PBG 650: Advanced Plant Breeding and Quantitative Genetics

Instructor: 
Jennifer G Kling
Term: 
Fall 2015
Syllabus: 

About

Telephone: 541-737-8277
E-mail: jennifer.kling@oregonstate.edu
Office: CRPS 249
Office Hours: By appointment

Lecture: MWF 1:00–1:50 CRPS 122  (CRN20576)
Recitation: W 4:00–5:00 and/or W 5:30–6:30 CRPS 150
Course Credit Hours: 3
Recitation Credit Hours: 1

The recitation is offered as a one-credit reading and conference course (PBG 599 ST/Advanced Plant Breeding Recitation, CRN 20578). This will provide for additional practice with calculations and more opportunity to ask questions about homework sets and course material. You are expected to attend the recitation for one hour per week.

Course Overview: Modern Plant Breeding requires an understanding of genetics at both the population and molecular levels. This course will emphasize concepts in population and quantitative genetics as they relate to plant breeding. Students will gain practical experience in analyzing data from genetic experiments and estimating genetic parameters and heritability. The design of efficient selection programs will be reviewed, including expected gains from various selection methods, and the choice of appropriate methods for specific crops, traits and environmental conditions. Factors to consider when developing inbred lines, hybrids, and synthetics will also be presented. Students will learn to apply techniques for multiple trait selection, including index and marker-assisted selection.  Approaches for controlling experimental error in breeding trials, and for analysis of genotype by environment interactions, will also be discussed.

Recommended Prerequisites
GEN 311 or CSS 430/CSS 530 (Genetics or Plant Genetics)
GEN 530 (Population Genetics)
CSS 450/CSS 550 (Plant Breeding)
ST 411/ST 511, ST 412/ST 512, and ST 413/ST 513 or equivalents

Online Resources
You can access the course website through the homepage for this class in Canvas or directly at this url:  http://cropandsoil.oregonstate.edu/content/pbg-650

We will use Canvas in this course for announcements and for submitting some of the homework assignments. The course is listed as PBG_650_001_F2015. For information on how to access and use Canvas, go to the OSU Extended Campus website http://ecampus.oregonstate.edu/
 
Textbooks
This course will draw on information from a number of texts and journal articles. The following text will be the primary reference:
Bernardo, Rex. 2010. Breeding for quantitative traits in plants, 2nd edition. Stemma Press, Woodbury, MN. (ISBN 978-0-9720724-1-0)

The book can be ordered directly from the publisher for $85.00 at http://stemmapress.com/.

The following text will be placed on reserve in the library.
Falconer, D.S. and T.F.C. Mackay. 1996. Introduction to Quantitative Genetics, 4th ed., Pearson Education Ltd., Essex, England.    QH452.7 .F34 1996

Problem Sets
You will be given about five problem sets to complete during the term, which will involve applications of genetic analyses presented in class. It is not assumed that you have knowledge of specific software prior to the class, although some experience with Excel, SAS, and R would be helpful. Recitations will be held in a computer lab to give you an opportunity to practice with the software that will be needed to complete your assignments. You may consult with your classmates regarding these assignments but are responsible for completing your own work.

Term Project
Students will work in pairs (or possibly in a trio) to develop 15-30 minute videos or narrated power point presentations on specific aspects of molecular breeding. These should be designed to cover basic principles that Plant Breeders need to know in order to apply molecular breeding techniques. Videos should be posted in Canvas by Wednesday, Nov. 25, 2015. Each team will also select a journal article that provides a case study for their topic. At a scheduled time during dead week, each team will lead a discussion on the journal article they have chosen. Everyone is expected to watch the videos and read the articles on the scheduled topics before coming to class each day.

Exams
For this class, you should strive to understand the concepts and how to apply them, but you will not be expected to memorize all of the formulae. For each midterm you may bring one 8.5” x 11” sheet of your notes along with you to the exam. Exam questions will be based primarily on material from the lectures and homework assignments. The final will be a take-home exam that may include a short answer section and one or more synthesis questions. It will be given to you on Friday of dead week and will be due by 9:30 am on Friday, December 11, 2015. The final will be open book, but you are expected to do your own work.

Recommended Reading
The table below is intended as a guide to provide background information and additional explanation of concepts presented in class.  In general, you can read texts by Bernardo or Falconer and Mackay. If you are unclear about a topic or want further detail, you may benefit from reading both texts.

Week Topic Reference
1 Hardy-Weinberg equilibrium, linkage disequilibrium • Bernardo Chapt. 1, 2
• Falconer and Mackay, Chapt. 1
2 Inbreeding and coancestry, effective population size • Bernardo, Chapt. 2
• Falconer and Mackay, Chapt. 3, 4, 5
2 Changes in gene frequency due to selection • Bernardo, Chapt. 2
• Falconer and Mackay, Chapt. 2
3 Average effects of genes, breeding values • Bernardo, Chapt. 3, 4
• Falconer and Mackay, Chapt. 7
4 Genetic variances, covariance between relatives, heritability • Bernardo, Chapt. 6
• Falconer and Mackay, Chapt. 8, 9, 10
5 Mating designs to estimate genetic variances • Bernardo, Chapt. 7
6 Mixed models, BLUP estimation • Bernardo, Chapt. 11
7 Expected gain from recurrent selection • Bernardo, Chapt. 10
• Falconer and Mackay, Chapt. 11, 16
7 Selection during inbreeding • Bernardo, Chapt. 9
7 Hybrid selection, inbred line development • Bernardo, Chapt. 12
8 Selection for multiple traits • Bernardo, Chapt. 11, 13
• Falconer and Mackay, Chapt. 13, 19
9 Genotype by environment interactions • Bernardo, Chapt. 8
9 Breeding for abiotic stress tolerance  

 
Supplementary Reading
Additional reading from journals will be assigned throughout the term. These references and pdf files will be posted in Canvas. One or more study questions will be provided with each reference. You will be expected to submit brief responses to questions for two articles of your choice during the term.



Student Assessment and Grading

Homework and class exercises 30%
Questions on assigned reading 5%
First exam 15%
Second exam 15%
Term project 20%
Take-home final 15%

Grades will be assigned according to the following point system:

97-100 = A+ 87-89 = B+ 77-79 = C+ 67-69 = D+ ≤59 = F
93-96 = A 83-86 = B 73-76 = C 63-66 = D  
90-92 = A- 80-82 = B- 70-72 = C- 60-62 = D-  

           
Lecture Topics                                          

Week 1-2 Breeding Populations and Mating Systems
•  Gene and genotype frequencies in random mating populations (Hardy-Weinberg equilibrium and assumptions)
•  Two loci (gametic phase equilibrium)                            
•  Inbreeding and coancestry                                
   - From pedigrees                                
   - Regular systems of inbreeding
   - Effective population size
•  Genetic diversity and distance
•  Changes in gene frequency due to selection                            
                                            
Week 3. Quantitative Genetics – Mean Performance of Populations         
•  Components of phenotypes
•  Genotypic values                                    
•  Average effect of a gene                                
•  Breeding values
•  Selection of parents

First Midterm

Week 4. Quantitative Genetics – Phenotypic and Genetic Variances        
•  Genetic variance: additive and dominance                        
•  Environmental variance                                
•  Covariance between relatives    
•  Heritability                                    
•  Genetic and phenotypic correlations                
                                            
Week 5-6. Estimation of Genetic Parameters    
•  Variance components
   - From paired matings and other family structures used in breeding programs    
   - North Carolina Designs I, II, III                            
   - Parent-offspring regression                            
   - Generation means analysis                            
   - Realized heritability from selection experiments                    
   - Designs for detecting epistasis                            
•  GCA and SCA
   - Diallel analyses                                
   - Testcross trials (progeny trials)
•  Degree of dominance, heterosis, inbreeding depression
•  Complex pedigrees – BLUP estimation
                                          
Week 7. Selection based on Phenotype                         
•  Expected gain from recurrent selection
•  Selection during inbreeding
•  Breeding inbred lines and hybrids
   - Testcross selection
   - Predicting performance of hybrids and synthetics
No class on Veteran’s Day, Wed., Nov. 11, 2015

Second Midterm

Week 8. Indirect  Selection and Selection for Multiple Traits                    
•  Family index - combining information from relatives                    
•  Selection for multiple traits (other types of selection indices)                
•  Indirect selection with correlated characteristics             

Week 8-9. Breeding for Diverse Environments        
•  Control of environmental variation in large field experiments
   - Augmented designs
   - Lattice designs
   - Spatial analysis
•  Stability, specific adaptation, and broad adaptation    
•  Analysis of genotype by environment interactions
•  Breeding for abiotic stress tolerance in a changing climate    
No class on Friday Nov. 27 – Thanksgiving Holiday

Week 10. Molecular Breeding - Possible Topics for Term Projects
•  QTL mapping with multi-parent advanced generation inter-cross (MAGIC) populations
•  Use of R/qtl software
•  Association studies (GWAS)
•  Marker assisted selection (MAB, MAS)
•  F2 enrichment
•  Genomic selection (GS)
•  Applications of genotyping-by-sequencing (GBS) in Plant Breeding
•  Breeding transgenic crops

Week 11. Final Exam
•  Take-home due by 9:30 am on Friday, December 11, 2015