F2 Designs for QTL Analysis

This chapter covers the procedure of mapping quantitative trait loci (QTLs) in an F₂ breeding design. I describe genetic design, general methods and software, and several commonly used approaches. The genetic design section includes F₂ population construction. Widely used methods and software are introduced in the section of general methods and software. Finally, composite interval mapping, penalized maximum likelihood, and empirical Bayes are described in detail. Some issues related to the F₂ design are discussed.