HORT 480 HORTICULTURAL GENOMICS/CROP BIOTECHNOLOGY SPRING 2011
Credits: 3
Goals
The course will:
1.
Explore the challenges and constraints in crop improvement
2.
Introduce concepts and approaches in the application of genetics, genomics, and bioinformatics to crop improvement
3.
Explore the controversy surrounding Genetically Modified Organisms (GMO) vs non
GMO approaches to crop improvement.
4.
Reinforce the need and opportunities for application of interdisciplinary scientific knowledge for crop improvement.
5.
Promote skills in critical thinking.
6.
Promote skills in research communication (written, visual, and oral).
7.
Promote scientific teamwork.
Instructor
Dr. Dorrie Main, 45 Johnson Hall, 335 2774, dorrie@wsu.edu
Office hours: Wednesday 11-12 and by appointment as needed
Class time
Lecture: Tu,Th 3.10–4.25 pm, Johnson Hall Room 24
Prerequisites
MBios 320
Text book
No prescribed text
Expected student learning outcomes
Through engagement in lectures, assignments, and other activities, students will:
1.
Demonstrate an understanding of the science and controversy involved in GMO and non-GMO approaches to crop improvement
2.
Demonstrate an understanding of the need for interdisciplinary solutions required for crop improvement
3.
Demonstrate teamwork, problem-solving, and communication skills.

LECTURE OUTLINE
Date Lecture topic
Jan 18 Course Introduction
20 Genomics Overview
25 Bioinformatics Overview
27 Biotechnology Overview
Feb 01 From Gene to Genome
03 Case Study: The Washington State Apple Breeding Program ( Dr. Evans)
08 DNA information for Tree Fruit Improvement (Dr. Peace)
10 Gene Functional Characterization (Dr. Neff)
15 The Challenges and opportunities facing WA Tree Fruit producers (Dr. McFerson)
17 Sequencing technology and application I
22 Translational genomics presentations and discussion
24 Case Study: Onion Genomics (Dr. Schroeder)
Mar 01 Sequencing technology and application I
03 Case Study: The Washington State Potato Research Program (Dr. Paveck)
08 Case Study: The Washington Spring Wheat Breeding Program (Dr. Humphrey)
10 Association Mapping, Extracting Useful Alleles from Germplasm (Dr. Coyne)
22 Case Study: The USDA-ARS Pulse Improvement Program (Dr. McGee)
24 Sequence Analysis I
29 GMO vs non GMO - The Class Debate
Apr 05 Sequence Analysis II
07 Comparative Genomics
12 Database Resources II
14 Groups Solution Poster Presentation
19 Class Project meeting I
21 Class Project meeting II
26 Class Solution Oral Presentation
28 Course Summary and Feedback

ASSESSMENT
Total = 200 pts
20 Assignment 1 – Translational Genomics in Crops
30 Assignment 2 – Gene Functional Characterization
40 Assignment 3 – GMO vs non GMO debate
30 Assignment 4 – Genome Annotation
80 Assignment 5 – Team Projects
Grading scale
100-93%
90-92%
86-89%
83-85%
80-82%
A
A-
B+
B
B-
76-79%
73-75%
70-72%
66-69%
62-65%
< 62
C+
C
C-
D+
D
F
Late assignments – Written reports are due at the beginning of class on their due date. Late assignments will result in a 10% grade penalty per day beginning the first day the assignment was due.
Assignment briefs
1.
Translational Genomics in Crops
Seek real world examples of successful translational genomics in crops of interest, for practical applications of diagnostics, therapeutics, transgenics (or cisgenics), and markerassisted breeding. Present these examples to the class on February 22.
2.
Gene Functional Characterization
Develop an experimental plan involving gene functional characterization to address a specific challenge in crop production. Written report due March 3.
3.
GMO vs non GMO debate
Two teams debate the pros and cons of GMO in crop improvement. Oral debate on March
29.
4.
Genome Annotation
Conduct genome sequence analysis to contribute to public annotation of an important crop genome. Written report due April 5.
5.
Team Projects
In teams, apply genetics, genomics, and bioinformatics approaches and techniques to seek solutions to a specific challenge in crop improvement, building on assignments 1-3. Each team presents a poster of proposed solution on April 14. Then, class discussions will lead to consensus on a single integrated solution. Course culminates in a single seminar presentation supported by the entire class on April 26.

Attendance
Attendance is expected and may sometimes be recorded. Attendance and participation in class sessions will be encouraged and may influence the course final grade. Absences because of illness, personal and/or family crises, mandated court appearances, university approved events, or similar reasons will be accommodated as long as such absences are not excessive and notification is provided to the instructor in advance. Excused absences should be arranged prior to any known or planned event. Required University activities will be excused absences if an official Class Absence Request form signed by the sponsoring faculty or organization is given to the instructor before the event.
Disability statement
Reasonable accommodations are available for students who have a documented disability.
Please notify the instructor during the first week of class of any accommodations needed for the course. Late notification may cause the requested accommodations to be unavailable. All accommodations must be approved through the Disability Resource Center (DRC) in
Administration Annex 206 (Tel. 335-1566).
Cheating (WAC 504-25-310)
Cheating is the intentional use of, or attempt to use, unauthorized material, information, or study aids in any academic activity to gain advantage. Cheating includes, but is not limited to, communicating improperly with others, especially other students, during tests or the preparation of assignments for classes; copying from books, notes, or other sources during a test when this is not permitted; copying from another student’s work (reports, laboratory work, computer programs, files, etc.); making improper use of calculators or other devices during a test; illegitimately procuring or using copies of current examinations; allowing a substitute to take an examination or write a paper for oneself.
Plagiarism (WAC 504-25-310)
Plagiarism is knowingly representing the work of another as one’s own, without proper acknowledgment of the source. The only exceptions to the requirement that sources be acknowledged occur when the information, ideas, etc., are common knowledge. Plagiarism includes, but is not limited to, submitting as one’s own work the work of a “ghost writer” or work obtained from a commercial writing service; quoting directly or paraphrasing closely from a source without giving proper credit; using figures, graphs, charts, or other such material without identifying the sources.
Academic Integrity Processes (WAC 504-25-315)
Every act of academic dishonesty affects academic evaluation of the student and also is a violation of the University’s standards of conduct. Responsible instructors retain the authority and responsibility to assign grades to students, considering from an academic standpoint the nature of the student’s action. This is the case even when the case is referred to the University
Academic Integrity Process. Students have recourse to appealing the responsible instructor’s assignment of grades according to usual academic policy. See Academic Regulation 104.

All clear instances of academic dishonesty shall be reported to the Office of Student Conduct as outlined in 504-35-335(2). The first reported instance at WSU of academic dishonesty by a student will be treated as purely an academic matter unless, in the judgment of the responsible instructor, more serious action should be taken through the disciplinary process. Any allegation of subsequent academic dishonesty will be treated as a matter to be referred to the Office of
Student Conduct
Reports of Academic Dishonesty (WAC 504-35-320)
Any member of the University community who witnesses an apparent act of academic dishonesty shall report the act either to the instructor responsible for the course or activity or to the Office of Student Conduct.