Plsc 751 Study Materials



PLSC 751- Advanced Genetics
Syllabus Spring Semester 2007

3 credits

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

 

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)

 

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.

 

Table of Contents

Study Materials

4

Terms and Principles

5

Homework 1

6

 
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

 

 

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

 

 

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

 
Double Cross-overs and Gene Mapping

Types of Double Cross-overs

121

Double Cross-over Detection

122

Interference

126

 
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

 
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

 
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

 
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

 
Autotetraploid Ratios

Definitions

233

Double Reduction

236

 
Linkage in Autotetraploids

Introduction

248

Single Coupling

249

Simplex Repulsion

250

Duplex Coupling-Simplex Coupling

253

Duplex-duplex Coupling

256

 

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.

 

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

E

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.

 

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.