Quantitative trait loci (QTL) detection in multicross inbred designs: recovering QTL identical-by-descent status information from marker data

Abstract

Mapping quantitative trait loci in plants is usually conducted using a population derived from a cross between two inbred lines. The power of such QTL detection and the parameter estimates depend largely on the choice of the two parental lines. Thus, the QTL detected in such populations represent only a small part of the genetic architecture of the trait. In addition, the effects of only two alleles are characterized, which is of limited interest to the breeder, while common pedigree breeding material remains unexploited for QTL mapping. In this study, we extend QTL mapping methodology to a generalized framework, based on a two-step IBD variance component approach, applicable to any type of breeding population obtained from inbred parents. We then investigate with simulated data mimicking conventional breeding programs the influence of different estimates of the IBD values on the power of QTL detection. The proposed method would provide an alternative to the development of specifically designed recombinant populations, by utilizing the genetic variation actually managed by plant breeders. The use of these detected QTL in assisting breeding would thus be facilitated.

Figure 1.—

If parents (P1, P2, P3, and P4) are considered as founders, only three types of relationships exist between individuals i and j of the mapping population. Notations Q₁, Q₂, Q₃, and Q₄ represent parents' QTL information while Q and Q′ (unknown) represent progenies' i and j QTL information. In the same manner, 1, 2, 3, and 4 represent parents' marker alleles information while A and A′ (supposedly known) represent progenies' i and j marker information. Q₁, Q₂, Q₃, and Q₄ are homozygous while Q and Q′ can be heterozygous. The possible genotypes at the QTL for the three cases are as follows:

Figure 2.—

Comparison of the LR profiles for (a) setting 1 under formulas 1, 2a, and 2b without selection; (b) setting 1 under formulas 1, 2a, and 2b with selection; (c) setting 2 under formulas 1 and 2b for three levels of QTL heritabilities (0.2, 0.1, and 0.05), without selection; and (d) setting 2 under formulas 1 and 2b for two levels of QTL heritabilities (0.1 and 0.05), with selection.