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.

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