1. Linkage analysis and genetic mapping
Marker assisted selection and “map-based” breeding
“Mendelizing” QTL

2. “Mendelizing QTL”

3. We can more completely characterize quantitative traits and the loci that confer quantitative inheritance
Identify the number of loci conferring a Quant. Trait
Identify gene action and estimate the magnitude of individual loci (VQTL/Vp)
Select for genotype when phenotypic selection is less efficient

4. New technology opens the possibility of “map-based” breeding.
How easy will it be to pyramid genes or break unfavorable linkage?

5. Synthesize information from numerous crosses to understand patterns of genome organization
Clusters of disease resistance genes
Candidate genes for Quant. Trait loci

6. Power of modern genetic mapping in breeding applications comes from:
Combining classical and new techniques
Placing “economic traits” onto maps
Working in genetic backgrounds that favor application

7. Building Genetic Maps Single-locus analysis Two-locus analysis
Measuring linkage distance
Linkage grouping
Gene ordering
Multi-point analysis

8. Building Genetic Maps Single-locus analysis Two-locus analysis
Measuring linkage distance
Linkage grouping
Gene ordering
Multi-point analysis

9. Definition of Genetic Linkage
The association of genes located on the same chromosome
The association or non-independence among alleles at more than one locus
Statistical definition

10. Linkage between qualitative traits
Does each locus segregate as expected?
Mendel’s first law
Do the loci assort independently?
Mendel’s second law
What is the distance between loci?

11. Estimation of linkage distance
Historical overview
Additive method
Weighted mean method
Product method
Maximum likelihood
Log of the odds

12. Keep in mind the following:
We are first going to cover the theory and practice of linkage analysis
Application of linkage data and “map-based” breeding are up to the creativity of the breeder
There are sometimes conflicting goals between breeding applications and genetic applications