Fig. 3: GWAS of neighbor genotype effects on herbivore damage and insect community composition on Arabidopsis thaliana genotype mixtures in Zurich and Otsu.
From: Reducing herbivory in mixed planting by genomic prediction of neighbor effects in the field
a–d, i–l Manhattan plots show the –log10(p) association score of the neighbor genotype effect \({\beta }_{2}\) across five chromosomes of A. thaliana at Zurich and Otsu. The horizontal dashed line indicates the Bonferroni threshold at \(p\) = 0.05 (see “Methods”). e–h, m–p The number and frequency of SNPs with the top 0.1% \(p\)-values and negative/positive \({\beta }_{2}\). All minor allele frequencies (MAFs) significantly differ between \({\beta }_{2} < 0\) and \({\beta }_{2} > 0\) (Mann-Whitney-Wilcoxon test, \(p\) < 0.05; see Supplementary Table 3 for the exact \(p\)-values) except for the individual number of other herbivores in Otsu. Numbers within parenthesis indicate the number of SNPs (sample sizes). Box plots visualize the median with upper and lower quartiles. Panels a-h and i-p show results from Zurich, Switzerland, and Otsu, Japan, respectively.
