CRS 7210 QUANTITATIVE GENETIC THEORY

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CRS 7210 QUANTITATIVE GENETIC THEORY
2. INSTRUCTOR:
Dr. Settumba B. Mukasa (Senior Lecturer),
PhD in Plant Virology (Swedish Univ. of Agric Science- Uppsala Sweden),
M. Agric St (Genetics & Plant Breeding) (Univ of Queensland, Australia),
BSc Agriculture (Makerere University)
3. COURSE TYPE:
CORE FOR: MSc Crop Science; MSc Plant Breeding and Seed Systems; PhD Plant Breeding and
Biotechnology
PREREQUISITES: CRS 7101
4. COURSE STRUCTURE
3 Credit units: 30 lecture hours (2 contact hour per week for 15 study weeks) and 30 Tutorial/Exercises
(equivalent 1 contact hour per week for 15 study weeks)
5. COURSE DESCRIPTION:
Students with will be equipped with techniques to plan and design breeding experiments by providing a solid
background in quantitative genetics and relevant statistical methodologies. The key topics to be covered include: An
introduction to statistical tools; Causes of genetic variation at single and multilocus; Linkage analysis and
chromosome mapping; Components of phenotypic variation; GxE interaction; The concept of heritability; Detecting
major genes; Resemblance between relatives; Analysis of line crosses; Expectations for line cross means; Analysis
of mating designs; Inbreeding and crossbreeding; Basic concepts of marker-based mapping; Mapping and
characterizing QTLs in inbred line crosses and outbred populations.
6. COURSE OBJECTIVES:
General objective
 The course will help students in making deduction of the consequences of Mendelian inheritance when
extended to the properties of populations, and quantitative traits of fundamental significance in the
application of genetics to breeding.
Specific objectives
 To explain the consequences of inbreeding and outcrossing on the population evolution
 To show how to estimate breeding values and to develop predictive models for crop improvement.
 To provide genetic techniques that will empower students in theoretical and empirical analysis in plant
breeding.
7. RECOMMENDED REFERENCES FOR READING
 Falconer, D.S. and Mackay, T.F.C. 1996. Introduction to Quantitative Genetics. 4th ed. Prentice Hall,
Harlow, U.K.
 Lynch, M. and Walsh, B. 1998. Genetics and analysis of quantitative traits. Sinauer Associates, Sunderland,
MA.
 Hartl, D.L. and Clark, A.G. 1997. Principles of Population Genetics. 3rd ed. Sinauer Associates, Inc.
Sunderland, Massachussetts.
 Sokal, R.R. and Rohlf, F.J. 1987. Introduction to Biostatistics Pub. WH Freeman & Co.
8. COURSE CONTENT, METHODS OF INSTRUCTION, TOOLS AND EQUIPMENT REQUIRED
TOPIC
CONTENT
1. Introduction
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2. An introduction to
statistical tools
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3. Gene models and
genetic variation
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4. Analysis of basic
generation variances
5. Selfing and full-sib
analysis
6. Half-sib mating
designs
7. Diallel Analysis
8. Linkage analysis
and mapping
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Definition of quantitative genetics
Quantitative vs qualitative traits
Historical development of quantitative
genetics
Assignment 1: Overview of Mendelian
genetics
Population distributions
Covariance, regression, and correlation
analysis
Recap on experimental designs
Exercise 1: Matrix algebra and multiple
regression
Single, and two gene models with additive
and dominance effects
Multiple gene models
Relationships between generation means,
and variances
Estimating genetic parameters
Exercise 2. Phenotypic and genetic
correlation of traits/characters
Variation in non-segregating generations
Estimating environmental variance
Variation in segregating generations
Genetic components and heritability
Exercise 3: Analysis of basic generations
Selfing: F3, F4 families etc
Variation between inbred lines derived from
an F2
Sib-mating: parent-offspring regression
Bi-parental mating design
Exercise 4: Variance component estimation
North Carolina experiment I: NCI
North Carolina experiment II: NCII
North Carolina experiment III: NCIII
Exercise 5: HS designs using inbred lines
from an F2 as parents
The diallel cross
Ggeneral and specific combining ability
Partial and full diallel
Assignment 2: Analysis of resemblance
between relatives
Genetic and molecular markers
Chiasmata and recombination
Mapping functions
Segregation distortion
METHOD OF
INSTRUCTION /
Time allocated
Interactive lecture (2
hrs)
TOOLS/
NEEDED
LCD Projector,
BB/Chalk.
Tutorial (2 hrs)
Lecture (2 hr)
LCD Projector,
BB/Chalk
Tutorial (2 hrs)
Lecture (2 hrs)
Practical -field tour (2
hrs)
Lecture (2 hrs)
Tutorial/ exercises (2
hrs)
Lecture (2 hrs)
Tutorial/ exercises (2
hrs)
Lecture (2 hrs)
Tutorial/ exercises (2
hrs)
Lecture (2 hr)
Tutorial (2 hrs)
Lecture (2 hrs)
Tutorial/ exercises (2
hrs)
LCD Projector,
BB/Chalk
LCD Projector,
BB/Chalk
LCD Projector,
BB/Chalk
LCD Projector,
BB/Chalk.
LCD Projector,
BB/Chalk.
LCD Projector,
BB/Chalk.
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9. QTLs and QTL
mapping
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10. Genotype x
Environment
Interaction
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11. Stability analysis
and selection
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12. Correlated and
threshold characters
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13. Analysis of line
crosses
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14. Multivariate
Analysis of Variance
in Plant Breeding
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15. Selection
methods
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Chromosome and genomic maps
Practical 1: Calculating recombination
frequencies
Definition of QTL
QTL mapping methodology
QTL and marker loci in segregating
generations
Assignment 3: Biometrical methods for
estimating gene number
Definition of GxE
Nature and causes of GxE
Interpretation of GxE analysis
Statistical estimation methods
Partitioning of phenotypic variance: genetic
and environmental variation
Exercise 6: Genotype x environment
interaction
Concept of phenotypic stability
Stability statistics
Selection in heterogeneous environments
Assignment 4: Genetic analysis of
agronomically important traits
Correlation between characters
Environmental and genetic correlations
Genetic covariation and design of
experiments
Threshold traits
Resemblance between relatives
Exercise 7: BLUP and REML estimation of
genetic values
Expectations for line cross means
Heterosis and inbreeding depression
Parent-offspring regression and ANOVA
estimation methods
Correlated response to selection
Tutorial 1: Heritability and genetic gain
estimation exercises
Analysis of variance
Cluster analysis
Maximum likelihood functions
Estimation of variance components using ML
and REML
Tutorial 2: Application of path coefficient
analysis in breeding programmes
Choice of breeding objective
Predicting the breeding potential of crosses
and response to selection
Indirect and multi-trait selection
Lecture (2 hr)
Tutorial/ exercises (2
hrs)
Lecture (2 hrs)
LCD Projector,
BB/Chalk.
BB/Chalk
Tutorial/ exercises (2
hrs)
Lecture (2 hr)
Tutorial/ exercises (2
hrs)
Lecture (2 hr)
LCD Projector,
BB/Chalk.
LCD Projector,
BB/Chalk.
Tutorial/ exercises (2
hrs)
Lecture (2 hr)
Tutorial (2 hrs)
LCD Projector,
BB/Chalk.
Interactive lecture (2 LCD Projector,
hrs)
BB/Chalk
Tutorial (2 hrs)
Interactive lecture (2 LCD Projector,
hrs)
BB/Chalk
Tutorial (2 hrs)
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16-17
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Marker assisted selection
Tutorial 3: Measure genetic variation and
relatedness using molecular makers
Revision Time
Final Examination
9. SUMMARY OF TIME NEEDED:
Lectures
Tutorials (and assignments)
Practicals
10. COURSE ASSESSMENT:
Quizzes tests:
Presentation
Assigment:
University Examination:
30 hrs
15 hrs
15 hrs
3 quizzes/tests arising from tutorials and assignments during
semester week 5, 10 and 15.
Presentation of selected topics
Students will write 2 assignment reports
Final examination during week 16-17 of the semester
END
20%
10
10%
60%
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