Extended Data Fig. 2: Dominance and additive QTL contrasts of allele frequencies, effect sizes, genotype group means, and p-values.
From: Non-additive association analysis using proxy phenotypes identifies novel cattle syndromes
a, Plot contrasting minor allele frequency (MAF) and absolute effect size (Effect size, kg) of QTL identified in the standard-additive model (blue), and the dominance model (red) for body weight. Note that for equitable effect size comparison both additive and dominance estimates are represented as allele substitutions (i.e. effect of the heterozygote compared to the reference homozygote), so dominance effects only represent half the effect observed in homozygous individuals. b, Chromosome-wide scatterplots contrasting P-values of the eight recessive QTL for the standard-additive model (p_standard_additive) and dominance model (p_additive/p_dominance). P-values were computed using Z-tests, the genome-wide significance thresholds of p = 5 × 10−8 are drawn in red, an x = y line is drawn in black. Note that only seven chromosomes are presented since two effects were identified on chromosome 2 (and thus are not readily differentiated). c, Box plots showing adjusted-bodyweight genotype means for the 8 non-additive loci in the discovery population (N=79,945 cows). Genotypes used for display represent putative causative mutations or lead associated variants where no obvious candidate was identified. Note the largely additive effect presented by the PLAG1 locus, highlighted in GWAS due to a partial dominance effect. Box plots show median (centre line), interquartile range (box limits), and upper and lower whiskers (maxima and minima data points).
