Course Description
Quantitative and population plant genetics and their interrelationship with plant breeding. Genetic and environmental variation and how they relate to selection procedures and choice of type of variety. Predictive plant breeding. QTL discovery, molecular breeding, and genomic selection in an applied breeding program.
Athena Title
Plant Quant Gen and Molec Bre
Prerequisite
PBGG(CRSS)(HORT) 4140/6140 and (STAT 6210 or STAT 6210E or STAT 6220)
Semester Course Offered
Offered spring
Grading System
A - F (Traditional)
Course Objectives
This course aims to: 1) provide students with a basic understanding of quantitative genetic theory and methodologies and their applications in plant breeding; 2) enable students to design, analyze, and interpret results of quantitative genetic experiments and develop a breeding strategy to maximum genetic gains; and 3) provide students with the ability to effectively utilize genomic tools including marker-assisted selection, marker-assisted backcrossing, and genomic selection in an applied breeding program. The course will cover quantitative and population plant genetics and their interrelationship with plant breeding; genetic and environmental variation and how they relate to selection procedures and choice of type of variety; predictive plant breeding; QTL discovery, molecular breeding, and genomic selection in an applied breeding program; and utilization of computer programs to analyze the quantitative data.
Topical Outline
1. Introduction and review of statistical concepts Review of statistical concepts Genetic basis of populations and quantitative genetics Importance of quantitative genetics Plant breeding vs. quantitative genetics Type of varieties - pure line, hybrid, synthetic, and clone 2. Genetics of breeding populations Genotype and allele frequency Hardy-Weinberg equilibrium Change of gene frequency Linkage and linkage disequilibrium Inbreeding coefficient Coefficient of parentage 3. Genetic variability in populations and heritability Means of genotypes Breeding value and the average effect Genetic variance Covariance among relatives Inbreeding Expected mean squares Heritability 4. Genetic mating design and estimating genetic variance Genetic mating design Combining abilities One factor design Nested mating design (NC I) Factorial mating design (NC II) NC III mating design Diallel mating design Generation means analysis Parent-offspring regressions analysis 5. Genotype x environment interaction Definition - genotype x environment interactions (G x E) Crossover and non-crossover interactions Effect of G x E on genetic variance Effect of G x E on decisions in a breeding program Stability theory and stability calculations 6. Trait selection Selection theory-single trait Selection theory-multi-traits Selection in self pollinators Phenotypic, genotypic, and environmental correlations Realized heritability and genetic gain Optimum generation to start selection for a yield of a self-fertilizing crop Recurrent selection Mass selection examples Gardner study (Yield in maize) Illinois Maize Oil/Protein long term selection experiment 7. Heterosis and choice of parents Theories of heterosis Heterotic patterns Classes of loci concept Improvement of inbred cultivars Improvement of parents of hybrids 8. Prediction and predicted gain Genetic prediction in plant breeding Introduction of matrix algebra for BLUP BLUP for self-pollinated crops BLUP for cross-pollinated crops BLUP for genome-wide selection 9. Molecular markers in plant breeding Types of molecular markers Use of molecular markers to characterize germplasm Genetic similarity and genetic distance measured by DNA markers Application of cluster analysis in plant breeding Use of molecular markers to map QTLs 10. Population design and development for QTL mapping Experimental design for QTL mapping Population development for QTL mapping Nested association mapping (NAM) design Multi-parent advanced generation intercross (MAGIC) population design 11. Deployment of molecular breeding in an applied plant breeding program Linkage disequilibrium and QTL analysis QTL x environment interaction QTL validation Marker-assisted selection Marker-assisted backcrossing Marker-assisted recurrent selection 12. Genomic selection and breeding by design in an applied breeding program Genomic selection Cross prediction-Breeding by design
Syllabus