neighbor_QTL

neighbor_QTL incorporates neighboring-genotype effects into quantitative trait locus (QTL) mapping by extending single-marker regression to interval mapping to analyze neighbor effects in sessile organisms such as plants, following the theoretical framework of Sato et al. (2020).

Key Features:

• Interval Mapping Extension: Extends single-marker regression to interval mapping to better capture the genetic architecture of traits influenced by neighboring genotypes.
• Conditional Self-Genotype Probabilities: Calculates conditional self-genotype probabilities based on recombination fractions between flanking markers.
• Neighbor Genotypic Identity Calculation: Computes the genotypic identity of neighboring plants using derived self-genotype probabilities.
• Estimation of Additive and Dominance Deviations: Estimates additive and dominance deviations for neighbor effects to quantify genetic contributions to phenotypic variation.

Scientific Applications:

• Plant neighbor-effect QTL mapping: Enables analysis of traits in which an individual's phenotype is affected by the genotypes of neighboring plants.
• Insect herbivory in Arabidopsis thaliana recombinant inbred lines: Applied to detect self QTLs and weak neighbor QTLs (notably on chromosome 4) and shown to increase detection power as the effective range of interaction decreases.

Methodology:

Computationally, neighbor_QTL obtains conditional self-genotype probabilities using recombination fractions between markers, derives neighbor genotypic identity from those probabilities, and estimates additive and dominance deviations for neighbor effects.