Interval Mapping with Regression Analysis

The genetic analysis of quantitative traits includes two major tasks: (1) identifying the location of QTLs affecting a quantitative trait using a genetic linkage map constructed from molecular markers, and (2) estimating the genetic effects of the QTLs on the phenotype. If the genotypes of a putative QTL were known for all individuals, its genomic location could be readily determined using a marker linkage analysis. Furthermore, the genetic effects of the QTL could be precisely estimated and tested by simple t tests or ANOVA. However, it is not possible for the genotypes of QTLs to be directly observed; instead they should be inferred from observed marker and phenotypic information. As was seen in Chapter 8, a marker analysis cannot unambiguously separate the genetic effects of a QTL from the recombination fraction between the markers and QTL.