Texas Tech University

PSS6001 - Molecular Basis of Plant Responses to the Environment

Special Topic in Plant and Soil Science


Dr. Benildo de los Reyes
Professor of Plant Genomics and Bayer CropScience Endowed Chair
Graduate Programs Director
Department of Plant and Soil Science
Texas Tech University

Experimental Sciences Building
Room 215, Mail Stop 2122
Lubbock, TX 79409-2122
Phone: +1 (806) 834-6421; Fax: 806-742-0775
Email: benildo.reyes@ttu.edu

Text Books

  1. Biochemistry and Molecular Biology of Plants, 2nd Edition (2015) by Buchanan BB, Gruissem W, Jones RL. American Society of Plant Biologists, John Wiley and Sons Ltd., ISBN:9780470714218; ISBN: 978-0-47071-422-5. (Highly Recommended)
  2. Plant Physiology, 5th Edition (2010), by Taiz L, Zeiger E. Sinauer Associates, Inc., ISBN: 978-0-87893-866-7.

All lecture materials will be provided in electronic form to the students.

Course description

Prerequisites: Consent of instructor; Credits: 3 credits including lectures, literature reading and class discussions

Plants adapt to changes in their environment through exquisitely coordinated and fine-tuned processes regulated at the cellular and molecular levels. Advances in genetics, genomics, biochemistry, and molecular biology during the last half century uncovered the molecular underpinnings of complex processes by which plants adjust their physiological status and biochemical attributes in order to cope with a plethora of biotic and abiotic insults. This course is a platform for integrating the advances in mechanistic and genome-enabled biology with the seminal science and classical paradigms of plant stress physiology towards appreciation of the 'cause-and-effect' relationships between the processes occurring at the cellular and genome levels and the phenotype observed at the whole-plant level. Stress is integral to almost all phases of plant growth and development. To address this dogma, the course will be presented in three modules. In the first module, students are led to the big picture of the molecular life of a plant, by dissecting the processes of growth and development, and the interaction between genetics and environmental factors in their regulation. Understanding the molecular basis by which plant growth and development are regulated by the environment sets the stage for dissecting the biochemical and molecular adaptive responses to abiotic and biotic stresses, and the genetic regulatory mechanisms that configure those processes. These aspects of plant stress physiology are covered in-depth in the second and third modules, respectively. Translation of molecular mechanisms to innovative genetic engineering strategies for enhancing the stress tolerance or disease resistance of crop plants sums up each module. Lessons on such topics provide students a basic understanding of how the outcome of functional genomics is directly applied to stress physiology and breeding.

Purpose of the course

The grand challenge to sustainable agriculture is to continuously make incremental enhancements in crop productivity in order to meet the food demands of the projected world population of 10 billion people by the middle of the 21 st century. This challenge is further complicated by the continuous marginalization of agricultural ecosystems, steady deterioration or depletion of natural resources, and rapidly changing dynamics of pest and pathogen populations, all of which are consequences of global climate change. Addressing such a challenge requires in-depth understanding of the fundamental mechanisms that are critical to plant resilience and productivity under sub-optimal environments, and the application of such knowledge to crop breeding and other innovative crop management approaches. With the burgeoning impact of climate change to plant agriculture, this course is very timely as it serves as a platform for educating graduate students interested in either fundamental plant biology or applied crop science on the mechanisms by which plants respond and adapt to various forms of stresses at the cellular level, and how these processes are integrated to configure whole-plant level defenses. Every student specializing in any sub-discipline of fundamental plant biology, agronomy, or horticulture must have a decent understanding of the mechanisms of how plants adapt to stresses and their genetic regulation. Therefore, this course aims to complement other applied courses in crop physiology taught in agronomy, horticulture and other fields of applied plant science, by presenting the mechanistic aspects. The goal is to illuminate the physiological processes observed at the whole plant or population level with molecular genetic and biochemical mechanisms to assist students in gaining appreciation of the potential of genetic technologies in developing the next generation of climate-resilient and disease-resistant crops.

Grading criteria and scale

Research paper presentation 10 %
Written critique of research papers 10 %
Participation in class discussions 10 %
Written research proposal 40 %
Oral presentation of research proposal 15 %
Written critique of research proposal 15 %

A = 85% to 100%;      B = 75% to 84%;        C = 65% to 74%;        D = 50% to 64%;        F = below 50%

Topic outline

Module-1: Environmental regulation of plant growth and development

  1. Growth regulation by hormones
    1. Overview of signal transduction.
    2. Auxin: Biosynthesis, degradation, signal transduction, gene expression.
    3. Gibberellin: Biosynthesis, degradation, signal transduction, gene expression.
    4. Cytokinin: Biosynthesis, degradation, signal transduction, gene expression.
  2. Phototropism and regulation of plant growth and development by light.
    1. Phytochrome signaling.
    2. Circadian rhythms.
    3. Genetic control of light regulated responses
  3. Environmental regulation of flowering
    1. Floral meristem, evocation, and floral organ development.
    2. Photoperiodism and the circadian clock.
    3. Florigen and long distance signaling.
    4. Vernalization.
    5. Regulation of gene expression during transition of the floral meristem.
  4. Maturation and senescence
    1. Programmed cell death during plant development.
    2. Regulation of gene expression during senescence.

Module-2: Plant responses to abiotic stresses

  1. Cellular dehydration are induced by water deficit/drought, salinity, and cold
    1. Common denominator: Reactive oxygen species and cellular toxicity.
    2. Physical and biochemical injuries to the cell.
  2. Hormonal regulation of plant responses to abiotic stresses
    1. Signal transduction: Ca2+ and oxidative signaling.
    2. Abscisic acid: Biosynthesis, degradation, and signal transduction.
    3. Ethylene: Biosynthesis, degradation, and signal transduction.
    4. Brassinosteroid: Biosynthesis, degradation, signal transduction.
    5. Coordination of transcription by stress hormones.
  3. Mechanisms of osmotic adjustment
    1. Osmotin and compatible osmolytes.
    2. Late Embryogenesis Abundant (LEA) proteins.
  4. Mechanisms of salinity tolerance and subcellular sequestration
    1. Ionic toxicity and osmotic stress.
    2. SOS signaling.
    3. Vacuolar transport and efflux mechanisms.
    4. Carriers, pumps, and membrane channels.
  5. Cold acclimation and thermotolerance
    1. Cell membrane stabilization
    2. Antifreeze proteins
    3. DREB/CBF gene regulon and its role in cold acclimation and drought tolerance
  6. Responses to flooding stress
    1. Anoxia and hypoxia.
    2. Role of ethylene.
    3. Sub1 genetic network and tolerance to anaerobic stress.
  7. Genetic engineering for stress tolerant crops
    1. Stress physiological genomics and quantitative trait loci.
    2. Agrobacterium-mediated transformation and regulon engineering.
    3. Post-transcriptional gene silencing and genome editing.


Module-3: Plant responses to biotic stresses

  1. Pathogen virulence mechanisms
    1. Bacteria.
    2. Fungi and oomycetes.
    3. Virus.
    4. Virulence molecules and effectors.
  2. Host plant responses and defense systems
    1. Baseline defenses.
    2. Oxidative burst and defense-associated programmed cell death.
    3. Secondary metabolites: Phenolics, alkaloids, terpenoids.
    4. Hypersensitive response (HR).
    5. Systemic acquired resistance (SAR).
    6. Hormones and elicitors: Ethylene, salicylic acid, jasmonic acid
  3. Genetic basis of plant-pathogen interaction
    1. Gene-for-gene mechanisms, R-genes, and R-gene-mediated disease resistance.
    2. Signal transduction mechanisms: NBS-LRR family of receptor kinases.
    3. Quantitative resistance mechanisms.
    4. Cross-talks, synergism, and antagonism of defense signaling pathways.
    5. Cross-talks of defense signaling against pathogens and abiotic stresses.