Plsc 751 Study Materials



PLSC 751- Advanced Genetics
Syllabus Spring Semester 2009

3 credits

Instructor: Dr. Ted Helms
Office: Loftsgard 374B
Phone: 231-8136
E-mail: Ted.Helms@ndsu.edu
Office Hours: by appointment

Class Time, Place: 9:00am, MWF, Loftsgard 102

 

No class:
Jan. 19 (Martin Luther King Day)
Feb. 16 (President’s Day)
Feb. 18 (I have a professional meeting)
March 16-20 (Spring break)
April 10-13 (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

5

Terms and Principles

6

Homework 1 7

Homework 2

8

Homework 3 9
 
Basic Statistics

Probability and Relative Frequency

10

Conditional Probability

11

Independent Events

19

Mutually Exclusive Events

21

Flower Color & Soybeans

23

Epistasis 24

Tri-hybrid Ratios

24

Branching Method

25

Review

27

Hypothesis Testing

29

Binomial Distribution

33

Homework 4

41

Chi-square Distribution

44

Contingency Test

45

Homogeneity Chi-square Test

52

Homework 5

55

Normal Distribution 57

Piosson Distribution

60

Homework 6

64

 

 

Linkage and Genetics

Meiosis

66

Crossing over

67

Two Strand Stage

68

Double-fertilization

71

Independent Assortment of Two Alleles

72

Detection of Linkage

73

Linkage in Testcrosses

77

Linkage in F2 Populations

80

Orthogonality

82

Short Formulas

84

Homework 7

88

 

 

Linkage Estimation

Estimation of Recombination

90

Product Method

90

Combined Estimate Recombination Using the Product Method

97

Concept Part III

100

Testcross Data

102

F2 Family Data

105

Probability of Crossover Event

107

Maximum Likelihood Method

111

Standard Error of Recombination Estimate

123

Combining Linkage Estimates

123

Example Using SSR Marker Data

125

Fisher’s Scoring Method

129

Fisher’s Score versus Product Method

136

Homework 8

138

 
Double Cross-overs and Gene Mapping

Types of Double Cross-overs

139

Double Cross-over Detection

140

Interference

144

 
Planning Experiments

Distinquish Between Two Segregation Ratios

147

Progeny Test

149

Amount of Information and Linkage

151

Coupling Phase Information

154

Repulsion Phase Information

154

Examples of Information Content

155

Standard Errors for Linkage Data

155

Minimun Sample Sizes for Mapping

158

Maximizing the Power to Detect QTL’s

159

Review

161

Homework 9

162

Percent Recombination versus Map Distance

163

Haldane’s Mapping Function

164

Poisson Distribution

171

Kosambi’s Mapping Function

174

Kosambi versus Haldane’s Function

176

Summary

178

Homework 10

180

Marker Coverage of the Genome

181

Number of Progeny Required for Minimum Confidence Interval

182

 
Mapping QTL's

LOD Score Concept

183

LOD Score Derivation

186

Maximum Likelihood Testcross Data

191

Plotting LOD Scores

192

Homework 11

195

Permutation Test

196

 
Marker Assisted Selection

Single Marker Analysis Using F2 Progeny

201

Conditional Probability and MAS

205

Mean Value of Each Marker Class

208

QTL Mapping and Marker Mean

208

Marker Assisted Selection

211

Conclusions About QTL Mapping

212

Factors that Affect the Efficiency of MAS

213

Genetic Proportions of Three Linked Loci

214

Flanking Markers to Map QTLs

218

QTL Confidence Interval

225

Review

229

Homework 12 & 13

230

Assumptions of MAS

232

 
Linkage and Inbreeding

Introduction

238

Number of Plants that Need to be Genotyped

238

Tables for Linkage and Inbreeding 241

Precision Associated with Estimation of Recombination

248

Diagrams of Confidence Intervals

255

 
Autotetraploid Ratios

Definitions

259

Random Chromosome 262

Double Reduction

265

 
Linkage in Autotetraploids

Introduction

275

Single Coupling

276

Simplex Repulsion

277

Duplex Coupling-Simplex Coupling

280

Duplex-duplex Coupling

284

 

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. 14 (Wednesday, 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, 2007 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.