Neighbor QTL: an interval mapping method for quantitative trait loci underlying plant neighborhood effects

Abstract Phenotypes of sessile organisms, such as plants, rely not only on their own genotypes but also those neighboring individuals. Previously, we incorporated neighbor effects into a single-marker regression using the Ising model ferromagnetism. However, little is known regarding how should be in quantitative trait locus (QTL) mapping. In this study, propose new method for interval QTL mapping effects, designated “neighbor QTL,” algorithm which includes: (1) obtaining conditional self-genotype probabilities with recombination fraction between flanking markers; (2) calculating genotypic identity probabilities; and (3) estimating additive dominance deviations effects. Our simulation F2 backcross lines showed that power to detect increased effective range decreased. The was applied insect herbivory Col × Kas recombinant inbred Arabidopsis thaliana. Consistent previous results, pilot experiment detected self-QTL effect at GLABRA1 locus. Regarding herbivory, observed weak top chromosome 4, self-bolting identified. available an R package (https://cran.r-project.org/package=rNeighborQTL), providing novel tool investigate studies.