Effect of population size on the estimation of QTL: a test using resistance to barley stripe rust

Abstract

The limited population sizes used in many quantitative trait locus (QTL) detection experiments can lead to underestimation of QTL number, overestimation of QTL effects, and failure to quantify QTL interactions. We used the barley/barley stripe rust pathosystem to evaluate the effect of population size on the estimation of QTL parameters. We generated a large (n = 409) population of doubled haploid lines derived from the cross of two inbred lines, BCD47 and Baronesse. This population was evaluated for barley stripe rust severity in the Toluca Valley, Mexico, and in Washington State, USA, under field conditions. BCD47 was the principal donor of resistance QTL alleles, but the susceptible parent also contributed some resistance alleles. The major QTL, located on the long arm of chromosome 4H, close to the Mlo gene, accounted for up to 34% of the phenotypic variance. Subpopulations of different sizes were generated using three methods-resampling, selective genotyping, and selective phenotyping-to evaluate the effect of population size on the estimation of QTL parameters. In all cases, the number of QTL detected increased with population size. QTL with large effects were detected even in small populations, but QTL with small effects were detected only by increasing population size. Selective genotyping and/or selective phenotyping approaches could be effective strategies for reducing the costs associated with conducting QTL analysis in large populations. The method of choice will depend on the relative costs of genotyping versus phenotyping.

QTL hotspots in eggplant (Solanum melongena) detected with a high resolution map and CIM analysis

“…However, it should be noted that the relatively small size of the mapping population (58 F 2 individuals) has several consequences. In such populations, minor QTL are more difficult to detect and major QTL effects are generally overestimated (Vales et al 2005). Thus the change in the magnitude of QTL effect may, in part, be explained by the elimination of false positives and minor QTLs.…”

Quantitative trait loci mapping of phenotypic plasticity and genotype–environment interactions in plant and insect performance

“…Firstly, the ability to detect QTL -trait associations is limited, because QTL are only detected where there is genetic variation at loci (between the two parental alleles), which has a significant effect on the measured trait. Each line in the mapping population is designed to contribute alleles from either parent, and each line will differ in which parental alleles they contribute at a small number of loci [22]. Therefore, fewer lines results in fewer genetically variable loci.…”

Quantitative trait loci (QTLs) analysis of palm oil fatty acid composition in an interspecific pseudo-backcross from Elaeis oleifera (H.B.K.) Cortés and oil palm (Elaeis guineensis Jacq.)

“…In that way, our experiment is a preliminary study where a certain number of QTLs with small or medium effects might not be detected. Studies showed that by increasing the population size, it is possible to increase the total number of QTLs detected and to reveal those with small effects (Vales et al 2005;Raghavan and Collard 2012). This is well known that the power to detect QTLs is rather low using a small number of individuals, depending on the trait heritability and QTL effects, with also the non-negligible risk to evidence false QTLs especially for those with weak effects (Beavis 1998).…”