PPATH 533 Course Syllabus

Fall 2016 PPATH 533 Molecular Genetics of Plant-Pathogen Interactions Course Syllabus

Course Logistics

Instructor: Seogchan Kang, Ph.D.

Location: 201 Buckhout Lab

Time: Tuesdays and Thursdays | 11:15-12:30 p.m.

Instructor contact information:
Office: 311 Buckhout Lab
Phone: (814) 863-3846

Course Objectives

This 3-credit course aims to help students understand different forms of plant-microbe and microbe-microbe interactions, various molecular and cellular mechanisms underpinning these interactions, how such interactions affect plant growth and health, and key experimental tools that can be applied to study plants, microbes, and their interactions. Another important goal is to improve their ability to identify interesting problems, develop relevant hypotheses, design appropriate experimental approaches, and formulate new questions and hypotheses based on resulting data, mainly through critical review of published research papers. Students completing this course will:

  1. Know current concepts and paradigms concerning diverse forms of plant-microbe and microbe-microbe interactions in light of plant growth and health and molecular mechanisms underlying these interactions;
  2. Be able to identify major gaps in our knowledge and emerging areas of research in plant-microbe and microbe-microbe interactions;
  3. Understand how various genetic/genomic/cytological tools work and can be applied to investigate the mechanism underpinning plant-microbe/microbe-microbe interactions and the biology, ecology, and evolution of individual organisms as well as their communities;
  4. Be familiar with the entire process of scientific discovery;
  5. Identify potential applications of various forms of plant-microbe and microbe-microbe interactions to help meet the steadily growing global need for quality food, fiber, and feed.

Rationale and Goals

Use of fertilizers and pesticides to support crop production represents one of the main pillars that have sustained the Green Revolution. However, multi-faceted negative impact from the heavy reliance on them has increased the call for alternative or complementary strategies to meet the steadily growing global need for quality food, feed, and fiber without overtaxing the environment and harming human and ecosystem health. Other intensifying threats to global crop production, such as water shortage, soil salinity, frequent movement of pathogens and pests via increasing global trade and travels, and climate changes, also call for novel strategies. Effective and sustainable solutions to these global challenges will be more forthcoming with enhanced understanding of the mechanisms underpinning diverse forms of plant-microbe and microbe-microbe interactions in agroecosystems.

The course will cover more than pathogenic interactions and pathogens, because plant health cannot be fully understood without taking into consideration other forms of plant-microbe interactions. It is rather simplistic and anthropocentric, but plant-associated microbes can be classified into "the bad, the good, and the unknown" in light of the resulting effect of their presence and activity to plant growth and health and collectively form the phytobiome. As demonstrated by many historical disease epidemics, diverse groups of pathogens can devastate crop production, drastically alter forest and urban landscapes, and also taint plant products by secreting metabolites toxic to animals and humans. In contrast, certain microbes are indispensable for plant growth and fitness, because they enhance plant’s stress resistance, stimulate plant growth, help scavenge nutrients, or confer combinations of these benefits. Deployment of such beneficial microbes has been promoted as a means for reducing the use of fertilizers and pesticides. However, difficulties in ensuring consistent benefit to plants under different conditions have hindered their wide adaption. Besides diverse pathogens and beneficial microbes, plants are also intimately associated with complex communities of other microbes whose roles in plant growth and health are poorly understood. However, rapidly increasing sequencing capacity and various omics tools are expected to help enhance knowledge about the nature and biology of these unknowns, how they interact with pathogens and beneficial microbes, and how their presence affects plant growth and health.

Research papers and review articles concerning these three groups of microbes, how they interact with plants and other microbes, and effects of their interactions on plant growth and health will be used to overview current concepts and models. Since various molecular and imaging tools have greatly advanced our understanding of the biology, ecology, and evolution of plants, microbes, and their interactions, the underlying principles, utilities, and limitations of key experimental tools will also be reviewed. Given the increasing importance of genomics, examples for how to use genomics data and tools to study plant-microbe/microbe-microbe interactions will be highlighted throughout the course.

Since the publication in 1995 of the first complete microbial genome sequences, that of a human pathogenic bacterium, Haemophilus influenzae, the number of sequenced genomes in multiple kingdoms has been growing exponentially. For fungi alone, hundreds of species already have been sequenced with thousands more species and different isolates of previously sequenced species currently being sequenced. Not surprisingly, many of the microbes targeted for genome sequencing are important plant or animal pathogens. Genome sequences across diverse microbial species has not only added much greater value than would be derived from a few model organisms alone, but also has significantly accelerated understanding of the biology and evolution of many lesser studied, yet equally important, relatives of the model organisms via comparative analyses. The microbial genome sequence data can now be exploited to unveil the evolution and mechanisms of different microbial life styles, such as pathogenesis, symbiosis, and the ability to proliferate in particular ecological niches. A better understanding of microbial biology based on their genome sequences and functional genomic analyses will not only advance our efforts to control pathogens, but also facilitate judicious use of beneficial microbes to improve the performance of crop plants and/or protect plants and the environment. The genomes of many plant species have also been sequenced. Collectively, insights, data, and tools derived from genomics have opened up many new opportunities to study and solve a wide range of plant heath-related problems.

Even though the main focus of the course will be on molecular, cellular, and evolutionary mechanisms underpinning plant-microbe and microbe-microbe interactions and research tools for studying such mechanisms, I hope that through the course students will learn to appreciate these interactions in broader contexts (e.g., global security, environmental sustainability, organismal biology, structure-function relationship, etc.). For the development and implementation of effective crop management strategies, integration and application of the knowledge and techniques from many areas of science (not just molecular tools) is essential. In addition, as the nature of research problems has become more complex, the need for interdisciplinary work spanning traditional scientific boundaries has also increased.

Course Organization

This course will consist of three main components:

  • lecture
  • student presentation
  • take-home assignments

Besides attending lectures on key findings from historical and contemporary studies, each student is required to lead a few discussions on research papers and actively participate in class discussion. Presentation schedule will be determined based on the timing of main topics covered in class.

Course Grading

ActivityGrade %
Class participation/attendance 10
Class presentation 30
Paper discussion 20
Take-home assignments 40


Basic knowledge of microbiology, molecular genetics, plant molecular genetics and physiology, and/or plant pathology is preferred but not required. The participants are expected to be familiar with basic concepts and terminologies in plant pathology. Plant Pathology (George N. Agrios, Academic Press), and selected review articles are recommended references. A list of core references for individual topics will be distributed.

Disability Statement

Penn State welcomes students with disabilities into the University’s educational programs. Every Penn State campus has an office for students with disabilities. The Student Disability Resources website provides contact information for every Penn State campus. For further information, please visit the Student Disability Resources website.

In order to receive consideration for reasonable accommodations, you must contact the appropriate disability services office at the campus where you are officially enrolled, participate in an intake interview, and provide documentation. If the documentation supports your request for reasonable accommodations, your campus’s disability services office will provide you with an accommodation letter. Please share this letter with your instructors and discuss the accommodations with them as early in your courses as possible. You must follow this process for every semester that you request accommodations.

Academic Integrity

Academic integrity is the pursuit of scholarly activity in an open, honest, and responsible manner. Academic integrity is a basic guiding principle for all academic activity at The Pennsylvania State University, and all members of the university community are expected to act in accordance with this principle. Consistent with this expectation, students should act with personal integrity, respect other students' dignity, rights, and property, and help create and maintain an environment in which all can succeed through the fruits of their efforts. Acts of dishonesty violate the fundamental ethical principles of the university community and compromise the worth of work completed by others. A lack of knowledge or understanding of the University’s Academic Integrity policy and the types of actions it prohibits and/or requires does not excuse one from complying with the policy.

Academic Integrity Guidelines for the College of Agricultural Sciences

Course Topics

Section 1. Introduction

  1. Key challenges to sustainable crop production
  2. Overview of central concepts and models underpinning plant-microbe interactions

Section 2. Research tools

  1. Genomics tools
  2. Molecular genetic, imaging and analytical chemistry tools for studying plants, microbes, and their interactions

Section 3. Molecular genetic basis of plant-microbe interactions

  1. Different forms of plant-microbe interactions and the nature of signals/effectors underpinning these interactions
  2. Gene-for-gene model
  3. Nature of pathogenicity/virulence factors and their mechanisms of action
  4. Secreted metabolites that participate in plant-microbe interactions

Section 4. Molecular and cellular basis of plant defense

  1. Non-host resistance
  2. Resistance gene-mediated defense responses
  3. Systemic resistance

Section 5. Applications to develop effective disease control strategies

  1. Chemical control
  2. Biocontrol
  3. Biotechnological approaches