PLSC 751- Advanced Genetics
Syllabus Spring Semester 2007
3 credits
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Instructor: Dr. Ted Helms
Office: Loftsgard 374B
Phone: 231-8136
E-mail: Ted.Helms@ndsu.ed
Office Hours: by appointment
Class Time, Place: 9:00am, MWF, Loftsgard 102
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No class:
Jan. 15 (Martin Luther King Day)
Feb. 19 (President’s Day)
Feb. 21 (I have a professional meeting)
March 12-16 (Spring break)
April 6, April 9 (Spring Holiday) |
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Lecture Syllabus
There is no text book. However, all the class notes are available online at: http://www.ag.ndsu.nodak.edu/plantsci/adv_genetics/genetics/main.htm When you go to this URL, click on the Plsc 751 Study Materials button near the top of the screen. User name and Password to access the online notes will be provided on the first lecture day. Homework will be assigned in class, so you can not necessarily go by the homework sets that are in the online document.
The syllabus will correspond closely to the index of the online document, which are also provided below. This year I plan to have many small group projects with verbal reports in class and a class discussion period.
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Table of Contents |
Study Materials |
4 |
Terms and Principles |
5 |
Homework 1 |
6 |
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| Basic Statistics |
Probability and Relative Frequency |
8 |
Conditional Probability |
9 |
Independent Events |
15 |
Mutually Exclusive Events |
16 |
Flower Color & Soybeans |
16 |
Duplicate Gene Action |
18 |
Tri-hybrid Ratios |
18 |
Branching Method |
19 |
Review |
21 |
Hypothesis Testing |
23 |
Binomial Distribution |
26 |
Homework 2 |
35 |
Chi-square Distribution |
36 |
Contingency Test |
37 |
Homogeneity Chi-square Test |
43 |
Normal Distribution |
48 |
Homework 3 |
47 |
Piosson Distribution |
50 |
Homework 4 |
53 |
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| Linkage and Genetics |
Meiosis |
55 |
Crossing over |
55 |
Two Strand Stage |
56 |
Double-fertilization |
58 |
Independent Assortment of Two Alleles |
60 |
Explanation of Linkage |
61 |
Linkage in Testcrosses |
65 |
Linkage in F2 Populations |
67 |
Orthogonality |
69 |
Short Formulas |
71 |
Homework 5 |
75 |
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| Linkage Estimation |
Estimation of Recombination |
76 |
Product Method |
76 |
Combined Estimate Recombination Using the Product Method |
82 |
Concept Part III |
84 |
Testcross Data |
86 |
F2 Family Data |
88 |
Probability of Crossover Event |
92 |
Maximum Likelihood Method |
94 |
Standard Error of Recombination Estimate |
104 |
Combining Linkage Estimates |
106 |
Example Using SSR Marker Data |
109 |
Fisher’s Scoring Method |
112 |
Fisher’s Score versus Product Method |
118 |
Homework 6 |
120 |
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| Double Cross-overs and Gene Mapping |
Types of Double Cross-overs |
121 |
Double Cross-over Detection |
122 |
Interference |
126 |
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| Planning Experiments |
Distinquish Between Two Segregation Ratios |
129 |
Progeny Test |
130 |
Amount of Information and Linkage |
132 |
Coupling Phase Information |
134 |
Repulsion Phase Information |
134 |
Examples of Information Content |
135 |
Standard Errors for Linkage Data |
135 |
Minimun Sample Sizes for Mapping |
138 |
Maximizing the Power to Detect QTL’s |
139 |
Review |
141 |
Homework 7 |
142 |
Percent Recombination versus Map Distance |
143 |
Haldane’s Mapping Function |
143 |
Poisson Distribution |
149 |
Kosambi’s Mapping Function |
152 |
Kosambi versus Haldane’s Function |
154 |
Summary |
156 |
Homework 8 |
158 |
Marker Coverage of the Genome |
159 |
Number of Progeny Required for Minimum Confidence Interval |
160 |
The Simple Ratio |
161 |
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| Mapping QTL's |
LOD Score Concept |
163 |
LOD Score Derivation |
165 |
Maximum Likelihood Testcross Data |
170 |
Plotting LOD Scores |
171 |
Homework 9 |
172 |
Permutation Test |
174 |
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| Marker Assisted Selection |
Single Marker Analysis Using F2 Progeny |
178 |
Conditional Probability and MAS |
182 |
Mean Value of Each Marker Class |
185 |
QTL Mapping and Marker Mean |
185 |
Marker Assisted Selection |
188 |
Conclusions About QTL Mapping |
189 |
Factors that Affect the Efficiency of MAS |
190 |
Genetic Proportions of Three Linked Loci |
191 |
Flanking Markers to Map QTLs |
194 |
QTL Confidence Interval |
202 |
Review |
206 |
Homework 10 & 11 |
207 |
Assumptions of MAS |
209 |
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| Linkage and Inbreeding |
Introduction |
214 |
Number of Plants that Need to be Genotyped |
216 |
Precision Associated with Estimation of Recombination |
217 |
Tables for Linkage and Inbreeding |
221 |
Diagrams of Confidence Intervals |
229 |
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| Autotetraploid Ratios |
Definitions |
233 |
Double Reduction |
236 |
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| Linkage in Autotetraploids |
Introduction |
248 |
Single Coupling |
249 |
Simplex Repulsion |
250 |
Duplex Coupling-Simplex Coupling |
253 |
Duplex-duplex Coupling |
256 |
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Study Materials
Texts On Reserve
Hartl, D.L. 1994. Genetics. Jones and Bartlett
Publishers, London.
Klug, W.S. and M.R. Cummings. 1997. Concepts
of Genetics. 5th ed. Prentice Hall, Upper
Saddle River, NJ.
Liu, Ben Hui. 1997. Statistical Genomics: Linkage,
Mapping, and QTL Analysis. CRC Press,
New York.
Strickberger, M.W. 1986. Genetics. The Macmillan
Co., New York. |
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Assessment:
Pre-test
This will be given the first class period, which is Jan. 10 (Monday 9 a.m.)
Not graded, only for assessment purposes.
Post-test
This will be given in the last week or two of the class.
Not graded, only for assessment purposes.
There will be three exams, two hourly exams and the final exam. Each exam will be given in class at the regular class meeting time. Each exam will be worth 25% of the final course grade. You will be given at least 10 days advance notice before each exam is given. I will announce the dates for the two hourly exams in class. The final exam will be given at the scheduled time, which will be announced in class. Exams will be mostly short answers of about one paragraph. I will pass out old exams before each test so that you can see what was covered in the Spring, 2005 class to help you study. The total value for all homework assignments will be 25% of the course grade. Exams will cover lecture material, online notes, handouts, and questions from the homework assignments.
Grade Categories |
Percent of Final Class Grade |
Points by Categories |
Exam 1 |
25 |
100 |
Exam 2 |
25 |
100 |
Final Exam |
25 |
100 |
Homework |
25 |
100 |
Exams will be completed individually and you will not be allowed to access books, notes, electronic devices, or other sources of information unless otherwise instructed. Calculators must only be used for basic calculating. Missed exams can be made up by appointment within two weeks of the scheduled exam date.
The following point totals are a guide for letter grades.
360 - 400 |
A |
320 - 359 |
B |
260 - 319 |
C |
200 - 259 |
D |
199 or less |
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Course Description:
We will study the mathematical and genetic basis of linkage between genes. Examples will be from plant species. The mathematics and concepts associated with molecular marker – quantitative trait associations will be discussed. The course is primarily oriented to diploid species, but there will be several lectures explaining the genetics and linkage relationships of autotetraploid species. |
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Course Objectives:
- To understand basic statistical concepts so that you can understand the rest of the course material.
- To be able to analyze and interpret the results of genetic experiments.
- To understand the technical and mathematical aspects of linkage genetics.
- To understand the value and limitations of marker-assisted selection.
- To be able to plan molecular marker and QTL experiments as well as other genetic experiments.
- To understand the more complex and challenging topics of autotetraploid genetics.
Cancellations:
Cancellation of a class meeting time automatically delays all scheduled activities, including exams, to the next scheduled meeting time.
Disability Accomodations:
Students that may require disability accommodations for this course are encouraged to speak with the instructor and/or the Disability Services Office (231-7671) as soon as possible to make appropriate arrangements.
Dishonesty:
The College of Agriculture, Food Systems, and Natural Resources has an Honor System (http://www.ag.ndsu.nodak.edu/colag/honor.htm), which believes that a student has the privilege and responsibility to perform honestly and responsibly. Exams will include the following pledge which students are required to sign before their exam will be accepted: “On my honor I have neither given nor received aid in completing this assignment.” An indication of dishonesty will be referred to the Honor Commission made up of students. The instructor also retains the privilege of deducting points if he deems that the action is warranted. |
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