves this by influencing air
turbulence, temperature, and precipitation.

5. Ethical Value for Every Form of Life in The Environment

Ecosystem’s right of an organism states that every form of life in any ecosystem is unique
and deserves respect from human beings. The right suggests that every organism on earth,
whether it is valuable to humans or not, has an inherent right to exist.

Besides, the present generation has a social responsibility towards future generations, including
protecting all living organisms in the world. Through biodiversity conservation, therefore, the
ethics of environmental sustainability and conservation can be encouraged.

6. Ecosystem Services Worth Billions of Dollars

Ecosystem services are processes that biodiversity provides to support human life. Perfect
examples include pollination, decomposition of waste, water purification, renewal of soil
fertility, and moderation of floods.

Ecosystem services can be separated into three categories:

 Provisioning services: These include anything related to the production of renewable

resources, like farming or energy production.
 Regulating services: They encompass anything that lessens environmental change.
 Cultural services: They are anything that provides direct value or enjoyment from
natural resources and beauty.

Unfortunately, ecosystem processes are not generally valued as part of the economy until they
cease functioning. When the economic value is assigned to these services, they are worth billions
of dollars.

For example, insect pollinators help in the production of many commercially important fruits
such as almonds, melons, blueberries, and apples. The global economic value of insect
pollination services has been valued at $217 billion per year.

Similarly, in other ecosystem services, water purification involves filtering rainwater by soil and
microbes that can break down nutrients and contaminants and reduce metal ions, slowing their
spread into the environment. Wetlands and riparian plants absorb nitrogen and trap sediments
that decrease water quality.

As human construction and development disrupt natural environments and all activity and
services related to this environment, we are forced to depend on artificial man-made services like
water filtration using filters and purifiers. These artificial services cost much more, while the
natural ecosystem services are free of cost.

7. Social and Spiritual Benefits

In human history, conservation also means protecting nature for its spiritual gifts and protecting
sacred places in the local landscape. The biodiversity effects on cultural development can be
shown by the heterogeneity of the world’s mythology, folk dances, and folk art, which contribute
to the richness of literature and global arts.

Different landscapes with different cultures influence our language, diet, occupation, and various
types of activity.

The uniqueness of each habitat consists of animals and plants present in each country and state
with their flagship animals and plants. Even during traveling, the sight of biological diversity,
different cultures, and landscapes motivates people.

Ecotourism is traveling with the aim of viewing, supporting, and sustaining the local
cultures and its natural ecosystem. Support from ecotourism can be very helpful to reduce
habitat destruction as well as to preserve endangered species.

Types of biodiversity conservation

There are many ways that you can classify types of biodiversity. There are two main broader
types of biodiversity conservation:

 In-situ: conservation of species in their natural environment.

 Ex-situ: conservation of species out of their natural habitat.

The conservation of biodiversity is a multifaceted process that encompasses sustainable

development. It involves both in-situ and ex-situ conservation approaches.

In situ conservation focuses on preserving and protecting ecosystems to safeguard

overall biodiversity. Conversely, ex-situ conservation steps in when specific organisms
are endangered.

As a result, biodiversity conservation methods aim to achieve preservation, maintenance,

conservation, recovery, and enhancement, as outlined below:
1. Protection Against Degradation and Destruction of Natural Ecosystems

Biodiversity conservation involves promoting a balance between the environment, society,

and development in line with the sustainable development goals. The present society should
develop conservation strategies that meet their need without compromising that of the future
generation.

A balance between the development of the environment and society ensures the achievement
of biodiversity conservation. Through properly enforced policies, sustainable development
can be achieved. Environmental institutions can enforce these conventions.

2. Maintain, Restore, and Increase Ecological Systems While Promoting the

Implementation of Better Conservation Practices

It involves the in-situ and ex-situ methods. In situ conservation involves the
conservation of the whole ecosystem and the natural habitats.

It also includes the maintenance and recovery of various species and degraded ecological
systems, such as damaged forest areas and heavily polluted lakes, rivers, and lands, among
other natural environments.

The ex-situ conservation involves strategically protecting biodiversity hotspots

for endangered species and habitats.

3. Identification and Protection of Endangered Species

Ex-situ biodiversity conservation aims to reduce the ongoing extinction by up to 30% or

higher by mainly focusing on two things.

First is the focus on conserving biodiversity in their natural habitats in places like museums,
arboretums, zoos, and gene banks. High-biodiversity areas should be covered in the form of
natural parks, sanctuaries, biosphere reserves, etc.

The second strategy focuses on captive conservation methods that involve the protection
of endangered species. This type of conservation is a collective responsibility of all nations.
An example is the Earth Summit, held in Rio de Janeiro, asking nations to take
appropriate measures to protect vulnerable habitats and species.

4. Establishing Buffer Zones to Prevent Any Alteration in The Balance of

Natural Ecosystems

Biodiversity conservation prioritizes establishing control measures that maintain the balance
of natural ecosystems, such as water balance, soil ecology, and genetic and species balance.
 It involves intragenerational and intergenerational equity that allows equitable sharing
of resources and the benefits derived from natural habitats to ensure social and
ecological stability.

Some of the conservation efforts that have been advanced under this category include the
World Conservation Union, the International Board for Plant Genetic Resources, and the
UNESCO Program on Man and Biosphere.

5. Science, Technology, and Research-Tools for Conserving Biodiversity

As our society develops, it leads to improved science and technology. Science, specifically
ecology, helps scientists understand the web of interactions in our biomes and pinpoint the
key species in ecosystems. This information is used to guide conservation efforts.

The same is also used to understand pollution and its cascading effects within an ecosystem,
as the Bio-magnification of toxins in a food chain can cause huge problems for top predators.

Technology is becoming vital in conservation biology. Sustainable technologies, like

renewable energies, biodegradable packaging, and recycling, help reduce human impact on
the environment. There are also technologies like cloning that allow scientists to bring back
species that are already considered extinct.

Research on how species interact within their environment is crucial for protecting organisms
and maintaining biodiversity. For example, the use of wildlife corridors in urbanized areas,
forming zoo and botanical gardens for research purposes, and collections of living organisms,
In vitro plant tissue, and microbial culture dramatically increase their populations.

6. Captive Breeding and Gene Banks

When animals are bred in captivity (often at zoos), it is called captive breeding. It
requires the capture of animals that are often near extinction. Captive breeding of animals
and artificial propagation of plants is somewhat controversial; however, on the positive side,
it provides the opportunity to increase the population of the species so that they can be
reintroduced into the wild.

It is very helpful to save a large variety of species of plants & animals in a very small space,
such as sperm and ova banks, and seedbanks.

Seed banks are areas where huge varieties of plant seeds are stored. Seed banks have
been collecting samples for many years, with some storing over 2 billion seeds at a time. If a
species goes extinct in nature, it provides a failsafe. The plant can be grown from saved seed
and reintroduced back into its habitat.

Examples of biodiversity conservation efforts

There are many ways biodiversity can be conserved and improved. These include:
  Reducing deforestation and promoting tree re-planting.
 The utilisation of Renewable Resources and reduction in non-renewable resource use.
 Protected sites such as Ramsar sites (wetlands of importance), National parks and
reserves.
 Protection of endangered species - European Red Lists, Invasive Alien Species,
Pollinators in Europe, Protected Areas and Natura 2000 etc.
 Public awareness by delivering lectures on numerous issues, providing workshops and
educating in schools.
 In everyday life, utilising "reduce, reuse, recycle" - may not look like much on the direct
effect of things. However, items which are thrown away and end up in landfills can often
end up in the ocean.

As well as these, you can join a volunteering organisation where you will directly contribute to
improving habitats or simply not cut the grass in your own garden to increase biodiversity.

PLANT BREEDING CONCEPTS AND

METHODS IN RELATION TO
BIODIVERSITY CONSERVATION

1. Introduction
There are now almost 7.25 billion human beings inhabiting this planet, and it has been projected
that world population growth may exceed 70 million annually over the next 40 years. The world
population will be approximately 9.2 billion in 2050, when the concentration of carbon dioxide
and ozone will be 550 ppm and 60 ppm, respectively and the climate will be warmer by 2ºC [1].
At that time it is expected that approximately 90% of this global population will reside in Asia,
Africa, and Latin American countries [2,3]. Currently, about 1 billion human beings suffer from
hunger; 3 billion malnourished people suffer one or more micronutrient deficiencies (especially
vitamin A, iodine and iron) and live with less than 2 US dollars per day; and anthropogenic
climate change continues to affect food output and quality [4,5]. By 2050, to sufficiently feed all
these people, the total food production will have to increase 60 to 70% to meet a net demand of 1
billion tonnes of cereal for food and to feed, and 200 million tonnes of meat [6-8], depending on
assumptions of population growth, income growth and dietary changes. This projected increase
of global crop demand is partly due to a growing global population, but a larger driver is
increasing global affluence and associated changes in diet due to higher incomes [4,8]. As global
incomes increase, diets typically shift from those comprised of mostly grains, to diets that
contain greater proportion of meat, dairy products, and eggs and more vegetables and fruits [4,8-
10].
In order to meet these demands, global livestock production systems are shifting from using
mostly marginal lands and crop residues to more industrial systems which require less land and
use of higher value feed crops [11,12]. Increasing demand for meat and dairy products is also of
importance to the global environment because their production requires more land, water and
other resources [13-15]. Livestock production is also responsible for other environmental
impacts. Besides livestock production is estimated to be responsible for 18% of total greenhouse
gas emissions [16], and animal products generally have a much higher water footprint than
vegetal products [17].

In 2008, the world’s arable land amounted to 1,386 M ha, out of a total 4,883 M ha land used for
agriculture [18]. Each year, arable and agricultural land is lost due to deforestation, overgrazing,
agricultural activities, gathering and overexploitation for fuel-wood, urbanization and
industrialization. The most direct negative impact of agriculture on biodiversity is due to the
considerable loss of natural habitats, which is caused by the conversion of natural ecosystems
into agricultural land. The arable land is limited. Increases in arable land can only be done by
deforestation. Agricultural production should be increased without further deforestation. This
requires innovation and better technologies, as well as substantial investment, to increase yields
on existing agricultural land.

Climate models predict that warmer temperatures and increases in the frequency and duration of
drought during the twenty-first century will have negative impact on agricultural productivity
[19-24]. For example, maize production in Africa could be at risk of significant yield losses as
researchers predict that each degree-day that the crop spends above 30°C reduces yields by 1% if
the plants receive sufficient water [23]. These predictions are similar to those reported for maize
yield in the United States [25]. Lobell et al. [23] further showed that maize yields in Africa
decreased by 1.7% for each degree-day the crop spent at temperatures of over 30°C under
drought. Wheat production in Russia decreased by almost one-third in 2010, largely due to the
summer heat wave. Similarly, wheat production declined significantly in China and India in
2010, largely due to drought and sudden rise in temperature respectively, thereby causing forced
maturity [26]. Warming at +2°C is predicted to reduce yield losses by 50% in Australia and India
[27,28]. Likewise, the global maize and wheat production, as a result of warming temperatures
during the period of 1980 to 2008, declined by 3.8% and 5.5%, respectively [24]. So climate
change poses a serious threat to species fitness [29,30], and to agro-ecosystems essential to food
production [31].

Climatic variation and change are already influencing the distribution and virulence of crop pest
and diseases, but the interactions between the crops, pests and pathogens are complex and poorly
understood in the context of climate change [32]. We will need to integrate plant biology into the
current paradigm with respect to climate change to succeed in defeating emerging pests and
pathogens posing a new threat to agriculture due to climate change [33-35].

In this context we can ask: can we feed and clothe the growing world population while
simultaneously preserving or improving ecosystems and the natural environment?

History shows that modern agriculture has the potential to feed the world population but also to
be worst and even catastrophically with the natural environment. Some examples are
deforestation, overgrazing and erosion, in many parts of the world, which contributed to the
outright collapse of ecosystems. One classical example is Madagascar's central highland plateau
that has become virtually totally barren (about ten percent of the country), as a result of slash-
and-burn deforestation, an element of shifting cultivation practiced by many natives.
Intensification of production systems have also led to reduction in crop and livestock
biodiversity, and increased genetic vulnerability and erosion. In contrast, the “Green
Revolution”, which began providing high-yielding crop cultivars and high-input management
techniques to developing countries in the 1960s, has prevented mass starvation and improved
living standards throughout the world [36]. Dwarfing, photoperiod insensitive genes and host
plant resistance genes to pathogens and pests were bred for various crops during the "Green
Revolution" [37]. Crop yields were increased in many nations of Asia and Latin America by
innovations of the “Green Revolution”. Calorie consumption would have dropped by about 5%
and the number of malnourished children would have increasing by at least 2%; i.e., the "Green
Revolution" helped to improve the health status of 32 to 42 million pre-school children. Since
the beginning of the "Green Revolution" in 1960, land devoted to crops increased some 10%,
land under irrigation has doubled, pesticide use by agriculture has tripled, fertilizer use is up 23-
fold, pesticide use is up by a factor of 53. Nowadays, forty per cent of crop production comes
from the 16% of agricultural land that is irrigated. Irrigated lands account for a substantial
portion of increased yields obtained during the "Green Revolution". The enhancement of yield
achieved in the "Green Revolution" (29% in food supplies per capita since 1960) may have been
associated with an increased level of greenhouse gas emissions associated with higher fertilizer
production and application, but, overall, its net effect has been calculated to have reduced CO 2
emission by some 161 gigatons of carbon (GtC) over the period 1961-2005 [38], implying that
gains in crop productivity can make a positive contribution to reducing greenhouse gas
emissions.

Developing sustainable agriculture in environmentally sensitive systems is the great challenge of

the coming decades. More food, animal feed, fiber, fuel, and forest products must be produced
with less available land, water, and nutrients, to meet basic human needs and improve the
sustainability of production [39]. In addition, pressure from an increasing global human
population will necessitate more efficient and diversified land use.

Identifying the most appropriate technologies and practices to achieve these objectives are
critical. This requires the building of a knowledge base to support such tasks. Agro-ecological
approaches are known to increase farming system productivity, to reduce pollution, and to
maintain biodiversity through careful management of soil, water, and natural vegetation. The
agenda for a new “Green Revolution” needs to consider new approaches to promote innovations
in plant science, agricultural and management practices and benefits to farmers and consumers.

Modern production agriculture in the developed world is highly industrialized. There is

considerable discussion about the inadequacy of the dominant model of agricultural
intensification and growth, which relies on increased use of capital inputs, such as fertilizer and
pesticides [40]. Technology and purchased inputs, e.g. fertilizer, pesticides and water are
required to maintain high levels of production, and use of these inputs continues to increase in
the developing world. Despite the critical need for agricultural production and continued
improvements in management practices, current systems are still not in “harmony” with the
environment because they can create many problems for ecosystems and human communities.
The generation of unacceptable levels of environmental damage and problems of economic
feasibility are cited as key problems with this model of industrial agriculture [39,41]. Specific
external costs of industrial agriculture which should be improved include soil deterioration,
erosion, declining surface water and groundwater quality, limited recycling of nutrients,
excessive use of off-farm fertilizers and pesticides, diminished biodiversity within the
agricultural system (both in terms of the variety of crops sown and coexisting species), lapses in
food safety, and the loss of rural employment. By developing new field crops, and trees that meet
societal needs, plant breeding plays a distinctive and crucial role in addressing these challenges,
which must be dealt with immediately to develop sustainable agronomic systems for the future.

In this article two general ways are described in which plant breeders can engage in
environmental issues: i) by breeding plants that are better adapted to environment and
environmental stresses, producing more with less and where productivity can be maintained in
the face of increasingly variable weather patterns and sub-optimal conditions, as well as pest and
disease pressures; and ii) by breeding plants that can alter and “improve” environments, as
breeding alternative crops and crops for new uses or breeding for local adaptation and
sustainable solutions. Previously, the concepts of crop biodiversity, soil biodiversity and agro-
biodiversity were briefly presented.

2. Crop biodiversity, soil biodiversity and agro-biodiversity

2.1. Crop biodiversity

Today, 150 plant species (out of 250,000 known plant species) dominate the world’s agricultural
landscapes, but only 12 crop species provide 80% of the world’s food chain [42]. Three main
cereals: wheat, rice and maize, provide about 50% of the energy we obtain from plants.

The wise use of crop genetic diversity in plant breeding can contribute significantly to protect the
environment. A major role of genetic resources will be to provide germplasm resistant to pests
and diseases, more efficient in their use of water and nutrients and less dependent on external
inputs to maintain current levels of productivity. Natural genetic diversity is becoming
increasingly important to understanding the ways in which we can improve plant breeding. There
is a continuing need to assemble and screen germplasm strategically and discover new sources of
variation that will enable developing new crop cultivars. Complex traits can be improved
dramatically by bringing novel alleles from diverse ecotypes into breeding material.

Crop genetic biodiversity is considered a source of continuing advances in yield, disease and pest
resistance, and quality improvement. It is widely accepted that greater varietal and species
diversity would enable agricultural systems to maintain productivity over a wide range of
conditions. The loss of biodiversity is considered one of today’s most serious environmental
concerns. In the last 50 years vegetable genetic resources have been lost, on a global scale at the
rate of 1-2% per year [43] and it has been estimated by FAO that 6% of wild relatives of cereal
crops (wheat, maize, rice, etc.) are under threat as well as 18% of legume species, and 13% of
solanaceous [44].
There is a growing world-wide awareness about the need to conserve plant germplasm for the
use of future generations. Consequently, considerable media attention has been given to the
creation of the Svalbard Global Seed Vault (see http://www.croptrust.org/main) and relates to
storage of seeds of many economically important crops [3,45]. Gene banks are crop genetic
diversity reservoirs and sources of alleles for sustainable genetic enhancement of crops [46].
Indeed breeding gains depend on capitalizing on the useful genetic variation present in the crop
gene pools, which for many crops is being conserved in gene banks. There are about 1,700 gene
banks and germplasm collections around the world (the number in FAO's database). They
maintain about 7.4 million accessions of plant genetic resources, with cereals and legumes
constituting 52% of the accessions [47]. The CGIAR consortium holds about 0.7 million
accessions of 3,446 species from 612 genera. The International Crops Research Institute for the
Semi-arid Tropics (ICRISAT) possesses one of the largest gene banks in the world with
approximately 115,000 accessions of cereals (sorghum, millets) and legumes (chick-pea,
groundnut, pigeon-pea) [48]. In spite of these large collections maintained ex situ, there are still
important collection gaps that must be addressed before these priceless genetic resources are lost
as a result of climate change or other driving forces leading to the genetic erosion and loss of
biodiversity [47,49]. These ex situ collections are to a large extent safe from the adverse impact
of climate change.

Ex situ collections should be subjected to phenotypic, disease resistance and molecular

characterization to facilitate the potential use of this genetic endowment for the amelioration of
crops. Plant breeders seldom access accessions from some gene banks with large collections. A
systematic assessment of the genetic diversity in such collections has helped to establish core
collections, which should be subsets of large collections [50-52], containing chosen accessions
that capture most of the genetic variability in the entire collection. A core collection therefore
improves the management and utilization of a germplasm collection. Genetic studies in selected
crops have shown that both common widespread and localized alleles occurring in the entire
collection are contained in the core collection subset. Only rare localized alleles may be excluded
during the aforementioned sampling process. The core collection subset often provides an entry
point to the entire collection for further investigation of the genetic diversity or for the utilization
of these resources. Core collections which are a priori selected by the curator are often of limited
use to those users of the gene bank germplasm collection who are interested in specific trait or
domain. The current revolution in information technology makes it possible for users to make
such selections themselves directly on the Worldwide Web using a stratified sampling in the
domain(s) of interest. This approach allows a more focused selection of the germplasm
accessions which shows variation for the trait of interest to the user compared with the use of
core collections. These smaller core collections are sometimes enough to capture most of the
useful variations.

Research undertaken on the large global collection of sorghum landraces and genetic stocks held
at ICRISAT (in excess of 35,000) demonstrates how the challenge of maintaining a large number
of accessions and the related information documented for this collection can be addressed by
gene bank curators. Different sampling strategies were proposed to obtain core collection subsets
of reduced size [53]. Three core collections subsets were established following: i) a random
sampling within a stratified collection (logarithmic strategy); ii) non-random sampling based
upon morpho-agronomic diversity (principal component score strategy); and non-random
sampling based upon an empirical knowledge of sorghum (taxonomic strategy). These core
collections subsets did not differ significantly in their overall phenotypic diversity according to
principal component representation of the morpho-agronomic diversity using the Shannon-
Weaver diversity indice. But when comparisons for morpho-agronomic diversity and passport
data were considered, the principal component strategy subset looked similar to the entire
landrace collection. The logarithmic strategy subset showed differences for characters associated
with the photoperiod reaction that was considered in the random sampling stratification of the
collection. The taxonomic strategy subset was the most distinct subset from the entire landrace
collection. It represented the landraces selected by farmers for specific uses and covered the
widest range of geographical adaptation and morpho-agronomic traits.

In the same sorghum landraces collection of ICRISAT, partial assessment of host response to
five sorghum diseases provided another means to quantify the importance of agro-biodiversity in
resistance [54]. Frequency distributions of host response to major sorghum pathogens were the
same between the entire collection and core collection subsets for all diseases, except between
the entire collection and the logarithmic core subset for grain mold. This was not surprising
because the sampling strategy for this core subset and the material included in the screening for
this disease did not match. The logarithmic core subset had the widest range of adaptation to
photoperiod whereas only photoperiod insensitive germplasm had been screened for grain mold.
The lack of accessions that fall in the highest resistance class for some diseases in the core
subsets is the result of sampling statistics, but the χ 2 tests for homogeneity clearly confirmed that
the entire collection and the core subsets included the same distribution of variation with only the
above stated exception for grain mold in the logarithmic strategy core subset. New accessions
with high resistance to specific diseases are likely to be identified by completing the screening of
the core subsets. This rational, targeted approach may also be cost-effective and more precise
than long term screening of the entire collection. Furthermore this analysis also shows that large
sample sizes do not appear to always be associated with capturing useful variation for disease
resistance (i.e., entire vs. core collections), neither when the sampling was defined by breeding
objectives (like the logarithmic strategy subset), a mirror of the entire collection (principal
component score strategy subset) or by maximizing farmer's landraces (taxonomic strategy
subset).

The latest database on world plant genetic resources highlighted that there are still large gaps,
more specifically in crop wild relatives and landraces, in ex situ gene bank collections preserved
across the globe [55]. Unlike cultivated germplasm, there are difficulties associated with ex situ
conservation of crop wild relatives due to their specific crop husbandry, tendency for natural pod
dehiscence, seed shattering and seed dormancy, high variability in flowering and seed
production, and rhizomatous nature of some of the species. Crop wild relatives have contributed
many agronomically beneficial traits in shaping the modern cultivars [56], and they will continue
to provide useful genetic variations for climate-change adaptation, and also enable crop genetic
enhancers to select plants which will be well-suited for the future’s environmental conditions
[57]. There is a growing interest that crop wild relatives should be preserved in situ in protected
areas to ensure the evolutionary process of wild species contributing new variants, which as and

agricultural production [58]. Worldwide, there are 76,000 protected areas, spread in ∼17 million
when captured by plant explorers, should be able to contribute to addressing new challenges to

km2, and several countries have taken initiatives to establish crop wild relative’s in situ
conservation [59-61]. Promoting in situ conservation may allow genes to evolve and respond to
new environments that would be of great help to capture new genetic variants helping to mitigate
climate-change impacts [62].

2.2. Soil biodiversity

Biodiversity and soil are strongly linked, because soil is the medium for a large variety of
organisms, and interacts closely with the wider biosphere. Soil biodiversity exceeds the
aboveground systems biodiversity, and is crucial for the sustainability of agro-ecosystems [63]. It
consists of macrofauna or soil engineers (earthworms and termites), mesofauna (microarthropods
such as mites and springtails), microfauna (nematodes and protozoans), and microflora (bacteria
and fungi). The soil organisms perform a number of vital functions such as: i) decomposition and
degradation of plant litter and cycling of nutrients; ii) converting atmospheric nitrogen into
organic forms (immobilization) and remineralization of mineral nitrogen, leading to the
formation of gaseous nitrogen; iii) suppression of soil pathogens through antagonism; iv)
regulating microclimate and local hydrological processes; v) synthesizing enzymes, vitamins,
hormones, vital chelators and allelochemicals that regulate population and processes; vi) altering
soil structure and other soil physical, chemical and biological characteristics; and vii) microbial
exudates have a dominant role in the aggregation of soil particles and the protection of carbon
from further degradation [64,65]. Biological activity helps in the maintenance of relatively open
soil structure; it facilitates decomposition and its transportation as well as transformation of soil
nutrients. It is not surprising that soil management has a direct impact on biodiversity. This
includes practices that influence global changes, soil structure, biological and chemical
characteristics, and whether soil exhibits adverse effects such as soil acidification.

Soil acidification has an impact on soil biodiversity. Roem and Berendse [66] in the Netherlands,
examined the correlation between soil pH and soil biodiversity in soils with pH below 5 in
grassland and heath land communities. A strong correlation was discovered, wherein the lower
the pH the lower the biodiversity. Soil acidification reduced the numbers of most macrofauna
and affected rhizobium survival and persistence. So extremely low pH soils may suffer from
structural decline as a result of reduced microorganisms. This brings a susceptibility to erosion
under high rainfall events, drought, and agricultural disturbance.

Land use pattern, plant diversity, soil desertification and pollution, including those resulting from
N enrichment, alter soil biodiversity [67-69]. The changes in soil biodiversity are also observed
through effects on soil organisms as a result of the changes in temperature and precipitation and
through climate-driven changes [like rising atmospheric/ambient CO 2 (hereafter aCO2) and
warming] in plant productivity and species composition.

Accumulated evidence so far reveals that soil biota is vulnerable to global changes and soil
disturbance. Castro et al. [70], in a multifactor climate change experiment, reported increased
fungal abundance in warmed treatments, increased bacterial abundance in warmed plots with
elevated atmospheric CO2 (hereafter eCO2) but decreased in warmed plots under aCO 2, changes
in precipitation altered the relative abundance of proteobacteria and acidobacteria where
acidobacteria decreased with a concomitant increase in the proteobacteria in wet relative to dry
treatments, altered fungal community composition due to the changes in precipitation, and
differences in relative abundance of bacterial and fungal clones varied among treatments. All
these observations led the researchers to conclude that climate change drivers and their
interactions among them may cause changes in the bacterial and fungal abundance, with
precipitation having greater effect on the community composition.

Dominique et al. [71] in their research, where the influence of plant diversity and eCO 2 levels on
belowground bacterial diversity were analyzed observed that the variability in plant diversity
level had significant effects on bacterial composition but no influence on bacterial richness. This
research therefore suggests that the soil microbial composition is mainly related to plant
diversity, assuming that different plant species might harbor specific rhizospheric microbial
populations, rather than altered soil carbon fluxes induced by eCO 2 which can lead to increased
photosynthesis. Bardgett [72] points out there is sufficient evidence to show that the transfer of
carbon through plant roots to the soil plays a primary role in regulating ecosystem responses to
climate change and its mitigation.

Very little is known about the influence of eCO 2 on the structure and functioning of below
ground microbial community. In a 10-year field exposure of a grassland ecosystem to eCO 2,
Zhili et al. [73] detected a dramatic alteration in the structure and functional properties of soil
microbial communities. They found the total microbial and bacterial biomass significantly
increased under eCO2, while the fungal biomass remained unaffected. Furthermore, the structure
of microbial communities was markedly different between aCO 2 and eCO2. More recently, using
tag-encoded pyrosequencing of 16S rRNA genes, Deng et al. [74] also found that the soil
microbial community composition and its structure were significantly altered under eCO 2. In
both studies, the changes in microbial structure were significantly correlated to soil moisture, soil
status relative to C and N contents, and plant productivity.

2.3. Agro-biodiversity

Agro-biodiversity is the result of the interaction between the environment, the variety and
variability of animals, plants and microorganisms that are necessary for sustaining key functions
of the agro-ecosystem, and the management systems and practices. It is the human activity of
agriculture which shapes and conserves this biodiversity.

Agro-biodiversity consists of the genetic diversity within the species, the species diversity, and
the ecosystem diversity, which comprises the variation between agro-ecosystems within a region.

There are several distinctive features of agro-biodiversity, compared to other components of

biodiversity: i) agro-biodiversity is actively managed by farmers and would not survive without
this human interference; ii) due to the degree of the human management and interference,
conservation of agro-biodiversity in production systems is inherently linked to sustainable use;
iii) many economically important agricultural systems are based on ‘alien’ livestock and crop
species introduced from elsewhere; iv) in regards to crop diversity, diversity within species is at
least as important as diversity between species; and v) as stated before in industrial-type
agricultural systems, much crop diversity is now held ex situ in gene banks or breeders’ materials
rather than on-farm.
Agro-biodiversity provides the main raw material for intensifying sustainable crop yields and for
adapting crops to climate change, because it can provide traits for plant breeders and farmers to
select input-efficient, resilient, climate-ready crop germplasm and further release of new
cultivars. Agro-biodiversity is crucial to cope with climate changes as the entire diversity of
genes, species and ecosystems in agriculture represents the resource base for food [58]. Many
farmers, especially those in environments where high-yield crop cultivars and livestock races do
not prosper, rely on a wide range of crop and livestock types. This is the best method for
increasing the reliability of food production in the face of seasonal variation. Diversified
agricultural systems not only render smallholder farming more sustainable, but also reduce the
vulnerability of poor farmers since they can minimize the risk of harvest failures caused by the
outbreak of diseases and pests, by droughts or floods, or by extremely high temperatures, all of
which will be exacerbated by climate change [75].

Monoculture means growing a single plant species in one area. Monoculture however should not
be regarded as synonymous to a single crop cultivar in a farmers’ field since monoculture can
present intra-specific genetic diversity. For instance, a crop under monoculture can be a mixture
of distinct cultivars or landraces having genetic variation within each population. Intra-specific
crop diversification can provide a means of effectively controlling diseases and pests over large
areas and therefore contribute to sustainable intensification of crop production. Nonetheless, an
agro-ecosystem with many species of different taxa will be richer in species diversity than
another agro-ecosystem where many species of the same taxon occur. Genetically diverse
populations and species-rich agro-ecosystems may show greater buffer potential to adapt to
climate change. Agro-biodiversity at the gene, species and agro-ecosystem levels increase
resilience to the changing climate. Promoting agro-biodiversity remains therefore crucial for
resilience of agro-ecosystems.

There is much evidence that global agriculture would benefit from an intensified utilization of
existing biodiversity. We need to shift the focus of agricultural research from genes alone to
management and their interactions. There is much to be gained with mixed cropping, as shown in
a study performed by Tilman et al. [76], where plots with 16 species produced 2.7 times more
biomass than monocultures. Bullock et al. [77] in comparing meadows with different number of
species, found, after 8 years experiment, that the richer meadows yielded 43 % more hay than
species-poor fields. Increased grassland diversity promotes temporal stability at many levels of
ecosystem organization [78]. Mixtures of barley cultivars in Poland generally out-yielded the
means of cultivars as pure stands [79]. The highly intensive agricultural system of home gardens
are some of the most diverse production systems in the world and also some of the most
productive [80,81]. Agro-biodiversity in home gardens reduces year-to-year variation, thus
contributing to stability in yield. Although they are usually highly labor intensive and small, they
provide income and nutrition for millions of small farmers throughout the world.

3. Plant breeding, agriculture and environment

3.1. Introduction

Farming and plant breeding have been closely associated since the early days when crops were
first domesticated. The domestication of staple crops, for example, rice and soybean in eastern
Asia; wheat in the Middle East; sorghum in Africa; and maize, beans, and potatoes in the
Americas [82], began independently, in multiple locales, 5000-12 000 years ago [82]. For
thousands of years, these crops were grown and morphologically altered by farmers, who
selected the most desirable and adaptable cultivars to plant in the next growing season. Without
understanding the science behind it, early farmers saved the seed from the best portion of their
crop each season. Over the years, they selected the traits which they liked best, transforming and
domesticating the crops they grew.

After the discoveries of Darwin and Mendel, scientific knowledge was applied to plant breeding
in the late 1800s [36]. Commercial hybridization of crop species began in the United States in
the middle of the 1920s with sweet corn and followed by onions in the 1940s [4]. With the
implementation of hybrid crop breeding, yield per unit land area rapidly increased in the United
States [83] and since that time, public and private breeding companies have been placing more
and more emphasis on the development of hybrids, and many species have been bred as hybrid
cultivars for the marketplace. Besides heterosis, hybrids also allow breeders to combine the best
traits and multiple disease and stress resistances. Furthermore, if the parents are homozygous, the
hybrids will be uniform, an increasingly important trait in commercial market production. The
creation of hybrid cultivars requires homozygous inbred parental lines, which provide a natural
protection of plant breeders’ rights without legal recourse and ensure a market for seed
companies.

In the 1970’s breeders’ rights protection has been provided through International Union for the
Protection of New Varieties of Plants (UPOV), which coordinates an international common legal
regime for plant variety protection. Protection was granted for those who develop or discover
cultivars that are new, distinct, uniform, and stable [84]. Cultivars may be either sexually or
asexually propagated. Coverage for herbaceous species is 20 years. Protective ownership was
extended by UPOV in 1991 to include essentially derived cultivars [84]. At the same time, the
farmer’s exemption (which permitted farmers to save seed for their own use) was restricted;
giving member states the option to allow farmers to save seed. Additionally, in Europe after
1998 and the United States after 2001, plant breeding companies can take advantages of patent
laws to protect not only the cultivar itself but all of the plant’s parts (pollen, seeds), the progeny
of the cultivar, the genes or genetic sequences involved, and the method by which the cultivar
was developed [85]. The seed can only be used for research that does not include development of
a commercial product i.e., another cultivar, unless licensed by the older patent. The patents are
considered the ultimate protective device allowing neither a farmer’s exemption nor a breeder’s
exemption (that permitted the protected cultivar to be used by others in further breeding to create
new cultivars) [86]. The use of patents for transgenic crops introduces additional problems
according to the IAASTD report [41] developed with the contribution from 400 scientists around
the world, and adopted by 58 governments. In developing countries, especially instruments such
as patents may boost up costs and restrict experimentation by individual farmers whereas
potentially undermining local practices for securing food and economic sustainability. Thus,
there is particular concern regarding present intellectual property rights instruments, which may
inhibit seed-saving, exchange, sale, and access to proprietary materials of vital importance to the
independent research community, specifically in view of the need for analyses and long term
experimentation on climate change impacts [84,85].
Research and development (hereafter R&D) for improved seed development is expensive. Such
product protection has presented a business incentive to corporations to invest in the seed
industry, which supported an enormous increase in private R&D leading to strong competition in
the marketplace between the major seed companies. The majority of current crop cultivars sold
nowadays are proprietary products developed by private R&D. A significant consequence of this
increase in R&D has been a reduction in public breeding programs. As a result, the cost for R&D
to develop new crop cultivars is shifting from the publicly supported research programs to the
customers of the major seed companies [4,87].

One of the main factors to determine success in plant breeding is crop biodiversity and genetic
capacity. Access to genetic variation, biodiversity, is required to achieve crop cultivar
improvement. No practical breeding program can succeed without large numbers of lines
(genotypes) to evaluate, select, recombine and inbreed (fix genetically). This effort must be
organized in order for valid conclusions to be reached and decisions to be made. Scientists,
breeders, support people and facilities, budgets, and good management are requirements to
assure success in the seed business. Science must be state-of-the-art to maximize success in a
competitive business environment. The continued need for fundamental breeding research is
critical to support development of new technology and expansion of the knowledge base which
supports cultivar development, competition among proprietary cultivar results in owner-
companies striving to do the best possible research to develop their own products and to compete
on genetic and physiological quality of crop seed in the marketplace. Reasonable profit margins
are essential to pay back the R&D costs to the owner and to fund future research on developing
even better crop cultivars to stay competitive. There is considerable genetic variation within the
numerous crop species, which can be exploited in the development of superior proprietary
cultivars. The consequences of this dynamic situation will mean relatively short-lived cultivars
replaced by either the owner of the cultivar or a competitor seed company. This intense
competition means constantly improved and more sophisticated cultivars. Seed companies are in
the business of manipulating genes to improve plant cultivar performance for a profit. The
success of the research is judged by the success of the product in making a reasonable profit. The
research must improve economic performance starting with the seed production costs and
including the farmer-shipper/processor and the end user. If any link in this sequence of events is
weak or broken, the new cultivar will likely fail [4,88].

Modern plant breeding is the science of improving plants to achieve farmer needs and better fit
production environments, but it is a long-term proposition. Each released cultivar represents a
culmination of a decade or more of work, from initial crosses through final testing. The rate of
improvement is a function of the amount of heritable genetic variation present in a population,
the time it takes to complete a breeding cycle (from seed production through selection to seed
production again), which can range from multiple generations per year (e.g. maize on field sites
in both hemispheres) to decades (some trees require 8 years of growth before flowering). In
hybrid crops, several years (multiple breeding cycles) are necessary to develop inbred lines that
must then be tested in hybrid combinations. Many years of testing under various environmental
conditions must be conducted to ensure that the new cultivar (inbred, hybrid, or population) will
perform well for the farmer, consumer, or end-user before any substantial additional investment
is made to increase production and distribution of the cultivar.
Biotechnology is a new and potentially powerful tool that has been added by all the major seed
corporations to their crop breeding research programs, and is part of an ongoing public research
for developing genetic engineered crop projects. It can augment and/or accelerate conventional
cultivar development programs through time saved, better products, and more genetic
uniformity, or achieve results not possible by conventional breeding [89]. Genetic engineering
provides innovative methods for modern plant breeding to adapt crops to agricultural systems
facing new challenges brought by the changing climate. New breeding methods, relying on
genetic engineering, can accelerate the pace to improve crops, or be more precise in transferring
desired genes into plant germplasm. Some limited target traits already available in transgenic
cultivars include those adapting agriculture to climate change and reducing their emissions of
greenhouse gases.

Plant breeding may benefit from recent advances in genotyping and precise phenotyping, and by
increasing the available agro-biodiversity through the use of genomics-led approaches. Today
marker-assisted breeding is applied to a broad range of crops and could facilitate domesticating
entirely new crops. Marker-assisted selection is particularly important for improving complex,
quantitatively inherited traits that alter yield, and for speeding up the breeding process [90]. Crop
genomics has also been improving in the last decade and today there are faster and cheaper
systems being increasingly used in gene banks, genetic research and plant breeding, e.g. for
studying interactions between loci and alleles such as heterosis, epistasis and pleiotropy, or
analyzing genetic pathways. Advances in crop genomics are providing useful data and
information for identifying DNA markers, which can be further used for both germplasm
characterization and marker-assisted breeding. Genomics- assisted breeding approaches along
with bioinformatics capacity and metabolomics resources are becoming essential components of
crop improvement programs worldwide [84,91].

Progress in crop genome sequencing, high resolution genetic mapping and precise phenotyping
will accelerate the discovery of functional alleles and allelic variation associated with traits of
interest for plant breeding. Genome sequencing and annotation include an increasing range of
species such as wheat, rice, maize, sugarcane, potato, sorghum, soybean, banana, cassava, citrus,
grape, among other species. Perhaps, one day further research on the genome of a plant species
from a drought-prone environment may assist in breeding more hardy and water efficient related
crops due to gene synteny.

Transgenic breeding involves the introduction of foreign DNA. While conventional plant
breeding utilizing non-transgenic approaches will remain the backbone of crop improvement
strategies, transgenic crop cultivars should not be excluded as products capable of contributing to
development goals. Available commercial transgenic crops and products are at least as safe in
terms of food safety as those ensuing from conventional plant breeding [89,92-94].

The use of transgenic crops remains controversial worldwide after almost two decades of
introducing them into the agro-ecosystems. Using plant-derived genes to introduce useful traits
and plant-derived promoters, may overcome some concerns about the development of genetically
engineered crops. In this regard, cisgenesis addresses some negative views regarding the use of
genes from non-crossable species for breeding crops. Cisgenesis involves only genes from the
plant itself or from a crossable close relative, and these genes could also be transferred by
conventional breeding methods. Crop wild relatives are therefore a valuable source of traits for
cisgenesis.

Plant breeders need to understand the various valuation strategies very early in the breeding
process if they are to direct long-term selection toward reducing agriculture’s negative
environmental impacts and achieving greater sustainability while maintaining productivity.
Regardless of method, breeding objectives can be broadened to include traits which reduce the
environmental footprint of traditional production systems (e.g. nutrient and water use efficiencies
that reduce off-farm inputs), to adapt crops to new climates, to host plant resistance to tackle old
and emerging pathogen epidemics, or new cultivars for new production systems (e.g. perennial
polycultures that mimic the biodiversity of natural systems), albeit with some reduction in rate of
gain for the traditional agronomic traits of interest. Interdisciplinary crop improvement strategies
accounting for ecological, socio-economic and stakeholder considerations will help identify traits
leading to plant cultivars using fewer inputs, less land, and less energy, thereby resulting in a
more sustainable agricultural ecosystem.

The impact of breeding on crop production is dependent upon the complex relationships
involving the farmers, the cultivars available to them, and the developers of those cultivars.
Farmers consist of commercial producers with varying size land holdings ranging from
moderately small farms to very large ones, and subsistence farmers with small farms often on
marginal lands. The subsistence farmers are usually poor. Several types of cultivars are available.
The least sophisticated in terms of methods of development are landraces, also known as local
cultivars. Modern cultivars consist of development by crossing and selection alone, those
developed by crossing and selection with specific important improvements are often obtained
from crosses with wild species or by transgenic methods, and F 1 hybrids between desirable
inbred lines. The developers of landraces are usually farmers themselves, and are obtained by
repeated simple selection procedures of generation after generation. Improved cultivars and
hybrids are created either by public sector breeders or seed companies.

Nearly 70% of the world's farmers, from 570 million world exploitations, are small/subsistence
and poor farmers. They feed 1,5 billion of the world's population. So they are also a key for
biodiversity and for improving the sustainability. For these farmers improved cultivars, hybrids
or transgenic seeds tend to be riskier than landraces, since the higher costs associated with seeds
and production impose a greater income risk. The lack of capital available denies them the
opportunity to invest in production inputs. Small farmers may have lower production costs with
landraces because they achieve adequate yields with fewer inputs. In addition, profits from
improved hybrid or transgenic cultivars tend to be more variable. Yields are often higher but
market prices tend to be inconsistent. For example in India states of Andhra Pradesh and
Maharashtra, farmers have been promised higher yields and lower pesticide costs when using Bt
cotton, thus they acquired loans to afford the costly seeds (Monsanto has control over 95 % of
the Indian Bt cotton seed market and this near monopoly has resulted in great increased prices).
When, in many cases, the farmers found the yields failed to meet their expected result, the
consequences were usually very serious and many farmers died by committing suicide over the
past 15 years, perhaps due to this reason. This situation of using Bt cotton seeds was explained
by the absence of irrigation systems combined with specialization in high-cost crops, and played
low market prices. Without collateral help these farmers are usually unable to secure a loan from
a bank or money lender [43,88]. Rates are often unmanageably high for those able to get a loan,
with strict penalties for late payments. Similarly, a lack of education, resources, skill training and
support prevent these farmers from using improved cultivars and then to generate a stable
income from their production. In addition, governments do not usually regulate the price of crops
or even provide market information. Improving market information systems for crops and
facilitating farmers’ access to credit are then essential components for a strategy to enable poor
farmers to grow improved cultivars. A major obstacle to success in crop production using
improved cultivars is the shortage of affordable credit. Desperate for cash, subsistence farmers
are forced to sell their crops immediately after the harvest to middlemen or their creditors at
unfavorable prices. Low cost quality seeds are essential for these poor farmers to improve their
life [43].

3.2. Breeding to adapt plants to the environment

3.2.1. Producing more with less

In the coming decades we will need to produce more with less. Fresh water suitable for irrigation
is expected to become increasingly scarce and the costs of fertilizer and other agricultural inputs
will increase as fossil-fuel costs rise. Nevertheless, continuing gains in production per hectare
must be realized to offset the loss of premium agricultural lands (e.g. from urbanization and
industrialization), while supplying a growing population. By developing resource efficient
plants, plant breeders can continue to improve the sustainability of agricultural ecosystems.
Plants requiring fewer off-farm input applications (specifically water, pesticides, nitrogen,
phosphorus, and other nutrients) decrease the cost of production, lower fossil energy use, and
reduce contamination of water systems, which help to improve public health and stabilize rural
economies [95,96].

Although modern plant breeding efforts initially focused on improving uptake of inputs, recent
efficiency gains have been made in physiologically increasing yield and biomass production
without further increasing inputs. Many crops already have genetic variation in nutrient use
efficiency, utilization, and uptake [97-99] and plant breeding will further improve these traits.
Intensive agro-ecosystems should emphasize improvements in system productivity, host plant
resistance and enhance use-efficiency of inputs such as water and fertilizers.

Water use-efficiency and water productivity are being sought by agricultural researchers
worldwide to address water scarcity. Under water scarcity, yields of crops, are a function of how
efficiently the crop uses this water for biomass-growth, and the harvest index. Water use
efficiency is the ratio of total dry matter accumulation to evapotranspiration and other water
losses. An increase in transpiration efficiency or reduction in soil evaporation will increase water
use efficiency. Water productivity is the ratio of biomass with economic value produced
compared to the amount of water transpired. Both water use efficiency and water productivity
may be improved through plant breeding. Farooq et al. [100] discuss the advances in transgenic
breeding for drought-prone environments. In their review, they noted the testing of 10 transgenic
rice events [unique DNA recombination taking place in one plant cell and thereafter to be used
for generating entire transgenic plant(s)] under water scarcity. It seems the transgenic expression
of some stress-regulated genes leads to increased water use efficiency.
Agriculture contributes significantly to greenhouse gas emissions. Nitrous oxide and dioxide are
potent greenhouse gases released by manure or nitrogen fertilizer, particularly in intensive
cropping systems. Nitrous oxide (N2O), which is a potent greenhouse gas, is generated through
the use of manure or nitrogen fertilizer. In many intensive cropping systems nitrogen fertilizer
practices lead to high fluxes of N2O and nitric oxide (NO). Several groups of heterotrophic
bacteria use NO3 as a source of energy by converting it to the gaseous forms N 2, NO, and NO2
(nitrous dioxide). N2O is therefore often unavailable for crop uptake or utilization.

Genetic enhancement of crops shows great potential for reducing N 2O emissions from soils into
the atmosphere. Some plants possess the capacity to modify nitrification in situ because they
produce chemicals which inhibit nitrification in soil. This release of chemical compounds from
plant roots suppressing soil nitrification has been called biological nitrification inhibition, which
seems to vary widely among and within species, and appears to be a widespread phenomenon in
some tropical pasture grasses, e.g. Brachiaria humidicola. Biological nitrification inhibition may
be an interesting target trait of crop genetic engineering for mitigating climate change.

Almost one-fifth of global methane emissions are from enteric fermentation in ruminant animals.
Apart from various rumen manipulation and emission control strategies, genetic engineering is a
promising tool to reduce these emissions. The amount of methane produced varies substantially
across individual animals of the same ruminant species. Efforts are ongoing to develop low
methane-emitting ruminants without impacting reproductive capacity and wool and meat quality.
A recent study by Shi et al. [101], to understand why some sheep produce less methane than
others, deployed high-throughput DNA sequencing and specialized analysis techniques to
explore the contents of the rumens of sheep. The study showed that the microbiota present in
sheep rumen was solely responsible for the differences among high and low methane emitting
sheep. It was further observed that the expression levels of genes involved in methane production
varied more substantially across sheep, suggesting differential gene regulation. There is an
exciting prospect that low-methane traits can be slowly introduced into sheep.

Crops are bred for nitrogen use efficiency because this trait is a key factor for reducing nitrogen
fertilizer pollution, improving yields in nitrogen limited environments, and reducing fertilizer
costs. The use of genotypes of same species efficient in absorption and utilization of nitrogen is
an important strategy in improving nitrogen use efficiency in sustainable agricultural systems.
Crops are being bred for nitrogen use efficiency because this trait will be a key factor for
reducing run-off of nitrogen fertilizer into surface waters, as well as, for improving yields in
nitrogen limiting environments. There are various genetic engineering activities for improving
nitrogen use efficiency in crops [98,102]. The gene Alanine aminotransferase from barley, which
catalyzes a reversible transamination reaction in the nitrogen assimilation pathway, seems to be a
promising candidate for accomplishing this plant breeding target. Transgenic plants over-
expressing this enzyme can increase nitrogen uptake especially at early stages of growth. This
gene technology was licensed to a private biotechnology company, and is slated to be
commercialized within the next six years [103]. A patent gave this biotechnology company the
rights to use the nitrogen use efficiency gene technology in major cereals, as well as, in
sugarcane.
Keeping nitrogen in ammonium form will affect how nitrogen remains available for crop uptake
and will improve nitrogen recovery, thus reducing losses of nitrogen to streams, groundwater and
the atmosphere. There are genes in tropical grasses such as B. humidicola and in the wheat wild
relative Leymus racemosus that inhibit or reduce soil nitrification by releasing inhibitory
compounds from roots and suppressing Nitrosomonas bacteria [104]. Their value for genetic
engineering crops for reducing nitrification needs to be further investigated.

3.2.2. Adapting to global climate change and for abiotic and biotic stress tolerance

Extreme weather events are expected to increase in both number and severity in coming years
[105]. Climate change impacts agro-ecosystems through changes over the long-term in key
variables affecting plant growth (e.g. rising temperatures) and through increasing the variability
(frequency and intensity) of weather conditions (rainfall, drought, waterlogging and elevated
temperatures). These changes affect both crop productivity and quality. In addition to physically
destroying crops, climate change has altered host-pathogen relationships and resulted in
increased disease incidence, in insect-pest borne stress in crop plants, and in invasive pests which
feed and damage them.

There are two ways to adapt crops to new environments: developing new crops (long-term
endeavor starting with domestication) and introducing target traits into existing crops through
plant breeding, which includes genetic engineering. However, the job of crop improvement is
becoming increasingly difficult. Cultivars which are not only high yielding but are also efficient
in use of inputs are needed, tailored to ever more stringent market demands, able to maintain
stability under increasing climate variability, and potentially contribute to climate mitigation.
These multi-trait demands for new cultivars provide significant challenges for crop breeders, and
standard selection approaches struggle under such complexity. To maintain productivity in the
face of increased climatic variability, both the population and the plant cultivars will need to be
continually developed to withstand “new” climate extremes and the stresses which these will
entail [106].

Many breeding programs are already developing plants which tolerate extreme weather
conditions, including drought, heat, and frost [107,108]. Plant breeders are also beginning to
address expected changes due to increased climate variability, by increasing genetic diversity
sources and by adjusting selection and testing procedures [109].

More frequent weather extremes will likely affect the existing ranges of not only agronomic
cultivars but also local native plant species [110]. Because some genetic variation useful for
climate change adaptation will be found only in wild plant relatives of cultivated crops,
preserving genetic biodiversity is essential in order for breeders to select plants that will be well-
suited for future environmental conditions [111].

Global climate change notwithstanding, additional stress tolerances in crop species are needed to
maintain productivity and survival. In the near future, tolerance to various soil conditions
including acidic, aluminum-rich soils (particularly in the tropics) and saline soils (especially
those resulting from irrigation), will be increasingly important for production on marginal
agricultural lands or as the salt content of irrigated lands increases [112]. Bhatnagar-Mathur et al.
[113] suggested that genetic engineering could accelerate plant breeding to adapt crops to
stressful environments. They further underline that engineering the regulatory machinery
involving transcription factors (TF; a protein binding specific DNA sequences and thereby
governing the flow of genetic information from DNA to messenger RNA) provides the means to
control the expression of many stress-responsive genes. There are various target traits for
adapting crops, through genetic engineering, to high CO 2 and high O3 environments of the
changing climate [114]. Ortiz [115], Jewell et al. [116], and Dwivedi et al. [117,118] provide the
most recent overviews on research advances in genetic engineering for improved adaptation to
drought, salinity or extreme temperatures in crops. The most cited include TF, and genes
involved in: i) signal sensing, perception, and transduction; ii) stress-responsive mechanisms for
adaptation; and iii) abscisic acid biosynthesis for enhanced adaptation to drought. Transporter,
detoxifying and signal transduction genes as well as TF are cited for tolerance to salinity. Genes
related to reactive oxygen species, membrane and chaperoning modifications, late abundance
embryogenesis proteins, osmoprotectants/compatible solutes and TF are pursued in crop genetic
engineering for temperature extremes.

Transgenic crops provide the means to adapt crops to climate change, particularly in terms of
drought and salinity. Duration and intensity of drought has increased in recent years, consistent
with expected changes of the hydrologic cycle under global warming. Drought dramatically
reduces crop yields. Genetic engineering may be one of the biotechnology tools for developing
crop cultivars with enhanced adaptation to drought [119]. It should be seen as complementary to
conventional plant breeding rather than as an alternative to it. The function of a TF such as the
Dehydration-Responsive Element Binding (DREB) gene in water stress-responsive gene
expression has been extensively investigated [120]. The main research goal was to gain a deep
understanding of TF in developing transgenic crops targeting drought-prone environments [121].
For example, the DREB1A gene was placed under the control of a stress-inducible promoter from
the rd29A gene and inserted via biolistic transformation into wheat bread [122]. Plants
expressing this transgene demonstrated significant adaptation to water stress when compared to
controls under experimental greenhouse conditions as manifested by a 10-day delay in wilting
when water was held. Saint Pierre et al. [123] indicated, however, that these transgenic lines did
not generally out-yield the controls under water deficit in confined field trials. Nonetheless, they
were able to identify wheat lines combining acceptable or high yield under enough irrigation
which also showed stable performance across the water deficit treatments used in their
experiments; i.e., severe stress, stress starting at anthesis, and terminal stress.

Soils affected by salinity are found in more than 100 countries, and about 1/5 of irrigated
agriculture is adversely affected by soil salinity. Therefore, breeding salt-tolerant crops should be
a priority because salinity will most likely increase under climate change. Mumms [124] lists
some candidate genes for salinity tolerance, indicating the putative functions of these genes in
the specific tissues in which they may operate. Genes involved in tolerance to salinity in plants,
limit the rate of salt uptake from the soil and the transport of salt throughout the plant, adjust the
ionic and osmotic balance of cells in roots and shoots, and regulate leaf development and the
onset of plant senescence. The most promising genes for the genetic engineering of salinity
tolerance in crops, as noted by Chinnusamy et al. [125], are those related to ion transporters and
their regulators, as well as the C-repeat-binding factor. The recent genome sequencing of
Thellungiella salsuginea, a close relative of Arabidopsis thriving in salty soils, will provide more
resources and evidence about the nature of defense mechanisms constituting the genetic basis
underlying salt tolerance in plants [126].

In the quest for breeding transgenic rice and tomato, advances showing salt tolerance have
occurred. Plett et al. [127] were able to show an improved salinity tolerance in rice by targeting
changes in mineral transport. They initially observed that cell type-specific expression of
AtHKT1 (a sodium transporter) improved sodium (Na+) exclusion and salinity tolerance in
Arabidopsis. Further research explored the GAL4-GFP enhancer trap (transgenic construction
inserted in a chromosome and used for identifying tissue-specific enhancers in the genome) to
drive expression of AtHKT1 in the root cortex in transgenic rice plants. The transgenic rice plants
had a higher fresh weight under salinity stress due to a lower concentration of Na + in the shoots.
They also noted that root-to-shoot transport of 22Na+ decreased and was correlated with an up-
regulation of OsHKT1, the native transporter responsible for Na+ retrieval from the transpiration
stream. Moghaieb et al. [128] bred transgenic tomato plants producing ectoine (a common
compatible solute in bacteria living in high salt concentrations). Ectoine synthesis was promoted
in the roots of transgenic tomato plants under saline conditions, which led to increased
concentration of photosynthesis in improving water uptake. Likewise, the photosynthetic rate of
ectoine-transgenic tomato plants increased through enhancing cell membrane stability in
oxidative conditions under salt stress.

Transgenic crops can also contribute to climate change mitigation efforts by reducing input use
intensity [129]. The integration of genetic engineering with conventional plant breeding, within
an interdisciplinary approach, will likely accelerate the development and adoption of crop
cultivars with enhanced adaptation to climate change related stresses [130]. Global warming will
reduce yields in many crops about 6% and 5% average yield loss per 1°C in C 3 and C4 crops,
respectively, whose optimum temperature ranges are 15–20°C and 25–30°C [131]. The extent of
yield loss depends on crop, cultivar, planting date, agronomy and growing area. For instance, an
increase of 1°C in the night time maximum temperature translates into a 10% decrease in grain
yield of rice, whereas a rise of 1°C above 25°C shortens the reproductive phase and the grain-
filling duration in wheat by at least 5%, thereby reducing grain yield proportionally. Heat stress
will exacerbate climate change impacts in the tropics, while it may put agriculture at risk in high
latitudes where heat-sensitive cultivars are grown today. Hence, new cultivars must be bred to
address heat stress. Ainsworth and Ort [132] suggested giving priority to traits improving
photosynthesis for adapting to heat stress. However, plants have various mechanisms to cope
with high temperatures, e.g. by maintaining membrane stability, or by ion transporters, proteins,
osmoprotectants, antioxidants, and other factors involved in signaling cascades and
transcriptional control [133,134]. Furthermore, Gao et al. [135] noted that bZIP28 gene (a gene
encoding a membrane-tethered TF) up-regulated in response to heat in Arabidopsis. Some of
these genes can be used in crop genetic engineering to enhance plant adaptation to heat stress.
For example, some stress-associated genes such as ROB5, a stress inducible gene isolated from
bromegrass, enhanced performance of transgenic canola and potato at high temperatures [136].
Likewise, Katiyar-Agarwal et al. [137] introduced hsp101 gene (a heat shock protein gene from
Arabidopsis) in basmati rice. This transgenic rice had a better growth in the recovery phase after
suffering heat stress.
Globalization has, among other consequences, led to the rapid spread of plant disease and
invasive pests. Being immobile, plants are unable to escape pathogens causing plant disease and
pests which feed and damage them. Plant disease is mainly caused by fungi, bacteria, viruses,
and nematodes. Approximately 70,000 species of pests exist in the world, but of these, only 10%
are considered serious [138]. Synthetic pesticides have been applied to crops since 1945 and
have been highly successful in reducing crop losses to some pest insects, plant pathogens, weeds
and in increasing crop yields [138]. One estimate suggests that without pesticides, crop losses to
pests might increase by 30%. Despite pesticide use, insects, pathogens and weeds continue to
exact a heavy toll on world crop production, approaching 40% [138,139]. Pre-harvest losses are
globally estimated at 15% for insect pests, 13% for damage by pathogens, and about 12% for
weeds [138]. Developing resistant cultivars reduces the need for expensive and environmentally
damaging pesticides to be applied. For example, a recent outbreak of Xanthomonas campestris
pv. musacearum led to the devastating Xanthomonas wilt of banana in the Great Lakes Region of
Africa, thereby threatening the food security and income of millions of East and Central African
people who depend on this crop. Transgenic banana plants with the hypersensitivity response-
assisting protein (Hrap) gene from sweet pepper did not show any infection symptoms after
artificial inoculation of potted plants with Xanthomonas wilt in the screen house [140]. Selected
transgenic banana plants with putative host plant resistance to Xanthomonas wilt are ongoing
confined field-testing in East Africa, where elevated temperatures, due to the changing climate,
will likely favor banana production.

Weather influences how pathogens and pests affect and interact with crops and their host plant
resistance, and thus climate change can also have wide-ranging impacts on pests and diseases
[118]. Late blight, which is caused by Phytophthora infestans, ranks as the most damaging
potato pest. Late blight accounts for 20% of potato harvest failures worldwide, translating into 14
million tonnes valued at 7.6 billion US dollars. Global warming will increase late blight spread,
e.g. expanding its range above 3,000 meters in the Andes [141]. Chemical control may lead to
more aggressive strains of the pathogen and chemical control is often regarded as being
environmentally damaging. Cisgenic potato cultivars with late blight resistance are becoming
available and will impact growers, consumers and the environment favorably [142]. Related wild
Solanum species can be a source of alleles to enhance host plant late blight resistance in potato.
For example, S. bulbocastum (a wild relative with high resistance to late blight from Mexico)
was used to breed the cultivar ‘‘Fortuna’’ using genetic engineering. Cisgenesis allows inserting
several host plant resistance genes from wild crop species in one step without linkage drag
(reduction in cultivar fitness).

3.3. Breeding plants to improve the environment

In general, plants are bred for their most obvious end products, including grain, fiber, sugar,
biomass yield, fruit quality, or ornamental qualities. However, plants deployed across the
landscape in agricultural or forestry settings affect the environment in measurable ways.
Perennial crops have environmentally beneficial properties not present in annual crops, such as
helping to prevent erosion in agricultural systems, providing wildlife habitat, and acting as sinks
for carbon and nutrients. Traditionally, perennial crops have not been a major focus of breeding
programs because they generally take more time and scientific knowledge to improve, and
therefore, products such as new cultivars are often not produced within the timeframe of funding
cycles. Current tree breeding programs are developing elms (Ulmus spp), chestnuts (Castanea
dentata), hemlocks (Tsuga spp), and other species which are resistant to introduced diseases and
insects [143,144]. As compared with natural selection, artificial selection via plant breeding has
overcome these stresses more effectively by rapidly incorporating diverse exotic genetic sources
of resistance, hybridizing to include multiple, different genetic resistances into the same plant,
and making use of off-season locations or artificial conditions to shorten generation cycles. A
more complex example which may be feasible in the future is tree breeding for larger and
improved root systems to decrease soil erosion, sequester carbon, and improve soil quality by
increasing soil organic matter.

New crop cultivars developed by plant breeders must help improve soil health, reduce soil
erosion, prevent nutrient and chemical runoff, and maintain biodiversity. The goal to breed
projects for forages, which include several species, is to produce a high yield of leaf and stem
biomass, as opposed to grain, for ruminant animals. In the tropics many forages are perennial,
providing year-round erosion control, improving water infiltration as compared with that, from
annual cropping systems, and in some cases, sequestering carbon. The forage breeding program
at the University of Georgia (UG) has developed cultivars in several species and has been
proactive in developing agreements with private-sector commercial partners to oversee seed
production and marketing of new cultivars. Among the cultivars developed at UG is ‘‘Jesup
MaxQ’’ tall fescue, a cultivar carrying a non-toxic endophytic fungus that was both highly
persistent under grazing and greatly improved animal weight gain and feed efficiency over
standard cultivars. In addition, this program developed the first true dual purpose, grazing and
hay, alfalfa cultivar ‘‘Alfagraze’’, followed by several further improved alfalfa cultivars like
‘‘Buldog 805’’ which persist through summer under cattle grazing [145].

Cover crops are annual species planted in rotation with crops to specifically improve soil
conditions and to control weeds, soil-borne diseases, and pests [146-148]. Continuous cover
crops can reduce on-farm erosion, nutrient leaching, and grain losses due to pest attacks and
build soil organic matter as well as improve the water balance, leading to higher yields
[149,150]. For instance, in Kenya, Kaumbutho and Kienzle [151] showed in two case studies that
maize yield increased from 1.2 to 1.8–2.0 t/ha with the use of mucuna legume as cover crop, and
without application of nitrogen fertilizer. Besides farmers who adopted mucuna legume as cover
crop benefited from higher yields of maize with less labor input for weeding.

Many current perennial and cover crop cultivars are essentially wild species bred from
germplasm collections and developed to increase success in managed agro-ecosystems. As
compared with non-native vegetation, plant species native to a particular region are generally
thought to survive on less water, use fewer nutrients, require minimal pesticide applications, and
be non-invasive; however, counter examples for both native and non-native species are plentiful
[152]. As potentially valuable species are identified, breeding to improve them for traits of
consumer importance will be needed to broaden available biodiversity in cultivated landscapes.
With a changing climate, species considered critical to the landscape may require human-assisted
hybridization with distant relatives to better ensure survival from threats posed by novel pests or
diseases.
Alternative crops are also being bred for new uses, such as removing toxic chemicals and excess
nutrients and improving degraded soils, including mine spoils [153]. Phytoremediation is a
biotechnology to clean the contaminated sites of toxic elements (e.g. Cd, Cu, Zn, As, Se, Fe) via
plant breeding, plant extracting, and plant volatilizing [154]. The last few years have seen a
steady expansion in the list of hyper-accumulator species, which could be valuable plant
resources for phytoremediation. For example an ecotype of the Zn/Cd hyper-accumulator
Thlaspi caerulescens from southern France was able to phytoextract Cd efficiently in field trials
through the different seasons with good growth of biomass [155,156]. The Chinese brake fern
Pteris vittata has a strong ability to hyper-accumulate arsenic (As) and shows promising
potential for phytoextraction of and from contaminated soils under field conditions [157,158].

A major goal of harmonizing agriculture with the environment is to “tailor” crops to individual
landscapes. Plant breeding has always maximized production by selecting for adaptation in the
target environments of interest, using local environmental forces for plant selection [131]. By
selecting breeding germplasm growing under local environmental conditions, individual cultivars
can be optimized for small regional areas of production that fit prevailing environmental and
weather patterns. Likewise, plants could be tailored to provide specific ecosystem services to
local environments, to address local needs. One cost-effective way to achieve this is through
participatory plant breeding, which involves local farmers in the breeding process.

Alternative crop rotations, planting densities, and tillage systems may make production more
environmentally benign but will require altering breeding targets and an understanding that
systems biology is complex and rarely has simple solutions. For example, no-tillage systems
used for soil conservation can lead to colder soils in spring and change the prevalence and onset
of various soilborne diseases, thus requiring the addition of specific disease resistances in the
breeding objectives [159]. Breeders must select from conditions prevailing under new
management practices to ensure cultivars will be optimally productive.

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4. Conservation and use of biodiversity – opportunities for

cooperation and new partnerships
Plant genetic resources for food and agriculture are the quintessential global public good. No
nation is self-reliant. A viable market for their conservation and trade does not exist. The
conservation of plant genetic resources is a prerequisite for addressing climate change, as well as
water and energy constraints, which will grow in importance in the next decades. The Svalbard
Global Seed Vault is an International Treaty which establishes a multilateral System to facilitate
access and benefit sharing of plant genetic resources. The Treaty has an insurance policy and
provides legal framework for a cooperative and global approach to manage this essential
resource. The Svalbard Global Seed Vault has a mechanism for ensuring the permanent
conservation of unique crop biodiversity, the Global Crop Diversity Trust, which is structured as
an endowment fund [45].
Plant breeding is vital to increase the genetic yield potential of all crops. As menthioned a result
of the Green Revolution was the increase of global productivity of the main food staples. Such
achievements ensued from crop genetic enhancement partnerships. These partnerships include
national agricultural research institutes and international agricultural research centers. For many
decades the global wheat yield increased due to an effective International Wheat Improvement
Network (IWIN) officially founded as an international organization in 1966 [160]. This wheat
network deployed cutting-edge science alongside practical multi-disciplinary applications,
resulting in the development of genetically enhanced wheat germplasm, which has improved
food security and the livelihoods of farmers in the developing world [161]. The spring wheat
germplasm bred in Mexico under the leadership of Nobel Peace Laureate Norman Borlaug was
further used for launching the Green Revolution in India, Pakistan and Turkey [162]. The
network was broadened during the 1970s to include Brazil, China and other major developing
country wheat producers. It resulted in wheat cultivars with broader host plant resistance
(especially to rusts), better adaptation to marginal environments, and tolerance to acid soils.
Nowadays IWIN, an international "alliance", operates field evaluation trials in more than 250
locations, in roughly 100 countries it tests improved breeding lines of wheat in different
environments. The number of wheat cultivars released annually in the developing world doubled
to more than 100 cultivars by early 1990s due to this networking and the strengthening of
national capacity [163]. The widespread adoption of newly bred wheat cultivars, especially in
South Asia and Latin America, due to yield increases, led to 50% average annual rates of
investment returns [164]. The urban poor also benefited significantly because grain harvest
increases drove wheat prices down. Every year, nursery sets and trials are sent to various
researchers worldwide, who share their data from these trials to catalogue and analyze. The
returned data are used to identify parents for subsequent crosses and to incorporate new genetic
variability into advanced wheat lines that are consequently able to cope with the dynamics of
abiotic and biotic stresses affecting wheat farming systems. The full pedigree and selection
histories are known and phenotypic data cover yield, agronomic, pathological and quality data
[161].

The International Network for Genetic Evaluation of Rice (INGER) is one more example of
world cooperation. It was established in 1975 as a consortium of national agricultural research
systems of rice-growing countries and Centers of today’s CGIAR Consortium. INGER was
initially founded as an International Rice Testing Program, but soon became an integral
component of world national rice breeding program. INGER partners can share rice breeding
lines. Every year partners provide about 1000 genetically diverse breeding lines, which have
been grown in about 600 experiment stations from 80 countries. This network facilitated the
release of 667 cultivars worldwide, which translated into 1.5 billion US dollars of economic
benefits. It was estimated that ending INGER could lead to a reduction of 20 rice cultivars per
year and to an economic loss of 1.9 billion US dollars [165]. Further analysis by Jackson and
Huggan [166] has shown how genetic conservation of landraces can lead to significant gains in
rice breeding.

Two other examples of cooperation and partnership are the Latin American Maize Project
(LAMP) and the Germplasm Enhancement of Maize (GEM). The LAMP was established as a
partnership between Latin America and the United States to assess national germplasm and
facilitate the exchange of maize genetic resources across the American continent [167]. The
United States Department of Agriculture, the participating national agricultural research systems
and a multinational seed corporation provided the funding. The aim of LAMP was to obtain
information about the performance of maize germplasm and to share it with plant breeders for
developing genetically enhanced open pollinated and hybrid cultivars. The maize germplasm was
tested for agronomic characteristics from sea level to 3300 m, and from 41°N to 34°S across 32
locations in the first stage and in 64 locations (two per region) in the second stage. These
locations were clustered according to five homologous areas: lowland tropics, temperate and
three altitudes.

There were a total five LAMP breeding stages [167]. In the first stage, 14,847 maize accessions
belonging to a region were planted for evaluation in trials using a randomized complete block
design with two replications of 10m2 plots at a single location, which was environmentally
similar to that from where these landraces were originally collected. The next step included the
assessment of the upper quintile (20%) of those accessions evaluated for agronomic performance
in the previous stage. These accessions were planted in two locations with two replications, and
the upper 5% were further selected according to their performance. These best selected
accessions of each country were interchanged among regions belonging to the same homologous
area in the third stage. They were tested in two locations with two replications in each region.
The selected maize accessions from the same homologous area were mated with the best tested
accession of the region in an isolated field within each region. In the fourth stage, combining
ability tests of 268 selected maize accessions were carried out with a local tester using two
replications at two locations within each region. The elite maize germplasm was integrated into
breeding programs in the fifth stage, which was the last. The best cross combinations and
heterotic pools were also determined by LAMP. Maize breeders obtained access to the most
promising accessions identified by LAMP to widen the crop genetic base. A LAMP core subset
has been made available for encouraging further use in broadening of maize genetic diversity
[168].

The GEM was set up to introgress useful genetic diversity from Latin American maize landraces
and other tropical maize donor sources (lines and hybrids) into United States’ maize germplasm,
to broaden the genetic base of the “corn-belt” hybrids [169,170]. GEM owes its existence to
LAMP because it has used the Latin American landrace maize accessions selected by LAMP in
crosses with elite temperate maize lines from the private seed companies in North America
[167]. GEM used a pedigree breeding system to develop S 3 lines. The GEM breeders arranged
their crosses into non-Stiff Stalk and Stiff Stalk heterotic groups [171].

LAMP provided the first step through the sharing of information needed to select gene bank
maize accessions for further germplasm enhancement. GEM completed the process by returning
to genetically enhanced breeding materials derived from gene bank accessions. This improved
germplasm can be further used in maize breeding in the United States and elsewhere. LAMP and
GEM are very nice examples of international and national public-private partnerships in crop
germplasm enhancement.

Agricultural plant breeding is a typical commodity- or species-oriented and solves problems

within a species, rather than making breeding choices based on system wide needs. For example,
maize breeders currently maximize the area in which maize can be grown, and maximize the
amount of maize produced throughout that area. If environmental harmony is to be a key
breeding objective, then a change in agricultural thinking to appropriately value whole cropping
systems will be required. Achieving these goals will require collaboration among the private,
public, and non-profit sectors, and with society as a whole. Programs within the private sector
excel at breeding major, profitable crops, and have economies of scale to increase the efficiency
of production and ultimately provide farmers with seed. As a valuable complement to
commercial breeding programs, public and non-profit breeding programs may focus on
developing alternative crops, breeding for small target regions, tackling long-term and high-risk
problems, evaluating diverse genetic resources, and, importantly, conducting basic research on
breeding methodology to enhance efficiency. Only publicly funded breeding programs, and in
particular those based at universities, can provide the necessary education and training in plant
breeding and in specialized fields such as ecology. Without trained students from public
programs, private commercial breeding programs suffer from an erosion of intellectual capital.
Conversely, without the private sector to commercialize public-sector-derived products,
beneficial traits and new cultivars cannot easily and quickly be put in the hands of farmers, as
has been seen in developing countries without a developed seed industry [172]. As stated, seed
production is high technology and a cost intensive venture and only well organized seed
companies with good scientific manpower and well equipped research facilities can afford seed
production.

Although due to globalization, most breeding research and cultivar development in the world is
presently conducted and funded in the private sector, mainly by huge multinational seed
companies. Public breeders, cultivar development activities and research are disappearing
worldwide. In general, this means there are fewer decision-making centers for breeding and
cultivar development. This has also resulted in the focus on relatively few major crops produced
worldwide, to the detriment of all the other cultivated crops. It is imperative that national
governments and policymakers, as part of a social duty, invest in breeding research and cultivar
development of traditional open-pollinated cultivars and in the minor crops. More investments in
this area will mean less expensive seed for growers to choose from, and an increased
preservation of crop biodiversity. To accomplish these goals new approaches may be required to
crop breeding research and development by both the public and private sector. Until recently,
breeding research and development which targets small-scale and poor farmers has largely been
undertaken by public sector institutions and national agricultural research institutes. However,
the capacity to undertake the work was mainly dependent on national or international funding
and expertise. The work has been limited by the capacity of these institutions to pay for it. As a
result, crop breeding advancement has varied enormously among countries and even within
regions in developed and still developing countries. In the area of plant breeding, the process to
produce improved cultivars is slow, and it requires long-term sustained commitment that may not
fit the continuing changes in the national and international politics to fund research. The
application of biotechnology promises acceleration in some aspects of plant breeding, but the
adoption of more advanced technology raises the cost of research significantly at a time when
investment funding has diminished. Public plant breeding remains a key component of crop
breeding research systems worldwide, especially in developing countries. However, the
increasing presence of private sector breeding and a decrease in national and international
support makes it difficult for the public sector to continue operating in the traditional manner.
Declining funding for public crop breeding coupled with the rapid increase of crop production
and an urbanizing population has created a difficult situation. Public sector breeding must be
strengthened. More public sector crop breeders are needed worldwide to select and to produce
non-hybrid cultivars of the minor crops. Breeding of major crops and other minor crops must
continue as a viable endeavor. This will benefit small farmers, and will safeguard biodiversity
and food security in developing countries.

While the maintenance of vigorous public sector breeding programs in areas where private
companies are not interested in providing low cost cultivars is highly desirable, an additional
approach to maximize crop and agricultural research input would be the development of global
programs with public-private partnerships. The public sector may support portions of crop and
agricultural R&D, unattractive to the private sector, and feed improved breeding lines and
systems to the private sector for exploitation in regions where the private sector is active, and
nurture private sector development in regions where it is lacking. In recent years, private plant
breeding programs have increased in number and size. Financial investment also increased, as
well as interest in intellectual property protection. The spirit of original attempts to protect plant
breeders’ rights was that granting a certificate of protection should not inhibit the flow of
information and products through continued research by the entire plant breeding community
[106,107]. In a classic sense, the patent is a defensive tool to prevent competitors from reaping
benefits which rightfully belong to the inventor. In the modern context, it is an offensive weapon,
to stifle competition, prevent further innovation by others and maximize income [106,108]. The
United States utility patent, it is a way to slow down the flow of progress in plant breeding
research, unless the research is within the company holding the patent. While obviously
benefiting that company, it is a big step backwards for the plant breeding community and by far,
for agriculture itself. The intellectual property protection must encourage research and free flow
of materials and information [106,108]. Protection should be for the cultivar only. There should
be no constraint against other breeders using that cultivar in further research, including further
breeding. Another breeder should be free to use the protected cultivar in a cross, followed by
further development through pedigree breeding. Another breeder should also be free to transfer
genes controlling economic traits into the protected cultivar by the backcross method or by
genetic transformation procedures [106,107