Course Syllabus

Welcome to Agronomy 511 at Iowa State University!

Instructor

Instructor: Dr. Deb Lee 
Phone: Phone conferences can be requested by email as needed.
Email
: deblee@iastate.edu (Please contact me by email.)

Office Hours: By appointment. Please feel free to email at anytime. I will do my best to respond as quickly as possible. If it turns out to be difficult to reach understanding through text, we can arrange a follow-up phone call.

 
 

Course Overview

Course Description: Basic principles in the genetic improvement of crop plants. Methods of cultivar development in self-pollinated and cross-pollinated crop species. Required course for the Master of Science in Agronomy degree program and Agronomy Graduate Certificate program.

Course Prerequisites: AGRON 181 or equivalent, MATH 140, CHEM 163, BIOL 101. Restricted to graduate students enrolled in MS Agronomy and Agronomy Graduate Certificate online degree programs at ISU. Students from other departments must get permission.

Please see my welcome messages in the Announcements section of Canvas. For those who are interested, there is a document outlining my background posted as an 'Announcement'. Finally, I request that you please complete the discussion topic ("Classmate Introduction") in the Introduction module.

The goal of this course is to help you develop a basic understanding of crop improvement objectives and techniques.

The fundamental aspects of crop improvement are:

  • To identify the desired goal(s) (increased grain yield, improved bread-making quality, disease and insect resistance, uniform maturation of vegetables to enable mechanical harvest, a prettier flower color. . . the list is endless).
  • To identify accessible, desirable genetic sources of variation for the desired traits.
  • To identify and/or develop parent stock with the desired traits
  • To create conditions for introduction/exchange of the desired genetic material.
  • To create conditions for reliable screening/identification and selection of progeny with the desired traits.
  • To evaluate and test the selected progeny to confirm performance.
  • To provide progeny in a form that is reliably reproducible at needed scale and cost.

Crop improvement is an ancient practice. The thread of this course will hopefully illustrate the increased sophistication of crop improvement techniques and objectives associated with our increased scientific understanding. There will be times in this course, especially in the beginning modules, when you will wonder how the material applies to crop improvement. When those moments occur, I suggest that you look back at the fundamental aspects listed above and consider the relationship between the subject matter and these fundamentals.

Crop improvement initially involved visual selection of desirable observed variation: the seed head that held together when ripe, rather than shattering to pieces, or conversely, that was easier to thresh to release the seed. . . or the plant that seemed to escape disease damage, for example.

As our understanding of classical genetics developed in the early 1900's, we began to understand the potential for systematic, predictable outcomes from controlled hybridization and the crossing of specific parental types.

As crop improvement programs expanded, various limitations to progress were encountered, including:

  • Difficulty finding desirable, accessible sources of genetic diversity for desired traits.
  • Ability to achieve reliable, consistent selection pressure at reasonable cost.
  • Speed of generation progression - how fast able to grow and harvest each generation.
  • Expense to screen and evaluate the necessary progeny numbers: space, labor, data processing.

Our ever-expanding understanding of molecular genetics, biochemistry, and computer technology has enabled increasingly sophisticated procedures to address these limitations.

A brief outline of the course modules is included below.  Textbook and supplemental readings are also assigned to reinforce and expand on the module content.

Module 1 provides an introduction to crop improvement, with a focus on two fundamental concepts – variation and selection. 

Module 1 also includes a review of the life cycle of a plant, with special focus on the fundamentals of reproductive biology: meiosis, floral anatomy, pollen formation, egg formation, pollination, fertilization, and seed development, as a foundation for learning about the genetic basis for crop improvement in future modules.

Modules 2 through 4 are designed to build an understanding of classical genetic principles. These principles form the foundation for crop improvement methods.

Modules 5 through 7 provide an introduction to crop improvement methods for self- and cross-pollinated crops.

Module 8 provides a more detailed examination of the specific objectives of breeding for disease and insect resistance.

Module 9 is designed to build an understanding of basic molecular genetic principles.

Modules 10 and 11 examine procedures that are utilized to expand sources of variation and to improve selection efficiency and effectiveness.

Module 12 provides an introduction to field experiment analysis.

Module 13 includes an overview of how cultivars are prepared for release and plant variety protection laws.

Module 14 provides an overview of how crop improvement programs are organized and current topics in crop improvement.

Course Objectives

Course Goal – Enable students to develop basic knowledge of crop improvement practices and the genetic principles underlying these practices.

Specific objectives include:

Students will demonstrate an understanding of crop improvement objectives.

Students will demonstrate an understanding of variation and selection in the context of crop improvement.

Students will demonstrate an understanding of the distinction between genetic and environmental sources of phenotypic variation.

Students will demonstrate an understanding of Mendelian, quantitative, population, and molecular genetic principles.

Students will be able to articulate ways in which our understanding of fundamental genetic principles guide crop improvement procedures.

Students will be able to describe the different types of polyploidy and the impact of polyploidy on crop improvement efforts.

Students will be able to list the different cultivar types and describe the distinctive characteristics of each cultivar type.

Students will be able to describe natural pollination methods and the impact of pollination method on individual and population genetic composition.

Students will be able to list and describe methods of pollination control.

Students will demonstrate an understanding of the impact of pollination methods on choice of cultivar development procedures and utilization of different cultivar types.

Students will be able to describe practices used for cultivar development in cross-pollinated crop species.

Students will be able to list and describe distinguishing features of methods used for cultivar development in self-pollinated species.

Students will demonstrate an understanding of crop improvement practices related to improved pest resistance.

Students will demonstrate an understanding of the resources required for the development and release of a new cultivar.

Students will demonstrate knowledge of crop improvement history, and of current and future challenges and opportunities.

Students will be able to describe current germplasm conservation activities and factors required for effective germplasm conservation and utilization.

Course Structure

The on-line portion of Agronomy 511 consists of 14 modules, three exams, and a final paper.

Each module is designed to take one week to complete.

Your activities for each module will include the following:

  • Reading the on-line Canvas module content and utilizing the included learning tools.
  • Reading the assigned textbook pages and other required readings.
  • Completing and submitting each Module Assignment. The assignments are designed to provide practice with concepts in the modules and, in some cases, to inspire deeper thought.
  • Completing and submitting each Module Reflection. The reflections are designed to help you think about the module concepts as a whole, to consider how the module concepts apply to practical applications, and to let me know what is still unclear to you and/or if something has sparked an interest and you want assistance finding resources to learn more about the topic.
  • Participating in discussion.  There will be graded class discussions as parts of modules 2, 5, 7, and 11.
  • Asking questions.  Your questions are welcomed at any time via email.

Module 8 is optional and can be completed at any time during the second half of the semester.  The assessments for Module 8 include a Reflection and a quiz. There is no Assignment for Module 8.

Required Textbook

  • Sleper, D.A., and J.M. Poehlman. 2006. Breeding Field Crops. 5th edition. Blackwell Publishing, Ames, IA.

Some modules will have required and/or suggested readings in addition to the textbook assignment. These readings will be available to you via the Course Reserves link in the main navigation of the course.

The required readings are very important to developing a full understanding of the course content. The on-line course content attempts to address the essentials. However, similarly to an on-campus course, where the instructor can't cover everything in three hours of lecture per week, the on-line course content can't cover everything. An additional benefit to reading the textbook and other sources is the opportunity to see the material presented in a different manner. Sometimes the 'aha' moment may occur when the concept is presented in a different context, with different examples.

Instructor Interactions

Office Hours: By appointment. Please feel free to email at anytime. I will do my best to respond as quickly as possible. If it turns out to be difficult to reach understanding through text, we can arrange a follow-up phone call.

Email: Feel free to message the instructor via the Canvas Inbox if you have any questions or concerns.

Discussions: Enter comments either in response to student comments; sometimes to pose additional questions. Provide an ‘Instructor Summary’ after the discussion closes.

Graded Feedback: All graded assessments will be returned with feedback within 7 days of the due date. Personalized feedback will be provided for each assignment and reflection. In addition, a 'Reflection Response' document addressing common questions and unclear content will be posted at the conclusion of each module.  Instructor comments will be posted at the conclusion of each discussion.

Grading Procedures

Your course grade will be based on your performance on the following assessments:

Assignments

13 required x 10 points each

130 points

Reflection

13 required x 10 points each

130 points

Discussions

4 x 10 points each

40 points

Exam 1

Genetic Foundations

50 points

Exam 2

Breeding Self- and Cross-Pollinated Crops

50 points

Exam 3

Focus on Variation and Selection

50 points

Final Paper

50 points

Total

500 points

 

Optional extra-credit assessments: Module 8 Reflection (10 points); Module 8 Quiz (10 points)

The following scale (with plus/minus grading) will be used to determine course grades:

A: 90% and above

B: 80 to 89.9%

C: 70 to 79.9%

D: 60 to 69.9%

F: Below 60%

Expectations

Completion of Module Components

All modules are designed to begin on a Monday and to be completed by the following Monday.  All modules, except for Module 8, ask that you submit an assignment and a reflection summary.  In addition, modules 2, 5, 7, and 11 ask that you participate in a class discussion.   Details regarding assignments, reflection summaries, and discussions are as follows:

Assignments

Each assignment is worth 10 points. There are a total of 13 required assignments.

Each assignment is due by 5 p.m. U.S. Central time seven days after the module start date.

Your assignment will be evaluated based on the accuracy and clarity of your answers.  In addition to point deductions for incorrect and/or incomplete responses, points will be deducted when the contents are unorganized or difficult to understand. Please make an effort to communicate your answers clearly and completely. I need to be able to discern whether or not you understand the concept(s) addressed in the assignment question in order to award full credit. 

There is no assignment for Module 8.  The assignment is replaced with an optional quiz worth 10 points.

Reflections

Each reflection is worth 10 points.  There are a total of 13 required and 1 optional reflections. Each reflection is due by 5 p.m. U.S. Central time seven days after the module start date, except for the optional Module 8 reflection, which must be submitted by the end of the semester (please see course calendar for specific date).  Up to 10 extra credit points will be given for submitting the Module 8 Reflection.

Your reflection will be evaluated based on accuracy and clarity.  Please make an effort to communicate clearly.  I need to be able to discern whether or not you understand the concepts addressed in the module in order to award full credit. 

The expected components of your Reflection response are:

  1. Summarize the main points - This summary should provide an overview of the module content in your own words, highlighting and concisely discussing the major concepts of the module. Your summary is expected to be in written paragraphs. Simply listing main points without some indication that you understand them will not receive full credit for content.
  2. Value or usefulness of concepts learned - Connect the information learned to the 'real world' and/or to other information you know.
  3. Unclear items - If anything remains hazy, or you are unsure about some point, please ask! This is another opportunity for you to verify your understanding and to solicit clarification from the instructor. This question also serves to identify those topics that need improved presentation. Future students thank you! If there is truly nothing that is unclear, use this opportunity to ask a question that goes beyond the course material OR simply state that you feel confident that you understand the module content.  Do not feel that you have to make something up.

Key elements to a successful Reflection response:

Reflect before writing:

Review the module headings and subheadings.

Think about each topic in relation to the context of the course…
how does the topic relate to understanding crop improvement goals and methods?

Strive for professional writing quality:

Use complete sentences.  Use professional vocabulary.

Write in paragraph format.  Do not submit your study notes or module outline as your Reflection summary.

Use your own words:  I understand that this can be a challenge when there is limited time to absorb the concepts before writing.  Please give it your best effort.

Proofread your work:

Read to confirm that your summary is arranged logically and flows smoothly.

Check for spelling and grammatical errors.

Submit on time:  Please make prior arrangements with me if you know in advance that you will not be able to submit your work by the due date.

Points will be deducted from the Reflection summary for the following:

  • Inaccurate statements
  • Unclear statements; when I am unable to determine whether or not you clearly understand the concept.
  • Multiple errors in spelling and/or writing mechanics.
  • Submitting lists, outlines, or a product that does not exhibit an effort to summarize the module content.

Discussions

There will be graded class discussions as parts of modules 2, 5, 7, and 11.

Participation in each discussion is worth a total of 10 points.

Full participation is considered posting an initial response to the discussion prompt and posting two additional comments in response to your classmates’ postings.

Expectations:

  • You are expected to post one response to the discussion prompt before 8:00 a.m. U.S. Central Time on Saturday morning of that discussion week. (maximum 6 points)
  • You are expected to post comments in response to two of your classmates’ postings before 5:00 p.m. U.S. Central Time on Monday afternoon of that discussion week. (maximum 2 points for each posting)

Discussion contributions will be evaluated based on depth and clarity.

Some of the discussion topics are designed to engage you more thoroughly with the course concepts.  Others are designed to encourage you to think about crop improvement in practice.  I have tried to make the topics interesting enough to encourage interaction. There are usually no right or wrong answers; the hope is to inspire you to share your experiences and thoughts so that you can learn from each other. I acknowledge that on-line discussions are not the same as being in a room together. Please give the discussions your best effort.

Exams

There will be three on-line exams during the course.

Additional details regarding these exams will be provided in Canvas two to three weeks prior to each exam period.

Exam 1
Exam 1 will cover topics from Modules 1 through 4 – content related to the genetic foundations of crop improvement.  Exam 1 is worth 50 points.  

Exam 1 will be available for a period of five days roughly coinciding with the week of Module 5.  

Check Canvas for the specific dates of Exam 1 availability.

Exam 2
Exam 2 will cover topics from Modules 5 through 7 – content related to crop improvement methods for self- and cross-pollinating crops.  Exam 2 is worth 50 points.  

Exam 2 will be available for a period of five days roughly coinciding with week 8.  

Check Canvas for the specific dates of Exam 2 availability.

Exam 3
Exam 3 will cover topics from Modules 9 through 11 – content related to molecular genetics and applications to expand variation and improve selection. Exam 3 is worth 50 points.  

Exam 3 will be available for a period of five days roughly coinciding with the week of Module 12.  

Check Canvas for the specific dates of Exam 3 availability.

Final Paper

The final paper will be based on your reading of a chapter of your choice of one of the following chapters from our textbook (Sleper and Poehlman, Breeding Field Crops):
    14. Wheat; 15. Rice; 16. Soybean; 17. Corn/Maize; 18. Sorghum; 19. Cotton

    20. Forages; 21. Potato; 22. Sugarcane

The final paper should include information on the following related to the crop you have selected: breeding objectives, basic genetics of the crop, breeding methods, crop history, and any unique challenges.  You are also asked to include comments on how your understanding of what you read was influenced by what you have learned in Agronomy 511.  In other words, where possible, try to make connections between what you learned about the specific crop and the concepts we have covered in Modules 1 through 14.  Are there examples of what you read about crop that you would not have understood prior to taking Agronomy 511; or that you would not have understood to the same degree?

The final paper is worth 50 points.  The paper will be due roughly one week after the completion of Module 14.  Please check Canvas for the specific due date for the final paper.

The final paper grade will be based on the following:

  • Degree of focus on crop improvement concepts
  • Depth/thoroughness and accuracy of coverage of the information in the reading
  • Communication quality – clear articulation of the concepts; complete sentences and evidence of proofreading
  • Relating what you read to what you have learned in Agronomy 511

Policies

Communication Policy

All communication within the course should adhere to university standards of Netiquette at ISU. Specifically, communication should be scholarly, respectful, professional, and polite. You are encouraged to disagree with other students, but such disagreements need to be based upon facts and documentation. It is the instructor’s goal to promote an atmosphere of mutual respect in our interactions. Please contact the instructor if you have suggestions for improving the interactions in this course.

Please contact me by email: Dr. Debra Lee; deblee@iastate.edu to ask questions. You can expect a response within 24 hours except when you have been notified in advance of travel times.

General announcements will be posted to the Announcements section of Canvas.

Be sure to properly configure your Notification settings or commit yourself to checking Canvas daily for new communication.

Feedback Policy

All graded assessments will be returned with feedback within 7 days of the due date. Personalized feedback will be provided for each assignment and reflection. In addition, a 'Reflection Response' document addressing common questions and unclear content will be posted at the conclusion of each module.  Instructor comments will be posted at the conclusion of each discussion.

Deadlines

All deadlines are posted on the course calendar in Canvas. Notification of any changes to deadlines will be communicated via an Announcement in Canvas.

Need extra time to meet a deadline? Explain the situation to your instructor IN ADVANCE and accommodation can be made.  The explanation doesn’t need to be extensive.  The important factor is to attempt to notify the instructor ahead of time.  I understand that emergencies occasionally occur.  Please find some way to make contact with the main office or the instructor as soon as possible in the event that an emergency is preventing timely completion of your course work.

Academic Integrity Policy

The class will follow ISU's policy on academic dishonesty. Anyone suspected of academic dishonesty will be reported to the Dean of Students Office. It is your responsibility to understand ISU's policy on academic plagiarism. All Discussions and Exam Questions will be screened for plagiarized content. There are several resources available to help you avoid committing academic misconduct.

Disability Accommodation

Iowa State University complies with the Americans with Disabilities Act and Sect 504 of the rehabilitation Act. If you have a disability and anticipate needing accommodations in this course, please contact the instructor to set up a meeting within the first two weeks of the semester or as soon as you become aware of your need. Before meeting, you will need to obtain a SAAR form with recommendations for accommodations from the Disability Resources Office, located in Room 1076 on the main floor of the Student Services Building. Their telephone number is 515-294-7220 or email disabilityresources@iastate.edu. Retroactive requests for accommodations will not be honored.

Harassment and Discrimination

Iowa State University strives to maintain our campus as a place of work and study for faculty, staff, and students that is free of all forms of prohibited discrimination and harassment based upon race, ethnicity, sex (including sexual assault), pregnancy, color, religion, national origin, physical or mental disability, age, marital status, sexual orientation, gender identity, genetic information, or status as a U.S. veteran. Any student who has concerns about such behavior should contact his/her instructor, Student Assistance at 515-294-1020 or email dsosas@iastate.edu, or the Office of Equal Opportunity and Compliance at 515-294-7612.

Religious Accommodation

If an academic or work requirement conflicts with your religious practices and/or observances, you may request reasonable accommodations. Your request must be in writing, and your instructor or supervisor will review the request. You or your instructor may also seek assistance from the Dean of Students Office or the Office of Equal Opportunity and Compliance.

Sample Study Plan

The following are suggested steps for working through each Module:

  1. Begin by reading the Module ‘Introduction’.  Take a brief moment to think about what you may already know about the Module topics.
  2. Read the Module ‘Learning Outcomes’.  Again, take a brief moment to think about what you may already know about the Module learning outcomes.
  3. Read through the Module content at browsing speed.  Take special note of the page and section headings.  The headings provide a structure for understanding the Module content. 
  4. Re-read the Module content.  Take notes.  Complete the Study Questions and Try This! exercises as you work through the Module.  After you complete this thorough reading of the Module, make note of any concepts that are unclear.
  5. Read the ‘Assigned Readings’.  The readings are an opportunity to reinforce the Module concepts.  At times, the readings may be helpful by presenting the concepts in a slightly different manner.  This may be just what is needed to help clarify your understanding.  
  6. Complete the Module ‘Assignment’.  The purpose of the Assignment is to provide an opportunity to practice with important Module concepts.  In most cases, the answers to the Assignment questions can be found directly in the Module content.  Remember to express the Assignment answers in your own words.
  7. Complete the Module ‘Reflection’ exercise.  The purpose of the Reflection Summary is to provide an opportunity to review the Module content, to confirm your understanding of the Module concepts and to practice expressing the content in your own words.  Writing a good summary requires that you understand the Module content well enough to write about it.  Please refer to the Agronomy 511 Syllabus for suggestions on writing a successful Reflection Summary
  8. When there is a Discussion Topic associated with the Module, challenge yourself to post your first comment before Thursday morning of the Module week.  The discussions tend to be most valuable the greater the amount of time for exchange of comments.
  9. Read the ‘Supplemental Readings’ as time permits.  The supplemental readings are provided to help reinforce concepts and to broaden your exposure to some of the Module topics.

Below is a suggested study plan of how you might structure your time.

Sunday

Monday

Tuesday

Wednesday

Thursday

Friday

Saturday

Week 1

 

Start Module 1

Read the Module 1 online materials at browsing speed


Take special note of the Introduction and Learning Outcomes


Post your classmate introduction

Read the Module 1 online materials, making notes to aid with Reflection summary


Read the Module 1 Assigned Readings

Begin Module 1 Assignment and Reflection

Week 2

Complete M1
Assignment and Reflection

Start Module 2


M1 Assignment, Reflection, and Classmate Introduction due

Read the Module 2 online materials at browsing speed


Take special note of the Module Introduction and Learning Outcomes


Post initial Module 2 Discussion response

​Read the Module 2 online materials, making notes to aid with Reflection summary


Read the Module 2 Assigned Readings

Initial Module 2 discussion response due


Begin M2 Assignment and Reflection


Post responses to classmate discussion comments

Week 3

Complete M2
Assignment and Reflection


Post responses to classmate discussion comments

Start Module 3


M2 Assignment, Reflection, and Discussion responses due


Review your M1 feedback

Read the Module 3 online materials at browsing speed


Take special note of the
Module Introduction and Learning Outcomes

Read the Module 3 online materials, making notes to aid with Reflection summary


Read the Module 3 Assigned Readings

Begin M3 Assignment and Reflection

Week 4

Complete M3
Assignment and Reflection

Start Module 4


M3 Assignment and Reflection due


Review M2 feedback

Read the Module 4 online materials at browsing speed


Take special note of the Module Introduction and Learning Outcomes


Post initial Module 4 Discussion comment

Read the Module 4 online materials, making notes to aid with Reflection summary


Read the Module 4 Assigned Readings

Initial Module 4 discussion response due


Begin M4 Assignment and Reflection


Post discussion responses to classmate comments

 

Support

Category Description Action

Course Content Support

Questions related to course content or grading should be directed to the course instructor. Instructor via Canvas Inbox

Student Support

The Center for Excellence in Learning and Teaching is an organization dedicated to supporting, promoting, and enhancing teaching effectiveness and student learning at ISU.

Self-guided orientation which you may find useful.

CELT: Online Learner Support

Self-Guided Orientation

Canvas Technical Support

If you experience any technical issues while using Canvas, contact the Solution Center. The Solution Center's hours are posted on their website.

Solution Center

Technology support

If you have any technical issues while using the University Library's Course Reserves system, please contact the The Library's Help Desk hours are posted on their website.

For all other technical issues, contact Agron DevLab Support. The Agronomy Development Lab staff is guaranteed to respond to requests within 24 hours during regular business hours. All requests made during the weekend will be addressed first thing Monday morning.

Agron DevLab Support

Library staff

Writing Support

The MS Agronomy program has built a Writing Guide to help answer some of the questions you may have while working on your courses.

Deborah Burns is available for one-on-one consultations and can assist you with any part of the writing process. Schedule an appointment with Deborah through the CELT's website (Links to an external site.) or via email.

Writing Guide

CELT Website (Links to an external site.) or email.

Library and research support

Anita Kay is the liaison librarian to the Department of Agronomy. She can help find any article, book or any other piece of information that you want assistance finding.  Anita has also built a really useful Agronomy Research Guide (Links to an external site.).

Anita Kay
Agronomy Research Guide (Links to an external site.)

Department Contact

Contact Dr. Allen Knapp, Associate Chair for Academics in Agronomy, if issues persist after working with the support systems listed above.

Dr. Allen Knapp

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