Syllabus

AppliedPlantBreedingSyllabusW2022v2.pdf

Applied Plant Breeding (APBI 318)

Winter 2022 TERM 1/Online and Flipped

Instructor

Andrew Riseman, Associate Professor, Plant Breeding and Agroecology

Primary Contact: e-mail: andrew.riseman@ubc.ca

Course Format and Times

This course uses a flipped format meaning students are required to watch pre-recorded

mini-lectures ahead of synchronous meetings and come prepared to discuss the topics

covered in the recordings.

Synchronous meetings are held Tuesdays and Thursdays at 9:30-11:00 Vancouver Time

Course Description

This course will give students working knowledge of small-scale classical (e.g., nonbiotechnological)

plant breeding and associated issues (e.g., plant reproductive biology,

genetics). It will use an application-oriented approach to enhance student understanding

of the techniques and procedures involved in reproductive biology (i.e., anatomy,

morphology, fertilization, genetics), in implementing a simple plant breeding program,

and in evaluating the impact of selection on breeding populations and desired outcomes.

Learning Outcomes

Upon successful completion of this course, the students should be able to:

• Design and implement a simple plant breeding program;

• Predict the potential for successful plant improvement for a particular breeding

objective, given the nature of the plant species and the genetic inheritance of the

trait;

• Create and manage plant populations in terms of specific genetic composition;

• Develop genetic hypotheses and apply the appropriate statistical methods for their

evaluation;

• Process seed for either seed saving or part of a breeding project.

Course Reading List

There is no required text for this course. Instead, students will engage with a coursespecific

manual and resources (posted on Canvas), supplemental readings, and the

primary literature.

Suggested Library Resources (non-reserved):

Textbooks:

Allard, R.W. 1960. Principles of Plant Breeding, John Wiley and Sons, NY

Chahal, G.S. and Gosal S.S. 2002. Principles and Procedures of Plant Breeding.

Biotechnological and conventional approaches. Alpha Science, Pangbourne, UK

Falconer, D.S. 1981. Introduction to Quantitative Genetics. 2nd ed. Longman, NY

Raven, P.H. et al. 1992. Biology of Plants. 5th ed. Worth Publishers

Simmonds, N.W. 1979. Principles of Crop Improvement, Longman, London

Journals

Theoretical and Applied Genetics Nature Biotechnology

Genome Plant Cell Reports

Plant Breeding Molecular and General Genetics

Plant Cell, Tissue and Organ Culture Can. J. Plant Science

J. American Soc. Hort Science HortScience

Crop Science Heredity

Experimental Agriculture Euphytica

There are also many relevant resource sites on the Internet. However, the credibility of

the content must be assessed considering the expertise and agenda of the source.

Course Format:

The course will include video recorded mini-lectures, synchronous discussions (recorded

and posted), writing assignments, computer simulation, term project, and at-home

laboratories.

Activities/labs (support information will be posted on Canvas)

GreenGenes Breeding Simulation, “2-minute Talks”, and Seed harvest, cleaning, and

viability testing.

Evaluation Procedures:

Students will be evaluated based on their comprehension of course material,

participation, and their ability to apply this information in addressing relevant problems

in plant breeding and crop improvement.

Critical Thinking/Word problem Assignments 20%

(1x written and 3x word problems @ 5% each)

GreenGenes Project 20%

Laboratory Reports (2@2.5% each) 5%

2-min Talks 15%

Term Project 40%

Crossword Puzzle (Bonus) up to 5%

Overall: 100%

Academic Honesty

Academic honesty is a core value of scholarship. Cheating and plagiarism (including

both presenting the work of others as your own and self-plagiarism), are serious academic

offences that are taken very seriously in Land & Food Systems. By registering for

courses at UBC, students have initiated a contract with the university that they will abide

by the rules of the institution. It is the student’s responsibility to inform themselves of

the University regulations. Definitions of Academic Misconduct can be found on the

following website:

http://www.calendar.ubc.ca/vancouver/index.cfm?tree=3,54,111,959#10894

If you are unsure of whether you’re properly citing references, please ask your instructor

for clarification before the assignment is submitted. Improper citation will result in

academic discipline.

Assignment 1: Critical Thinking Assignments

Assignment 1 (written): Topic: My perfect plant.

In under 1000 words, describe your perfect plant, its attributes, phenotypes, capabilities,

and uses. Knowing there are genetic engineering tools that allow trans-species genetic

exchange, you are free to dream big. If you have seen a particular trait in some other

biological organism, it can be included. However, please note 1) it must maintain the

essence of a plant (e.g., no walking plants with legs) and 2) you are bound by all laws of

nature (e.g., no anti-gravity potatoes 😉).

Assignments 2, 3 and 4: Genetic Word Problems

Complete the assigned genetic word problems. Complete in sufficient detail to allow me

to understand how you answered the problem. Show all calculations, summaries,

hypotheses, statistics, and conclusions.

Greengenes Breeding Simulation:

Each student will receive a unique web-based breeding problem designed to emulate an

actual breeding program but without the time required to grow populations. You will be

asked to determine the genetic control of simply inherited traits, identification of

interactions between genes (epistasis) and calculation of co-segregation (linkage) if

present. Additional information will be posted on Canvas.

Laboratory Reports:

My Seed Diary Parts I and II. See Assignment in Canvas for details.

2 min Talks:

See Assignment in Canvas for details.

Term Project Description

Each student will select a crop (that is or could be grown at in SW British Columbia) and

write a paper that details the development of a breeding program for it. We will

brainstorm ideas as a group but plan to have your choice of crop and breeding objective

ready by October 18.

Your term project should include the following sections:

• Title page: Title, name and student number; executive summary of project (~1/2

page); and 6-8 key words (10%).

• Introduction (~1-2 pages) (20%)

o Economic (e.g., sales, value added), environmental (e.g., ecological

services), and/or social (e.g., pedagogy, ritual) importance of growing this

crop compared to other similar crops (10%);

o Environmental requirements for crop production (i.e., feasibility

assessment) (5%);

o Extent of its current cultivation (local, regional, national, and

international) (5%);

• Literature review (~1-3 pages) Relevant literature, including the most recent

publications (last 5 years) should be consulted and cited as appropriate (20%).

o Basic botany including family, order, class, genus, species, etc. with

scientific and common names; characterization of flower (e.g., perfect),

fruit (e.g., capsule), and pollen (e.g., bi-nucleate) (5%).

o Evolutionary background of the crop and cytogenetic relationship with its

related wild/cultivated species (2.5%);

o If known, the genetic control of important traits (1.5%);

o Pertinent Canadian and International breeding programs including their

locations (1%);

o Current commercial breeding objectives (5%);

o Reproduction system (i.e., outcrosser or selfer) and typical breeding

methods used on this crop (5%).

• Breeding program description (? pages) (45%)

o Vision: detail your ideal plant/cultivar profile (10%);

o Variation: germplasm sources, cultivar/accession lists, and acquisition

strategies (5%);

o Techniques (5%)

o Crossing techniques

o Pollination control techniques (i.e., mechanical, spatial, temporal)

o Description of the selection pressure environment relevant to your ideal

cultivar

o Seed harvest, cleaning, and storage techniques

o Breeding strategy and selection criteria (15%)

o General description of recommended breeding strategy (e.g., MS,

Pedigree, SSD)

o Planting design and isolation requirements

o Year-by-year activities (e.g., when to increase heterozygosity, when to

increase homozygosity, and when to select)

o Seed production requirements (i.e., number of plants per generation

required to achieve goals)

o Cultivar stabilization and stock seed production procedures (10%)

• References (5%)

Course Schedule:

Date (Day), Discussion Topic Mini-lectures to Watch Before

Synchronous Discussion

Week 1:

Sept 6

Imagine Day (No Class)

Week 1:

Sept 8

Course Introduction, Goals and

Critical Thinking

Student introductions, goals, and

favorite plant

Course Logistics

Week 2:

Sept 13

Impacts of domestication and

plant breeding

Introduction to Plant Breeding

Important Historical Events

Week 2:

Sept 15

Flowers and the female

gametophyte

Flower Structure

Megasporogenesis

Week 3:

Sept 20

The male gametophyte and the

cool world of pollen

Assignment 1 Due: Topic: My

perfect plant

Microsporogensis

Pollen Overview

Microspore Embryogenesis

Week 3:

Sept 22

Sex, fertilization, and the

consequences….

Discuss your perfect plants

Fertilization

Seeds

Week 4:

Sept 27

Fruit diversity and breeding

Fruit Types

Seed Dispersal

Week 4:

Sept 29

Seeds and early growth Seed Physiology

Seed Testing

Week 5:

Oct 4

Practical seed cleaning My Seed Diary Part I

Week 5:

Oct 6

Class discussion Breeding

Projects

Week 6:

Oct 11

Breeders work with natural

breeding systems, until they

don’t….

Natural Breeding Systems

Self Incompatibility Overview

Week 6:

Oct 13

Self Incompatibility Morph and Dev

Mech

Self Incompatibility Genetic Mech

Variants in the Reproductive Process

Week 7:

Oct 18

Mendel and his genetics

When things don’t work out,

linkage?

Genetic Word Problem-

Qualitative Inheritance Due

Introduction to Qualitative

Inheritance

Mendelian Genetics

Chi Square Analysis

Linkage and Recombination

Three Point Test Cross

Detecting Linkage

Week 7:

Oct 20

When things really don’t work

out, lethality, epistasis,

modifiers, oh my….

Altered Ratios Lethality

Altered Ratios Epistasis

Altered Ratios Modifiers

Week 8:

Oct 25

Introduction to Greengenes

Genetic Word Problems-

Linkage and Epistasis Due

Greengenes Document Mastering

Mendel’s Magic

Week 8:

Oct 27

Class discussion Breeding

Projects

Week 9:

Nov 1

Dissecting complex traits, the

quantitative way….

Greengenes Due

Introduction to Quantitative

Inheritance

Quantitative Distributions

Number of Genes Formula

Allelic Contributions

Week 9:

Nov 3

Alleles are the basis of

populations

Allelic Frequency

Hardy Weinberg Equilibrium

Population Equilibrium

Effect of Selection on Allelic

Frequency

Week 10:

Nov 8

Populations are made up of

individuals that breeders

select….

And…

The royals come to plants…

Variance Overview

Genotypic Variance

Model of Genotypic Variance

Number of Genes Formula

Heritability and Selection Pressure

Inbreeding Depression

Heterosis and Hybrid Vigour

Week 10:

Nov 10

No Class- Winter Break

Week 11:

Nov 15

Breeding strategies for Self-

Pollinated Crops

Breeding Schemes Overview

Breeding Schemes Mass Selection

Breeding Schemes Pure Line

Breeding Schemes Bulk Method

Week 11:

Nov 17

Breeding strategies for Cross

Pollinated Crops

Breeding Schemes Pedigree

Selection

Breeding Schemes Single Seed

Descent

Breeding Schemes Backcross

Breeding

Combining Ability

Recurrent Selection

Week 12:

Nov 22

Doing the actual work in the

field

Field Plot Technique

Experimental Design

Week 12:

Nov 24

Example breeding scenario:

Breeding for Disease Resistance

Introduction

Disease Development

Vertical and Horizontal Resistance

Disease Resistance Mechanisms

Sources of Resistance

Screening Techniques

Week 13:

Nov 29

Example breeding scenario:

Breeding for Disease Resistance

(continued)

2 min Talks Due (Dec 6)

Breeding Strategies for Resistance

Marker Assisted Selection for

Resistance

Somaclonal Variation

Genetic Engineering for Resistance

Managing for Disease Resistance

Week 13:

Dec 1

Catch up day

Week 14:

Dec 6

Class wrap-up 2 min Talks