Fig. 6: Pilot GWAS of leaf damage scores on field-grown Arabidopsis thaliana.
a Proportion of phenotypic variation explained (PVE) by the self-genotype (red) or neighbor effects (blue). The PVEself was represented by the single PVEself that represented additive genetic variance, while the net contribution of the neighbor effects was evaluated using the net PVEnei = total PVE − single PVEself. Asterisks highlight a significant fraction with stepwise likelihood ratio tests, from simpler to complex models: **p value < 0.01. b, c Manhattan plots for the self or neighbor effects. The first to fifth chromosomes are differently colored, where lighter plots indicate smaller MAF. Horizontal dashed lines indicate the threshold after Bonferroni correction at p value < 0.05. The red vertical line in panel b indicates an SNP position near the GS-OX2 locus, while the three circles highlighted by a black outline in panel c indicates the variants subject to the post hoc simulation (Fig. 7). Results of the self and neighbor effects are shown at s = 0 (i.e., standard GWAS) and s = 1, respectively.
