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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 2. An introduction to statistical tools 3. Gene models and genetic variation 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 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. 9. QTLs and QTL mapping 10. Genotype x Environment Interaction 11. Stability analysis and selection 12. Correlated and threshold characters 13. Analysis of line crosses 14. Multivariate Analysis of Variance in Plant Breeding 15. Selection methods 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) 16-17 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%