COURSE SYLLABUS. Dr. Ron Lewis, Associate Professor, Animal Genetics

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1 MODULE 4: SPRING 2011 DESIGN OF ANIMAL BREEDING PROGRAMS COURSE SYLLABUS INSTRUCTOR Instructor: Dr. Ron Lewis, Associate Professor, Animal Genetics Address: Virginia Tech, Department of Animal and Poultry Sciences (0306), 3100 Litton-Reaves Hall, Blacksburg, VA, Telephone: (540) TEACHING ASSISTANT Assistant: Ms. Gabi Márquez Betz, PhD student Address: Virginia Tech, Department of Animal and Poultry Sciences (0306), 214 Litton-Reaves Hall, Blacksburg, VA SCHEDULE AND CREDIT This online course will begin on Monday, February 21, 2011 and last 5 weeks. The ending date for the course is Friday, April 1, 2011, which allows for a one-week spring holiday. The content of this course is consistent with a one-credit graduate level course. COURSE GOAL The overall goal of this course is to increase your skills and knowledge related to the design of animal breeding programs. The focus will be on the application of index theory to the definition of breeding objectives in animal agriculture. The course will also consider the derivation of economic weights, discounting and gene flow, which are useful when predicting economic response to selection. TEXTBOOK No textbook is required for the course, although the following book is recommended as a useful general reference: 1

2 Mrode, R. A Linear Models for the Prediction of Animal Breeding Values, 2 nd Edition. CAB International, Wallingford, Oxfordshire, UK (ISBN ) LEARNING OBJECTIVES Lesson One: Introduction to Design of Animal Breeding Programs 1.1. Describe and distinguish a breeding goal and breeding strategy 1.2. Identify constraints in breeding programs 1.3. Define the meaning of an economic selection index Lesson Two: Review of Expected Values and Selection Response 2.1. Apply six key rules to obtain expected values 2.2. Define the meaning of selection response Derive selection response using linear regression Show the generality of the derivation Predict response to phenotypic selection Characterize truncation selection Describe selection response per unit of time Lesson Three: Economic Selection Indices 3.1. Derive an economic selection index Define an aggregate genotype Find coefficients for an economic selection index Predict response to selection on an economic index Derive an economic selection index 3.2. Apply constraints to selection indices Derive a restricted index Define a desired gains index 3.3. Recognize sensitivities in selection indices Test sensitivities to estimates of co-variances Ascertain the impact of uncertainties in economic weights 3.4. Deriving indices using predicted breeding values 2

3 Combination of predicted breeding values and economic weights Equivalency with classic index methodology Lesson Four: Multiple-stage Selection 4.1. Distinguish stages of selection Recognize one- versus two-stage selection Incorporate an index into an index 4.2. Adjust for prior selection 4.3. Derive a two-stage selection index Lesson Five: Deriving Economic Weights 5.1. Define a profit equation Describe the relationship between profit and genetic change Identify relevant management systems and economic environments 5.2. Derive economic weights from profit equations Distinguish linear and non-linear profit functions Find solutions for such profit functions 5.3. Differentiate perspectives toward animal breeding programs 5.4. Recognize unifying principles for deriving economic weights Distinguish fixed versus variable costs Identify the consequences of rescaling a breeding program Discriminate absolute versus relative economic weights Lesson Six: Discounting and Gene Flow (time allowing) 6.1. Define the use of economic discounting Describe the process of discounting Recognize useful cumulative discounting expressions Choose relevant discounting rates in animal breeding 6.2. Utilize gene flow methods Delineate inheritance of genes from particular groups Define the flow of genetic improvement over one or more rounds of selection 3

4 6. 3. Discount gene expression TOOLS REQUIRED You will need a current version of Flash Player installed on your computer to see the audio-. 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 your work. This course will also require use of software for matrix manipulation. You are welcome to use any software at your disposal for doing so (e.g., Excel; SAS; System-R; Matlab; Octave). 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. One Beginning Date Activities Assignments Feb. 21 Syllabus Entry Knowledge Quiz to be completed online audio before starting any other course work, and by Thurs., Feb. 24, 8:00 p.m. Eastern Standard Time (EST) Introduction online audio Listen to the four Audio-Presentations related to this week s topics by Fri., Feb. 25 Two Feb. 28 Review of Expected Values and Selection Response two online audio Economic Selection Indices (I, II and III) three online audio First Homework Assignment posted by Wed., Mar. 2 Make a posting to the Forum by Mon., Feb. 28, 8:00 p.m. EST Complete Quiz #1 by Tues., Mar. 1, 8:00 p.m. EST Listen to the three Audio-Presentations related to this week s topics by Fri., Mar. 4 Make a posting to the Forum by Mon., Mar. 14, 8:00 p.m. Eastern Daylight Time (EDT) Complete Quiz #2 by Tues., Mar. 15, 8:00 4

5 Three Beginning Date Activities Assignments Mar. 7 or Mar. 14 Economic Selection Indices (IV, V and VI) two online audio Second Homework Assignment posted by Fri., Mar. 18 Submit first Homework Assignment by Wed., Mar. 16, 8:00 Listen to the three Audio-Presentations related to this week s topics by Fri., Mar. 18 Make a posting to the Forum by Mon., Mar. 21, 8:00 Four Mar. 21 Multiple-stage Selection (I and II) two online audio Complete Quiz #3 by Tues., Mar. 22, 8:00 Listen to the two Audio-Presentations related to this week s topic by Fri., Mar. 25 Submit second Homework Assignment by Fri., Mar. 25, 8:00 Make a posting to the Forum by Mon., Mar. 28, 8:00 Five Mar. 28 Economic weights (I and II) online audio Discounting and Gene Flow (time allowing) online audio Complete Quiz #4 by Tues., Mar. 29, 8:00 Listen to the three Audio-Presentations related to this week s topics by Fri., Apr. 1 Make a posting to the Forum by Mon., Apr. 4, 8:00 Complete Final Exam by Tues., Apr. 5, 8:00 The two start dates for week three, and the associated due dates for assignments, are intended to allow flexibility for different schedules for spring break at different Universities. For students with spring break during the week of March 14, you may well wish to complete assignments earlier than the deadline specified to avoid disruption of your holiday. PREREQUISITES Module 1 (Quantitative Genetics Applications of Matrix Algebra) and Module 3 (A Primer to Quantitative Genetics), which are offered in the Animal Breeding and Genetics Online curriculum, are prerequisites for this course. Equivalent courses can be substituted given the approval of the Instructor. 5

6 FORM OF ASSESSMENT Your performance will be evaluated based on: a weekly submission to the Forum (worth, in total, 10% of grade); four online quizzes (worth, in total, 40% of grade); two homework assignment (worth, in total, 30% of grade); and, an online final exam at the end of the course (worth 20% of grade). Forum. You are expected to make one posting to the Forum each week. Each week s activity is worth 2% of your grade. The purpose of the Forum is to provide practice so that you may develop skills in the design of animal breeding programs that are defined as learning objectives for this course. Each week, questions will be posted by the Instructor on the course Forum on Scholar. 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 will certainly be encouraged. You are expected to make one posting to the Forum each week. Each week s posting is worth 2% of your grade, and is due each Monday by 8:00 p.m. Eastern Daylight or Standard Time, as appropriate. On-line quizzes. One hour will be allowed for each on-line 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 on-line quiz is worth 10% of your grade. Each week s quiz will be available by 5:00 p.m. Eastern Daylight or Standard Time, as appropriate, on Friday. The quiz must be taken by 8:00 p.m. Eastern Daylight or Standard Time, as appropriate, 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 module. The assignments will be posted at least one week before they are due. 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. The grades on each homework assignment will be worth 15% of your final grade. The first homework assignment will be due by 8:00 p.m. Eastern Daylight Time on Wednesday, March 16, The second homework assignment will be due by 8:00 p.m. Eastern Daylight Time on Friday, March 25,

7 Final exam. Two hours will be allowed for the final exam, which will be taken on-line. The exam must be completed individually during the time period announced. The final exam will cover material from the entire module, although with a greater focus on the materials presented in week five. You may use your class notes for this exam. The final exam will be available by 5:00 p.m. Eastern Daylight Time on Friday, April 1, The final must be taken by 8:00 p.m. Eastern Daylight Time on Tuesday, April 5, STUDENT EVALUATION OF COURSE There will be opportunities at the middle and end of the course for you to evaluate its instruction, flow and content. These evaluations will be entirely anonymous and managed by Dr. Barbara Lockee, a colleague in the School of Education at Virginia Tech. She will be in contact with specific instructions at the times these evaluations are sought. Bonus credit will be awarded for submission of each course evaluation. GRADING Final grades will be determined by the number of credits (expressed as percentages) earned over the five-week course. You are assured of earning a final grade within a category shown below by earning the number of credits specified. Credits Grade category % A 80-89% B 70-79% C 60-69% D < 60% F Plus (excluding A) and minus grades will be given within a grade category. HONOR CODE The Virginia Tech Graduate Honor Code will be enforced in this course. All assignments (i.e., quizzes; homework assignment; final exam) will be subject to the stipulations of the Graduate Honor Code. For more information on the Graduate Honor Code, refer to 7

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