(Last revised: Jan. 6, 2016) 1 Instructor: Dr. Ron Lewis, Professor

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(Last revised: Jan. 6, 2016)
A PRIMER TO QUANTITATIVE GENETICS
SPRING 2016
COURSE SYLLABUS
INSTRUCTOR
Instructor:
Dr. Ron Lewis, Professor, Animal Breeding and Genomics
Address:
A218i Animal Science Bldg., P.O. Box 830908
University of Nebraska-Lincoln, Lincoln, NE 68583-0908
Telephone:
Email:
(402) 472-6378
[email protected]
SCHEDULE AND CREDIT
This online course will begin on Monday, January 11, 2016, and last five weeks. The ending
date for the course is Friday, February 12, 2016. The content of the course is consistent with
a one-credit graduate level course.
COURSE GOAL
The goal of this course is to provide students with an introduction to the language and basic
principles of quantitative genetics. Its purpose is to develop foundational knowledge for
students entering a graduate program in animal breeding and genetics. Topics included will
be the basic model for quantitative genetics (additive and non-additive genetic effects,
including Mendelian sampling, and environmental effects), sources of variation, heritability,
family resemblance and repeatability, selection response, and family selection. Expected
values and concepts in applied statistics (e.g., linear regression) will also be considered. The
course materials will be presented using online tools prepared by the Instructor.
PREREQUISITES
Quantitative Genetics Applications of Matrix Algebra, which is offered in the Animal
Genetics and Genomics Online curriculum, is a prerequisite for this course. An equivalent
course can be substituted given the approval of the Instructor.
COURSE ACCESS
Access to course will be through Blackboard via the URL https://my.unl.edu/.
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LEARNING OBJECTIVES
Lesson One: Summation and dot notation
Upon completion of this lesson, you will be able to:
1.1. Describe computations in a succinct yet comprehensive way
1.2. Characterize the summation
1.2.1. Define three key rules of the summation
1.2.2. Describe the properties of the summation
1.2.3. Evaluate the summation
1.3. Apply dot notation
Lesson Two: Expected values
Upon completion of this lesson, you will be able to:
2.1. Define six rules for expected values
2.2. Derive expected values
2.3. Apply the rules to:
2.3.1. Expected value of an observation
2.3.2. Expected value of an observation squared
Lesson Three: Average effects (additive, dominance and epistatic effects)
Upon completion of this lesson, you will be able to:
3.1. Characterize the various genetic effects
3.1.1. Describe additive genetic effects
3.1.2. Describe dominance effects
3.1.3. Describe epistatic effects
3.2. Characterize how the genetic effects contribute to the basic genetic model
Lesson Four: The basic model of quantitative genetics
Upon completion of this lesson, you will be able to:
4.1. Characterize the basic genetic model
4.1.1. Describe assumptions of the genetic model
4.1.2. Describe the genetic effects that are (not) transmitted
4.2. Characterize Mendelian sampling
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Lesson Five: Sources of variation
Upon completion of this lesson, you will be able to:
5.1. Characterize sources of phenotypic variability
5.1.1. Describe the biological factors influencing performance
5.2. Characterize the effects determining maternal influence on performance
5.3. Characterize the effects determining producing ability
5.4. Characterize the differences between permanent and temporary environmental effects
Lesson Six: Heritability
Upon completion of this lesson, you will be able to:
6.1. Characterize the concept of heritability
6.1.1. Describe alternative definitions of heritability
6.1.2. Evaluate heritability given population (co)variances
6.2. Characterize the importance of heritability from an animal production perspective
6.2.1. Describe the importance of heritability to selection
6.2.2. Describe the importance of heritability to prediction
6.2.3. Describe the importance of heritability to management
Lesson Seven: Selection response
Upon completion of this lesson, you will be able to:
7.1. Characterize the concept of direct selection
7.1.1. Describe the influence of variability on genetic progress
7.1.2. Describe the selection criterion
7.1.3. Describe the concept of superiority
7.1.3.1. Evaluate superiority
7.1.4. Describe the concept of generation interval
7.1.4.1. Evaluate generation interval
7.1.5. Describe the concept of accuracy
7.1.5.1. Describe the contributors to accuracy
7.2. Derive the key equation for genetic improvement
7.3. Evaluate alternative selection decisions for their effect on rate of genetic improvement
Lesson Eight: Family resemblance
Upon completion of this lesson, you will be able to:
8.1. Characterize sources of information useful for identifying family resemblance
8.1.1. Recognize possible sources of information
8.1.2. Delineate the emphasis that should be placed on each source
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8.2. Define the concept of family resemblance
8.2.1. Describe reasons for family resemblance
8.2.2. Define the intra-class correlation
8.3. Predict selection response
8.3.1. Evaluate the regression of ‘true’ breeding value on sources of information
8.3.2. Determine the accuracy of selection
Lesson Nine: Selection index
Upon completion of this lesson, you will be able to:
9.1. Define selection response
9.1.1. Delineate true and expected breeding values
9.1.2. Explain Mendelian sample
9.2. Derive the prediction of selection response
9.2.1. Use linear regression in the derivation
9.2.2. Illustrate the generality of this derivation
9.3. Describe a selection index
9.4. Derive index coefficients considering:
9.4.1. Properties of index coefficients
9.4.2. Maximization
9.4.3. Unbiased prediction
9.4.4. Normal equations
9.5. Predict response to index selection considering:
9.5.1. Variance in the index
9.5.2. Covariance and correlation between breeding value and index
9.5.3. Selection response
9.5.4. Accuracy of selection
9.6. Apply index theory to:
9.6.1. Phenotypic selection
Lesson Ten: Repeatability
Upon completion of this lesson, you will be able to:
10.1. Define repeatability
10.1.1. Interpret its meaning
10.1.2. Recognize its properties
10.1.3. Delineate its importance in culling and prediction
10.2. Derive repeatability in the context of:
10.2.1. Index coefficients
10.2.2. Accuracy of selection
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Lesson Eleven: Family selection
Upon completion of this lesson, you will be able to:
11.1. Define family selection
11.2. Derive a family selection index based on:
11.2.1. Individual’s own record and that of siblings
11.3. Illustrate application of a family index obtaining:
11.3.1. Index weights
11.3.2. Accuracy of selection
TEXTBOOKS
No textbook is required for the course, although the following books are recommended as
useful references:
Mrode, R. A. 2014. Linear Models for the Prediction of Animal Breeding Values, 3rd
Edition. CAB International, Wallingford, Oxfordshire, UK [ISBN 978-1-84593-981-6
(paperback); ISBN 978-1-78064-391-5 (hardback)]
Van Vleck, L. D. 1993. Selection Index and Introduction to Mixed Model Methods for
Genetic Improvement of Animals: the Green Book. CRC Press, Inc., Boca Rotan, Florida
(ISBN 0-84938-762-0)
A digital copy (pdf) of the Green Book is available for download at
http://www.enbgeo.soe.vt.edu/greenbook.php.
COURSE SCHEDULE
Course material will be made available on a weekly basis. This pacing is intended to maintain
course continuity by engaging all students in the same material at the same time.
Week
One
Beginning
Date
Activities
Jan. 11
Overview of Syllabus
 online audio
presentation
Summation and dot
notation
 online audio
presentation
Expected values
 online audio
presentation
Assignments
Entry Knowledge Quiz to be completed before
starting any other course work, and by Thurs.,
Jan. 14, by 11:59 p.m. (your local time zone)
Listen to the three Audio-Presentations related
to this week’s topics by Fri., Jan. 15
Make a posting to the Forum by Mon., Jan. 18,
by 11:59 p.m. (your local time zone)
Complete Quiz #1 by Tues., Jan. 19, by 11:59
p.m. (your local time zone)
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Week
Two
Beginning
Date
Activities
Jan. 18
Average effects
 online audio
presentation
Basic genetic model
 online audio
presentation
Assignments
Listen to the three Audio-Presentations related
to this week’s topics by Fri., Jan. 22
Make a posting to the Forum by Mon., Jan. 25,
by 11:59 p.m. (your local time zone)
Complete Quiz #2 by Tues., Jan. 26, by 11:59
p.m. (your local time zone)
Sources of variation
 online audio
presentation
Three
Jan. 25
First Homework
Assignment posted
by Wed., Jan. 20
Heritability
 online audio
presentation
Selection response
 online audio
presentation
Family resemblance
 online audio
presentation
Four
Feb. 1
Second Homework
Assignment posted
by Fri., Jan. 29
Selection index
(parts I, II &III)
 online audio
presentations
Submit first Homework Assignment by Wed.,
Jan. 27, by 11:59 p.m. (your local time zone)
Listen to the three Audio-Presentations related
to this week’s topics by Fri., Jan. 29
Make a posting to the Forum by Mon., Feb. 1, by
11:59 p.m. (your local time zone)
Complete Quiz #3 by Tues., Feb. 2, by 11:59
p.m. (your local time zone)
Submit second Homework Assignment by Fri.,
Feb. 5, by 11:59 p.m. (your local time zone)
Listen to the three Audio-Presentations related
to this week’s topic by Fri., Feb. 5
Make a posting to the Forum by Mon., Feb. 8, by
11:59 p.m. (your local time zone)
Complete Quiz #4 by Tues., Feb. 9, by 11:59
p.m. (your local time zone)
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Week
Five
Beginning
Date
Activities
Feb. 8
Repeatability
 online audio
presentation
Family selection
 online audio
presentation
Assignments
Listen to the two Audio-Presentations related to
this week’s topics by Fri., Feb. 12
Make a posting to the Forum by Mon., Feb. 15,
by 11:59 p.m. (your local time zone)
Complete Final Exam by Tues., Feb. 16, by
11:59 p.m. (your local time zone)
TOOLS REQUIRED
This module will require use of software for matrix manipulation (e.g., Excel; SAS; R;
MathCad). You will need a current version of Flash Player installed on your computer to
“see” the audio-presentations. You will also need Adobe Acrobat Reader to view Portable
Document Files (PDF) contained within the course. Finally, you will need to be able to create
PDF files for homework assignments. This process can be accomplished within Microsoft
Office software through the Print menu. If you choose a different software package to
complete your homework assignment, you may need the full version of Adobe Acrobat to
create a PDF of the work, or compatible freeware.
FORM OF ASSESSMENT
Your performance will be evaluated based on:
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a weekly submission to the Forum (worth, in total, 10% of grade or 100 points);
four online quizzes (worth, in total, 40% of grade or 400 points);
two homework assignments (worth , in total, 30% of grade or 300 points); and,
an online final exam at the end of the course (worth 20% of grade or 200 points).
In total, 1,000 points will be available.
Forum. You are expected to make one posting to the Forum each week. Each week’s activity
is worth 2% of your grade (20 points).
The purpose of the Forum is to provide practice so that you may develop the requisite
foundational skills in quantitative genetics that have been defined as learning objectives for
this course. The other purpose is for you to gain experience discussing ideas across electronic
media from remote locations; given changes in how grants are awarded, and research teams
interact, this skill is becoming increasingly important.
Each week, questions will be posted by your Instructor on the course Forum on Blackboard.
These may entail extending on material presented in the course, and/or a practice exercise.
You may respond to these postings, or preferably begin your own discussion thread. The
latter is certainly encouraged.
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Your contribution to the Forum will be graded based on its relevance to the week’s materials,
and the comprehensiveness of the posting itself. Postings are due each Monday by 11:59 p.m.
your local time.
Although response times may be quicker, the Instructor will respond to Forum postings (and
email correspondences) within 24 hours. The exception may be weekends, and so please plan
accordingly.
Online quizzes. One hour will be allowed for each online quiz. These must be completed
individually during the time period announced. These weekly quizzes will focus on material
presented that week. You may use your class notes for these quizzes. Each online quiz is
worth 10% of your grade (100 points).
Each week’s quiz will be available on Friday of that week. The quiz must be taken by 11:59
p.m. (your local time zone) on the subsequent Tuesday.
Homework assignments. There will be two homework assignments, one due during the
second week and the other during the fourth week of the course. The assignments will be
posted at least one week before they are due. Each homework assignment will be worth 15%
of your final grade (150 points).
You are permitted, even encouraged, to discuss your homework assignment with other
students in the course. However, you must prepare and submit your own assignment.
Completed homework files will need to be saved in PDF format and submitted online within
the Assignments folder on the course Blackboard site. Details of the submission process will
be included in the preface to the assignment.
The first homework assignment will be due by 11:59 p.m. (your local time zone) on
Wednesday, Jan. 27, 2016. The second homework assignment will be due by 11:59 p.m.
(your local time zone) on Friday, Feb. 5, 2016.
Final exam. Two hours will be allowed for the final exam, which will be taken online. The
exam must be completed individually during the time period announced. The final exam will
cover material from the entire module. You may use your class notes for this exam. The final
exam will be worth 20% of your final grade (200 points).
The final exam will be available on Friday, Feb. 12, 2016. The final must be taken by 11:59
p.m. (your local time zone) on Tuesday, Feb. 16, 2016.
STUDENT EVALUATION OF COURSE
There will be an opportunity at the end of the course for students to evaluate its instruction,
flow and content. This evaluation will be entirely anonymous. You will be contacted with
specific instructions at the times when the evaluation is sought.
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GRADING
Final grades will be determined by the number of points earned over the five-week course.
You are assured of earning a final grade within a category shown below by earning the
number of points specified.
Points
930 or above
900 - 929
870 - 899
830 - 869
800 - 829
770 - 779
730 - 769
700 - 729
670 - 699
630 - 669
600 - 629
599 or below
Grade category
A
AB+
B
BC+
C
CD+
D
DF
EMERGENCY RESPONSE INFORMATION (for students’ resident at University of NebraskaLincoln)




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Fire Alarm (or other evacuation): In the event of a fire alarm: Gather belongings
(Purse, keys, cellphone, N-Card, etc.) and use the nearest exit to leave the building. Do
not use the elevators. After exiting notify emergency personnel of the location of persons
unable to exit the building. Do not return to building unless told to do so by emergency
personnel.
Tornado Warning: When sirens sound, move to the lowest interior area of building or
designated shelter. Stay away from windows and stay near an inside wall when possible.
Active Shooter
o Evacuate: if there is a safe escape path, leave belongings behind, keep hands visible
and follow police officer instructions.
o Hide out: If evacuation is impossible secure yourself in your space by turning out
lights, closing blinds and barricading doors if possible.
o Take action: As a last resort, and only when your life is in imminent danger, attempt
to disrupt and/or incapacitate the active shooter.
UNL Alert: Notifications about serious incidents on campus are sent via text message,
email, unl.edu website, and social media. For more information go to:
http://unlalert.unl.edu.
Additional Emergency Procedures can be found here:
http://emergency.unl.edu/doc/Emergency_Procedures_Quicklist.pdf
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STUDENTS WITH DISABILITIES
Students with disabilities are encouraged to contact the instructor for a confidential
discussion of their individual needs for academic accommodation. It is the policy of the
University of Nebraska-Lincoln to provide flexible and individualized accommodation to
students with documented disabilities that may affect their ability to fully participate in
course activities or to meet course requirements.
For students’ matriculated at the University of Nebraska, to receive accommodation services,
students must be registered with the Services for Students with Disabilities (SSD) office, 132
Canfield Administration, 472-3787 voice or TTY.
STUDENT CODE OF CONDUCT
Students are expected to adhere to guidelines concerning academic dishonesty outlined in
Section 4.2 of the University’s Student Code of Conduct (http://stuafs.unl.edu/dos/code).
Students are encouraged to contact the instructor for clarification of these guidelines if they
have questions or concerns.
ACADEMIC DISHONESTY
Academic dishonesty can involve cheating; fabrication or falsification of information;
plagiarism, including copying of written materials or “cutting and pasting” from websites
without proper referencing; destroying, defacing, stealing, or making inaccessible library or
other academic resource material; complicity in the academic dishonesty of others; falsifying
grade reports; or misrepresenting illness, injury, accident, etc., to avoid or delay an
examination or the timely submission of academic work.
Consequences of academic dishonesty in Animal Science courses, depending on the degree
of severity as interpreted by an instructor, may range from a warning to assigning an F for the
course. The instructor may also choose to assign a zero or partial credit for a specific
assignment, quiz, examination or laboratory report in which dishonesty was involved. Before
imposing an academic sanction the instructor shall first attempt to discuss the matter with the
student. In all cases the instructor must document the instance(s) of student activity, which
constitutes academic dishonesty. Documentation must be kept by the instructor for a
minimum of one year and must be made available to appropriate department, college, and
UNL authorities if cases of academic dishonesty result in disciplinary hearings and/or
appeals at those levels. When an academic sanction is imposed that causes a student to
receive a lowered course grade, the instructor shall make a report in writing of the facts of the
case, and of the academic sanction imposed against the student, to the Animal Science
Department Head and the UNL Director of Student Judicial Affairs. The student shall be
provided with a copy of this report. Further, the instructor may recommend the institution of
CASNR or UNL disciplinary proceedings against the student for violation of the Student
Code of Conduct if the instructor, in the exercise of his or her professional judgment,
believes that such action is warranted.
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If a student facing sanctions due to academic dishonesty in an Animal Science Department
course wishes to appeal such a sanction, the following process must be followed. First is a
written appeal to the chief instructor of the course. Failing obtain resolution the student can
appeal (in writing) to the Animal Science Department Head. The Department Head will refer
the appeal to the Animal Science Curriculum Committee who will interview both the student
and instructor, review all pertinent documentation, and then issue a decision. If a member of
the Animal Science Curriculum Committee is also an instructor of the course in which
academic dishonesty has been reported, the Animal Science Department Head will
temporarily appoint a different faculty member to the committee hearing the appeal. If a
solution satisfactory to the student is not achieved at the department level, the student may
then appeal through the CASNR Dean’s office and the University Director of Student
Judicial Affairs, in that order and subject to the processes and requirements of those offices.
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