PLNT*6160 Advanced Plant Breeding II

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The following description is for the course offering in Winter 2023 and is subject to change. It is provided for information only. The course outline distributed to the class at the beginning of the semester describes the course content and delivery, and defines the methods and criteria to be used in establishing the final grades for the course. Offered in odd-number years.

The course is designed to familiarize plant breeding graduate students with the theory and application of quantitative genetics in plant breeding, help them understand the fundamentals of population genetics, and explore how quantitative genetics principles and modern tools can help a plant breeder design and implement a breeding program to improve quantitative traits and to study complex traits. The course is intended to provide opportunities for continued learning, critical questioning and discussion of research findings and communication skills. Emphasis is placed on gaining hands-on experience data management and analysis that resembles real-life plant breeding and quantitative genetic problems and situations.


Teaching Assistant:

Credit Weight:


Course Level:

  • Graduate

Academic Department (or campus):

Department of Plant Agriculture



Semester Offering:

  • Winter

Class Schedule and Location:

Please refer to WebAdvisor for class schedule and location.

Learning outcomes:

At the end of this course, students should be able to:

  1. understand the fundamentals of Population and Quantitative Genetics applied to plant breeding situations,
  2. know how to critically review and discuss scientific literature addressing quantitative genetics problems in plant breeding,
  3. have had hands-on experience with quantitative management, analysis and interpretation of quantitative data from plant breeding populations; and
  4. understand, with hands-on experience, the application of genomics data in the analysis of quantitative plant breeding data.

Lecture Content:

Lecture Content:
Theme I: Plant Breeding, Quantitative Genetics, and Population Genetics
  • Lecture: Introduction to quantitative traits, gene frequency, and genetics of breeding populations
  • Preparation for stats analysis for the upcoming sessions, planning paper discussions and other assignments
  • Lecture: Resemblance among relatives, identity by state and identity by descent, coefficient of co-ancestryAssignment I (due in two weeks)
  • Hands on Experience with Computer Program; Analysis of relatedness data and Cluster analysis (read papers/manuals before class).
  • Paper discussion
  • Lecture: Review of statistical Concepts: Frequency Distribution, parameters and statistics, ANOVA, correlation, regression, Experimental designs and field plot techniques to phenotype plant breeding populations for quantitative traits
  • Paper Discussion

Theme II. Variation in Breeding Populations and Selection Efficiency

  • Lecture: Variation in breeding populations, phenotypic and genetic variances and heritability, Methods to estimate Variance components and heritability - Assignment II (Due in two weeks)
  • Hands-on experience to estimate heritability
  • Paper Discussion
  • Lecture: Genotype by Environment Interaction, stability and adaptation - Assignment III (due in two weeks)
  • Hands on experience with G by E data
  • Paper Discussion
  • Lecture: Response to direct selection, correlated response to selection, and multiple trait selection in plant breeding populations
  • Hands-on experience: Genetic and Phenotypic correlation data analysis
  • Paper Discussion

Theme III. Marker-Trait Association and Genomic Selection

  • Lecture: Fundamentals of marker-trait association, Linkage mapping, and QTL analysis
  • Paper Discussion
  • Hands-on experience: linkage mapping and QTL analysis software - Assignment IV (due in two weeks)
  • Lecture: Fundamentals of Association Mapping
  • Paper Discussion
  • Hands-on experience – Association mapping software
  • Lecture: Genomic selection in Plant Breeding
  • Paper Discussion
  • Student Presentations (20 min each; peer grading)
Labs & Seminars:

Hands-on data analysis will form the lab component of this course. Datasets and sample SAS programs will be provided.


Each student is to pick one of the topics of the course and prepare a 20-minute presentation, in which they will review the recent pertinent literature and present research examples output.  (Peer Graded)

Course Assignments and Tests:

Assignment or Test Contribution to Final Mark Learning Outcomes Assessed

Quizzes (5x)

20% 1-4
Assignments (4x)


Paper discussion and participation 20%


Seminar 20%


Additional Notes:

Best four of five quizzes counted towards final grade.

Four assignments will be handed out in class (see course content) each will require students to write a report. The report is due back in two weeks. Please send electronic reports saved as *.pdf (no hard-copy required) to on or before the deadline by 12:00 (AM).

Assignment Handed out Due Marked by

















Final examination:

There is no final examination scheduled for this course.

Course Resources:

Required Texts:


Recommended Texts:

Falconer, D.S. and T.F.C. Mackay. 1996. Introduction to Quantitative Genetics. 4th edition Pearson Prantice Hall. Essex, England.

Kang, M.J. (Ed.) 2003. Handbook of formulas and software for plant geneticists and breeders. Food Products Press. The Haworth Reference Press, New York

Hallauer, A.R. and J.B. Miranda (eds.) 1988. Quantitative genetics in maize breeding. 2nd ed., Iowa State University Press, Ames, IA

Bernardo, R. 2002. Breeding for quantitative traits in plants. Stemma Press, Woodbury, MN

Lynch, M. And B. Walsh. 1998. Genetics and analysis of quantitative traits. Sinnauer Associates, Inc. Publishers. Sunderland, MA

Liu, B. H. 1998. Statistical Genomics. 2nd Edition. CRC Press Boca Raton, NY.

Lab Manual:

Software manuals and instructions will be provided.

Other Resources:


Field Trips:


Additional Costs:


Course Policies:

Grading Policies:

Homework assignments will be assigned at the time of lecture on each topic and will be due in class three weeks afterwards.

Assignments (40% of the final mark): Four homework assignments (each worth 10% of the final mark) will be handed out in class. For each assignment, students will be supplied with a data-set and in some cases sample analysis SAS codes/software. Students are asked to write a report, in which they will follow the format of a scientific paper with Introduction, Materials and Methods, Results (including tables and Figures), Discussion, and References. Students will need to go over the basics of the analysis, discuss several relevant papers, and then and interpret the results.

Paper Discussion and Participation (20% of the final mark): Each paper discussion will have one moderator, leading the discussion, and the rest of the class will actively participate in discussions. Students will be marked for both their moderator role and discussion participant role.

Student Presentations or tutorial videos (20 % of the final Mark – Peer-graded): Each Student is to pick one of the topics of the course and prepare a 20 Min presentation to review the recent pertinent literature. Alternatively, they can work with a team of three students and make a tutorial video for a software.

Quizzes (20% of the final Mark): Students will write 5 Quizzes throughout the semester. Students will be informed one week before. 4 quizzes will be counted towards 10% of the total mark.

Discussion of Research Papers: Research articles will be discussed as part of the class. Students will be expected to thoroughly read and prepare for a discussion of all papers as their participation (emphasis on relevance and quality of contribution rather than time spent discussing it) will make up part of their overall grade for the course. Discussion of papers should take into consideration such items as objectives and purpose of the research, adequacy of the methodology used, and the scientific impact of the results.

A discussion moderator will be assigned for each paper. Their role will be to make sure that all relevant points in the paper are discussed. Their role is not to present the paper to class but to involve all students in the discussion by asking questions and making references to concepts, data and its interpretation in the paper.

Note: Papers will be handed out in class or via e-mail, and will also be posted on the course website on CourseLink.

Course Policy on Group Work:


Course Policy regarding use of electronic devices and recording of lectures:

Electronic recording of classes is expressly forbidden without consent of the instructor.  When recordings are permitted they are solely for the use of the authorized student and may not be reproduced, or transmitted to others, without the express written consent of the instructor.

Other Course Information:

University Policies

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