Fig. 4

Genotype-phenotype associations. a Exemplar Manhattan plot of the genome-wide −log₁₀ p values of association (logP) between the height to ear tip phenotype from year 2 (HET_2) and 55,067 LD-pruned SNP dosages (dots) or founder haplotype dosages (line). The horizontal lines show the 5% genome-wide significance thresholds for SNPs (dotted) and founder haplotypes (dashed). b The 193 non-zero LASSO SNP effect estimates for HET_2. c The 40 genomic locations where genome-wide significant SNP associations were found for at least one phenotype, classified by effect size (logP; x-axis) and genomic interval width (Mb; y-axis). Each circle represents one locus, and its size shows the number overlapping QTLs; the smallest interval width and most significant logP is shown where there are multiple overlapping phenotype associations. Labels indicate QTLs that colocalize with previously described QTLs or candidate genes; green indicates high-confidence colocalization (n = 11) and purple low-confidence colocalization (n = 10). d Pleiotropy across 40 loci: those loci without official names are labelled by chromosome and position in Mb, and 73 phenotypes. Shades indicate the significant (p < 0.05) locus phenotypic effects expressed as the number of standard deviations (Z-score). Genome-wide significant QTLs are highlighted with boxes