Plants, Genes, and Agriculture

Description

Presenting and integrating information from many disciplines, this book invites readers to consider the complexity of feeding humanity and increasing food production sustainably. Topics covered include:

-- the development, physiology, and nutrition of plants
-- human nutrition and food safety
-- photosynthesis and energy transformations
-- genetics, molecular biology, and genomics, including the techniques of genetic transformation (gene silencing, gene editing with CRISPR) used in modern crop breeding
-- crop domestication and plant breeding
-- soil ecosystems
-- the biotic (animal pests, diseases, and weeds) and abiotic (drought, flooding, temperature extremes, and soil degradation) stresses that limit crop production
-- technological advances and how new innovations (equipment, chemical products, and improved plant varieties) reach farmers and eventually affect what we eat; also discusses legal aspects (e.g., patents) relevant to agricultural innovations
-- plants as sources of pharmaceuticals and specialty chemicals

Although publicized in the controversies surrounding "genetically modified organisms" (GMOs), the applications of modern biotechnology to agriculture extend far beyond GMOs, and include crop improvements that rely on knowledge of the plant's genomes and its analysis by bioinformatics. This unifying theme of the text is stressed in coverage of a number of issues that appear throughout the chapters, including:

-- how crop plant breeders look for specific traits to solve practical problems
-- genetic engineering of crops as a useful way to supplement conventional plant breeding
-- the nature of agribusiness in industrialized countries
-- the vital contributions of developing countries and their smallhold farmers, and the unique challenges facing them

Challenging and controversial topics such as the safety of pesticides and GMOs, the increasing demand for animal products and the stresses this puts on agricultural output, organic farming and foods, and patenting new crop varieties are dealt with in a balanced way, inviting teachers and students to consider all the implications of these serious questions.

Table of Contents

Chapter 1. The Human Population and Its Food Supply in the 21st Century, Maarten J. Chrispeels and Hanya E. Chrispeels
1.1 Hunger and Malnutrition Persist in a World of Plenty
1.2 Human Population Growth Is Slowing
1.3 By How Much Does the Food Supply Need to Increase to Satisfy Future Demand?
1.4 Agriculture Must Become More Sustainable in the Future
1.5 An Uncertain Climate Presents Challenges to Food Production
1.6 Urbanization and Rising Living Standards Are Changing the Demand for Agricultural Products and the Way They Are Brought to Market
BOX 1.1 Food Deserts in America
1.7 Government Policies Play Pivotal Roles in Global Food Production
1.8 Agricultural Research Is Vital If We Are to Maintain a Secure Food Supply
BOX 1.2 International Agricultural Research Institutes of the CGIAR Consortium
1.9 Can Other Agricultural Methods and Policies Contribute to Feeding the Population?
1.10 Biotechnology Is Crucial for the Future of Food Production

Chapter 2. A Changing Global Food System: One Hundred Centuries of Agriculture, H. Maelor Davies and Paul Gepts
2.1 Hunting and Gathering Were the Methods of Food Procurement for Much of Human History
2.2 Agriculture Began in Several Places Some 10,000 Years Ago
2.3 Plants Are the Principal and Ultimate Source of All Our Food
2.4 Crop Production Today Takes Several Forms That Differ Dramatically in Productivity
BOX 2.1 Intensification of Agricultural Productivity in the Brazilian Cerrado
2.5 Science-based Agricultural Practices Have Led to Significant Increases in Productivity
BOX 2.2 Some Inventions and Innovations through the History of Agriculture
2.6 Farming and the Postharvest Food Delivery Pathway Combine to Provide Consumers with an Abundance of Different Foods
BOX 2.3 Agricultural Intensification and New Business Opportunities: The Pacific Fruit Express
2.7 Agriculture and Food Production Are Significant Players in the Economic Systems of Developed Countries
2.8 Intensive Agriculture Has Environmental Effects That May Limit Its Long-term Sustainability

Chapter 3. Plants in Human Nutrition, Diet, and Health, Maarten J. Chrispeels
3.1 Animals Are Heterotrophs, Plants Are Autotrophs
3.2 Carbohydrates Are the Principal Source of Energy in the Human Diet
BOX 3.1 Lactose Tolerance: A Case of Human Evolution in Action
3.3 Fats Are a Source of Energy, Structural Components, and Essential Nutrients
3.4 Diets High in Energy Are Linked to Major Diseases
3.5 To Make Proteins, Animals Must Eat Proteins
3.6 Vitamins Are Small Molecules That Plants Can Make, but Humans and Other Animals Generally Cannot
BOX 3.2 Vitamin D: A Vitamin or a Hormone?
3.7 Minerals and Water Are Essential for Life
3.8 Plants Produce Bioactive Molecules that Can Affect Human Health
3.9 The Consequences of Nutritional Deficiencies Can Be Severe and Long Lasting
BOX 3.3 Gluten Sensitivity and Celiac Disease
3.10 Millions of Healthy Vegetarians and Vegans Are Living Proof that Animal Products Are Not a Necessary
Component of the Human Diet
3.11 Are Organically Grown Plants and Products from Animals Fed with Organic Feed Worth the Additional
Price?
3.12 The Intestinal Microbiome Significantly Influences Health

Chapter 4. Genes, Genomics, and Molecular Biology: The Basis of Modern Crop Improvement, Kranthi K. Mandadi and T. Erik Mirkov
4.1 Traits Are Inherited from One Generation to the Next
4.2 Genetic Information Is Replicated and Passed to New Cells during Cell Division
BOX 4.2 Chromosomes, Chromatids, and Meiosis
4.3 Genes Are Made of DNA
4.4 Gene Expression Involves RNA Synthesis Followed by Protein Synthesis
4.5 Gene Expression Is a Highly Regulated Process
4.6 Mutations Are Changes in Genes
4.7 Much of the Genome's DNA Does Not Code for Proteins
4.8 DNA Can Be Manipulated in the Laboratory Using Tools from Nature
4.9 Creating GE Plants Depends on the Application of Naturally Occurring Horizontal Gene Transfer
BOX 4.3 Selectable Markers
4.10 Genome Sequencing and Bioinformatics Are Important Tools for Plant Biologists and Plant Breeders
4.11 Gene Editing Technologies Allow Us to Make Targeted Changes in an Organism's DNA

Chapter 5. Growth and Development: From Fertilized Egg Cell to Flowering Plant, Maarten J. Chrispeels
5.1 The Plant Body Is Made Up of Cells, Tissues, and Organs
BOX 5.1 The Structures of a Living Plant Cell
5.2 Development Is Characterized by Repetitive Organ Formation from Stem Cells
BOX 5.2 Plant Tissue Systems and Cell Types
5.3 Gene Networks Interact with Hormonal and Environmental Signals to Regulate Development
BOX 5.3 Plant Hormones
5.4 In the First Stage of Development, Fertilized Egg Cells Develop into Embryos
5.5 Deposition of Food Reserves in Seeds Is an Important Aspect of Crop Yield
5.6 Maturation, Quiescence, and Dormancy Are Important Aspects of Seed Development
5.7 Formation of the Vegetative Body Is the Second Stage of Plant Development
5.8 Secondary Growth Produces New Vascular Tissues and Results in the Formation of Wood
5.9 Reproduction Involves the Formation of Flowers with Male and Female Organs
5.10 Fruits Help Plants Disperse Their Seeds
5.11 Developmental Mutants Are an Important Source of Variability to Create New Crop Varieties
5.12 Plant Cells are Totipotent: A Whole Plant Can Develop from a Single Cell

Chapter 6. Converting Solar Energy into Crop Production, Donald R. Ort, Rebecca A. Slattery, and Stephen P. Long
BOX 6.1 Efficiency of Food Production from Solar Energy to People
6.1 Photosynthetic Membranes Convert Light Energy to Chemical Energy
6.2 In Photosynthetic Carbon Metabolism, Chemical Energy Is Used to Convert CO2 to Carbohydrates
6.3 Sucrose and Other Polysaccharides Are Exported to Heterotrophic Plant Organs to Provide Energy for
Growth and Storage
6.4 Plants Gain CO2 at the Cost of Water Loss
6.5 Plants Make a Dynamic Trade-off of Photosynthetic Efficiency for Photoprotection
6.6 Abiotic Environmental Factors Can Limit Photosynthetic Efficiency and Crop Productivity
6.7 How Efficiently Can Photosynthesis Convert Solar Energy into Biomass?
6.8 Opportunities Exist for Improving the Efficiency of Photosynthesis
6.9 Global Climate Change Interacts with Global Photosynthesis

Chapter 7. The Domestication of Our Food Crops, Paul Gepts
7.1 Wheat Was Domesticated in the Near East
7.2 Rice Was Domesticated in Asia and Western Africa
7.3 Maize and Beans Were Domesticated in the Americas
7.4 Domestication Is Accelerated Evolution Involving Relatively Few Genes
7.5 Crop Evolution Was Marked by Genetic Bottlenecks That Decreased Diversity
BOX 7.1 Genetic Uniformity and the Irish Potato Famine
7.6 Hybridization Plays a Role in the Appearance of New Crops, the Modification of Existing Crops, and the
Development of Some Troublesome Weeds
7.7 Polyploidy Led to New Crops and New Traits
7.8 Sequencing Crop Plant Genomes Provides Insights into Plant Evolution

Chapter 8. From Classical Plant Breeding to Molecular Crop Improvement, Paul Gepts and Todd Pfeiffer
8.1 Plant Breeders Have a Long Wish List
8.2 Plant Breeding Involves Introduction of Genetic Diversity, Hybridization, and Selection of New Gene
Combinations
BOX 8.1 Who Owns the World's Genetic Resources?
8.3 Genetic Variation Manipulated by Selection Is the Key to Plant Breeding
BOX 8.2 Johannsen and the "'Princess": Defining Variation for Plant Breeders
8.4 The Breeding Method Chosen Depends on the Pollination System of the Crop
8.5 F1 Hybrids Yield Bumper Crops
8.6 Backcrossing Comes as Close as Possible to Manipulating Single Genes via Sexual Reproduction
8.7 Quantitative Traits Are More Complex to Manipulate Than Qualitative Traits
8.8 The Green Revolution Used Classical Plant Breeding Methods to Increase Wheat and Rice Yields
8.9 Tissue and Cell Culture Techniques Facilitate Plant Breeding
8.10 The Technologies of Gene Cloning and Plant Transformation Are Powerful Tools
to Create GE crops
8.11 Marker-assisted Breeding Helps Transfer Major Genes
BOX 8.3 Karl Sax and the Principle of QTL Analysis
8.12 Genome Sequencing Has Become an Essential Tool of Plant Breeding Programs
8.13 High-Throughput Trait Measurement Facilitates Phenotyping for Crop Breeding

Chapter 9. Plant Propagation by Seeds and Vegetative Processes, Kent J. Bradford and Maarten J. Chrispeels
9.1 Commercial Seed Production Is Often Distinct from Crop Production
BOX 9.1 Where Do the Seeds to Grow Seedless Watermelons Come From?
9.2 Seed Certification Programs Guarantee and Preserve Seed Quality
9.3 Saving Seeds Securely Is an Important Aspect of Agriculture in Developing Countries
BOX 9.2 Storing Seed for the Next Season: Challenges Faced By African Farmers
9.4 Seed Germination, Seedling Establishment, and Seed Treatments Are Important Agronomic Variables
9.5 Enhancing Microbial Biofertilizers in the Soil Is an Important Technology for Crop Production
9.6 Seed Banks Preserve Genetic Diversity for the Future
9.7 Sterile Tissue Culture Is Used for Micropropagation and the Production of Somatic Embryos
9.8 Grafting Is Widely Used in the Fruit Industry to Propagate Superior Varieties
9.9 Apomixis Is a Unique Way in which Some Plant Species Reproduce

Chapter 10. Innovations in Agriculture: How Farm Technologies Are Developed and How They Reach Farmers, H. Maelor Davies
10.1 Biological and Technological Innovations Have Improved Farming Practices since the Early Days of
Agriculture
BOX 10.1 Synergy between Plant Breeding and Technology Development
BOX 10.2 The Agricultural Services Industry
10.2 Innovations in Agriculture Require Substantial Research in Many Fields
10.3 Patents Stimulate Invention and Improvements
10.4 Farmers Obtain Seeds in Different Ways
10.5 Minor Crops and New Production Methods Are Important
10.6 Agricultural Technologies and Practices Are Subject to Oversight and Regulation

Chapter 11. Soil Ecosystems, Plant Nutrition, and Nutrient Cycling, Eric M. Engstrom
11.1 Soil Ecosystems Are Fundamental to Agriculture
BOX 11.1 Animal, Vegetable, Mineral?
11.2 Particles Created by Weathering Are the Medium of Soil Ecosystems
11.3 Living Organisms and Their Remains Are Important Components of Soil Ecosystems
11.4 Plants Need Six Mineral Elements in Large Amounts and Eight Others in Small Amounts
11.5 Productivity May Be Limited by the Availability of Soil Water and Nutrients
11.6 Soil Organic Matter Is the Key Determinant of Soil Fertility
11.7 Roots Are the Foundation of Soil Food Webs and Soil Adhesion
11.8 Phosphorus Is the Rock-Derived Nutrient That Most Commonly Limits Crop Productivity
BOX 11.2 Terra Preta Do Indio
11.9 Nitrogen-fixing Bacteria and Industrial Nitrogen Fixation Drive the Nitrogen Cycle
11.10 Mycorrhizae Are Plant-Fungi Mutualisms That Help Plants Acquire Nutrients

Chapter 12. Biotic Challenges: Weeds, Patrick J. Tranel
12.1 Weeds Are Plants Adapted to Environments Disturbed by Humans
12.2 Weeds Interfere with Crop Plant Growth
BOX 12.1 Weeds That "Don't Fight Fair"
12.3 Weed Control Is Achieved by Cultural, Mechanical, Biological, and Chemical Practices
12.4 Herbicides Kill Plants by Interfering with Vital Plant-specific Processes
BOX 12.2 Herbicide Properties Depend on Their Chemistry
12.5 First Chemistry and then Biotechnology Transformed Weed Control
12.6 Weeds Adapt to Our Attempts To Control Them
12.7 Herbicide Resistance and a Lack of New Herbicides Are Challenges to Weed Control
BOX 12.3 Dioecious Pigweeds Are Particularly Well Equipped to Evolve Herbicide Resistance
12.8 New Methods of Weed Control Are Emerging

Chapter 13. Plant Diseases and Strategies for Their Control, Andrew F. Bent
13.1 Microbial Infections Diminish Crop Yields, but Plants Fight Back
13.2 Disease Epidemics Occur When Multiple Factors Converge
13.3 Viruses and Viroids Have Only a Few Genes
13.4 Cellular Pathogens Use Effector Proteins That Act in the Host Plant
13.5 Plant-pathogenic Bacteria Cause Many Economically Important Diseases
BOX 13.1 The Value of Sequencing a Pathogen Genome
13.6 Pathogenic Fungi and Oomycetes Collectively Cause the Greatest Crop Losses
BOX 13.2 Cereal Rusts Are among the Most Crop-destructive Diseases on the Planet
13.7 Chemical Strategies for Disease Control Can Be Effective but Problematic
13.8 Plants Mount Defenses to Ward Off Pathogens; Successful Pathogens Elude the Defenses
13.9 Resistance to Pathogens Can Be Introduced into Plants by Breeding and Genetic Engineering
13.10 The Plant Immune System Can Be Activated So Subsequent Infections Are Met with a Stronger Response

Chapter 14. Biotic Challenges: Pests, Georg Jander
14.1 Arthropod Pests Cause Substantial Crop Losses
14.2 Parasitic Nematodes Cause Substantial Crop Losses
14.3 Plants Have Chemical Defenses against Pests
BOX 14.1 Some Legal and Illegal Drugs Are Natural Insecticides
14.4 Improved Cultural Practices Can Help Control Pests
BOX 14.2 Push-pull Systems for Pest Control
14.5 Integrated Pest Management Can Control Outbreaks
14.6 Plant Breeding Methods Accelerate the Development of Pest-resistant Crop Varieties
14.7 Properly Applied, Synthetic Chemicals Can Provide Effective Pest Control
14.8 Genetically Engineered Plants Provide New Opportunities
BOX 14.3 Bt Toxins Have Both Positive and Negative Consequences for Farmers
14.9 Evolution Keeps Chemists, Plant Breeders, and Molecular Biologists Busy

Chapter 15. Abiotic Stresses and How They Affect Crop Yield, Maarten J. Chrispeels
15.1 Plants Sense Abiotic Stresses and Respond to Them
15.2 Plant Growth Depends on an Active Transpiration Stream
BOX 15.1 The Ogallala Aquifer
BOX 15.2 Water Potential, Osmosis, and Turgor Pressure
15.3 The Molecular Responses to Water Deficit Involve Signals from the Root
15.4 Too Much Water Depletes Oxygen in the Roots and Leads to Cell Death
15.5 Crops Experience Osmotic Stress and Sodium Toxicity
15.6 Plants Sequester Toxic Ions in Vacuoles
15.7 Heat Stress During Reproductive Growth Severely Diminishes Crop Yield
15.8 Many Crop Plants That Originated in Tropical Regions Are Sensitive to Cold
15.9 The Crops That Feed Humanity Are Not Well Adapted to Alkaline or Acidic Soils
15.10 Agricultural Practices and Global Climate Change May Exacerbate Abiotic Stresses

Chapter 16. Introduced Traits That Benefit Farmers and Industry, Maarten J. Chrispeels and Eliot M. Herman
16.1 Crops Bred Using Genetic Engineering Approaches Were Introduced in the Mid 1990s
BOX 16.1 Genetically Engineered Trees Saved Hawaii's Papaya Industry
16.2 Herbicide-tolerant GE Crops Facilitate Weed Management
16.3 Genetic Engineering of Insect Resistance Decreases Pesticide Use on Several Major Crops
16.4 Alleviating Water-deficit Stress Is an Increasingly Important Goal of Crop Improvement
16.5 Common Bean Provides an Example of Protecting against Virus
16.6 Uptake and Assimilation of Nitrogen Can Be Enhanced by Genetic Transformation
16.7 Phosphate Uptake Can Be Improved by Transgenic and Traditional Approaches
16.8 Pod Shatter-resistant Canola Prevents Seed Losses and Increases Yield
16.9 Genetically Engineered Forest Trees Are a New Frontier in Biotechnology
16.10 Male-sterile Lines and Fertility-restorer Genes Facilitate Hybrid Seed Production

Chapter 17. Introduced Traits That Benefit the Consumer, Maarten J. Chrispeels and Eliot M. Herman
17.1 Enhancing Essential Nutrients or Eliminating Harmful Ones Creates Functional Foods
17.2 Golden Rice is the Poster Child for Genetic Engineering in the Service of Humanity
17.3 Biofortifying Crops with Iron Is a Major Goal of Nutritionists
17.4 Heat-stable Vegetable Oils Are Better Suited for Deep-frying
17.5 Biotechnology Can Help Eliminate Food Allergens, But These Innovations May Not Come to Market
17.6 Acrylamide Can Be Eliminated from Processed Foods
17.7 Genetic Engineering Can Help Reduce Postharvest Food Losses
17.8 Conquering Citrus Greening Disease Could Lower the Price of Orange Juice
17.9 Are Tastier Tomatoes in Our Future?

Chapter 18. Food Safety: Are Foods Made from GE Crops Safe to Eat? David Tribe
18.1 Humans Have Continuously Been Exposed to Novel Foods
BOX 18.1 Kiwifruit: Entirely New Foods Occasionally Come into Our Stores
18.2 The Safety of Genetically Engineered Food Crops Has Been Extensively Debated
18.3 Genetically Engineered Food and Feed Crops Have an Excellent Safety Record
18.4 Specific Principles of Food Safety Assurance Apply to Foods and Feeds Developed Using Biotechnology
BOX 18.2 Internationally Accepted Guidelines for Risk Assessment of Foods
18.5 Evaluation of Variability Is a Major Tool to Limit Unintended Changes in GE Crops
18.6 Molecular Characterization of Intended Changes and Added Proteins Is a Necessary Component of Safety Assessment
18.7 Chemical Risk Evaluation Involves Investigating the Relationship between Degree of Exposure and Harmful Effects
18.8 Food Safety Experiments Demand High Standards of Experimental Design and Interpretation
18.9 Perspectives on the Impacts of Crop Biotechnology on Human and Animal Health Are Changing

Chapter 19. Challenges and Solutions for Subsistence Farmers, Manish N. Raizada
19.1 Subsistence Farmers Grow a Diversity of Crops to Maintain Resiliency
BOX 19.1 The Orphan Crops of Smallholders
19.2 Intensifying Agricultural Output on Smallholds Must Be a Priority
19.3 Water Is a Challenge for Smallhold Farmers
19.4 Degraded Soils and Soil Erosion Are Life-threatening Issues for Smallholders
19.5 Weed Control Is a Major Burden on Women and Girls in Developing Countries
19.6 Indigenous Farmers Have Strategies to Combat Pests and Diseases
19.7 There Are Hazards and Drudgery in Harvest and Postharvest Work
19.8 Maximizing Profit after Harvest Is Critical
19.9 The Public-Private Sector Job Creation Model Can Apply to Smallholders

Chapter 20. Plants as Chemical Factories, Krutika Bavishi and Birger Lindberg Moller
BOX 20.1 The Elixir of Poppies
20.1 Plant Secondary Metabolism Is a Treasure Chest of High-value Chemicals
BOX 20.2 Cannabis, Cannabinoids, and the "Entourage Effect"
20.2 Several Different Platforms Are Used to Produce Plant Secondary Metabolites for Human Use
BOX 20.3 "Hairy Roots" Produce Novel Chemicals
20.3 Plant Cells Cultured in Bioreactors Constitute Sustainable "Green Factories"
20.4 Metabolic Engineering of Plants Results In Higher Yields And Superior Quality Chemicals
BOX 20.4 Pink or Blue? Economics in the Floral Industry
20.5 Transferring Metabolic Pathways into Microorganisms Is a Promising Approach to Producing Secondary Metabolites
20.6 Microalgae Are Potentially Renewable Resources for a Bio-based Society
20.7 The World Needs Biodegradable Plastics

Chapter 21. Plants as Factories for the Production of Protein Biologics, Qiang Chen
21.1 Plants Can Be Used as Factories for Protein Biologics
21.2 There Are Several Production Strategies for Making Protein Biologics in Plants
21.3 Agroinfiltration Is an Effective Way of Delivering Transgenes into Plants
21.4 New Vectors for Gene Delivery Are Being Developed
21.5 The Plant Host and Plant Organs Used to Produce Biologics Must Be Chosen Carefully
BOX 21.1 A Primer on Adaptive Immunity, Immunoglobulins, and Monoclonal Antibodies
21.6 Monoclonal Antibodies and Vaccine Candidates Can Be Produced in Plants
BOX 21.2 Plant-produced MAbs Show Promise in the Fight against Ebola
21.7 A Plant-manufactured Biologic Has Been Approved to Treat a Genetic Disease in Humans

Chapter 22. Sustainable Food Production in the 21st Century, Maarten J. Chrispeels
22.1 Agricultural Intensification and Sustainability Are Equally Important
22.2 Can We Decrease the Yield Gap?
22.3 Smarter Agronomy Can Deliver Higher Yields
22.4 Wider Acceptance of GE Technology Is Essential if We Are to Increase Food Supplies
22.5 Research Is Key to Increasing the Intensity of Crop Production
22.6 Education at All Levels Is Essential if We Are to Increase Food Production
22.7 Maintaining the Resource Base Is Essential for Food Production
22.8 We Must Diminish Agriculture's Contribution to Climate Change and Global Pollution
22.9 Sustainability Will Require Greater Attention To Food Waste

Glossary
About the Chapter-Opening Photos
Illustration Credits
Index