Accuracy of mapping quantitative trait loci in autogamous species

Abstract

The development of linkage maps with large numbers of molecular markers has stimulated the search for methods to map genes involved in quantitative traits (QTLs). A promising method, proposed by Lander and Botstein (1989), employs pairs of neighbouring markers to obtain maximum linkage information about the presence of a QTL within the enclosed chromosomal segment. In this paper the accuracy of this method was investigated by computer simulation. The results show that there is a reasonable probability of detecting QTLs that explain at least 5% of the total variance. For this purpose a minimum population of 200 backcross or F2 individuals is necessary. Both the number of individuals and the relative size of the genotypic effect of the QTL are important factors determining the mapping precision. On the average, a QTL with 5% or 10% explained variance is mapped on an interval of 40 or 20 centiMorgans, respectively. Of course, QTLs with a larger genotypic effect will be located more precisely. It must be noted, however, that the interval length is rather variable.

Identification of quantitative trait loci function through analysis of multiple cuticular hydrocarbons differing between Drosophila simulans and Drosophila sechellia females

“…Significance levels at P ¼ 0.05 (Table 1) for all CHC were calculated from 1000 permutations of the trait data among marker classes (Churchill and Doerge, 1994). Boundaries of QTL were determined by finding the highest peak and then extending the QTL for 2-LOD (logarithm of odds) around the peak, which is a conservative estimate of the location (van Ooijen, 1992;Manichaikul et al, 2006). When peaks were adjacent, if there was not a 2-LOD drop between them, the QTL region was combined.…”

QTL analysis of an intervarietal set of substitution lines in Brassica napus: (i) Seed oil content and fatty acid composition

“…In segregating populations the precision of QTL mapping methods are relatively poor, and rarely fall below a 95% CI of about 20 cM (van Ooijen, 1992;Hyne et al, 1995;Burns, 1997). The CI in the substitution lines is defined precisely as the upper limits of extent of the donor segments as indicated in Figure 1.…”

“…However, all of these methods can suffer from lack of precision of QTL mapping owing to a number of factors. These factors include: the heritability of the trait; the total number of QTL governing the trait, the distribution of these QTL over the genome, their interactions with each other, the random variation because of the environment and other unlinked genetic factors, the type and size of the population studied, the genome size, and the number and distribution of marker loci (van Ooijen, 1992;Darvasi et al, 1993).…”

Genetic Architecture of NaCl Tolerance in Arabidopsis

“…QTL likelihood plots were constructed from the LOD scores obtained, using the SigmaPlot 2000 program (v6.0, Statistical Products and Service Solutions, Chicago). One and two LOD support intervals were established as 90% and 95% confidence intervals, respectively (Van Ooijen, 1992). The MapQTL program was also used to obtain estimates of the additive effect and the percentage of variance explained by each QTL, as well as the total variance explained by all of the QTL affecting each of the traits were analyzed.…”