The phenotypes and genotypes of representative hybrids with the highest BPH or the lowest BPH. (A) Growth vigor of two representative Arabidopsis hybrids, Col-0 × Per-1 and Col-0 × Aa-0, at 14 DAS. (Bar, 1 cm.) (B) Col-0 × Per-1 exhibits the highest BPH for biomass, whereas Col-0 × Aa-0 shows no significant BPH for biomass. The data are presented as the means ± SD; n > 30. **P < 0.01 between the hybrids and parents (Student’s t test). (C) Silhouette images showing differences in the size of the first leaf of plants in A. (Bar, 0.5 cm.) (D) Col-0 × Per-1 accumulates more total, missense, and GWAS-associated SNPs than Col-0 × Aa-0. (E) Genes with multiple missense SNPs (>10) are significantly enriched in defense pathways, which were more evident in Col-0 × Per-1.