Sample sizes are N=306 for leaves and N=310 for roots. (a) Estimates of broad-sense heritability (H2) of individual OTUs are plotted for leaves (top) and roots (bottom). The bottom and top edges of the boxes mark the 25th and 75th percentiles (that is, first and third quartiles). The horizontal line within the box denotes the median. Whiskers mark the range of the data excluding outliers that fell more than 1.5 times the interquartile range below the first quartile or above the third quartile (dots). (b) Between-sample diversity of the leaf microbiome is plotted as least-squares mean PCo1 of the weighted UniFrac distance for each plant genotype in each site, showing the genotype-by-site interaction after controlling for other sources of variation in a LMMs, including the constitutive effect of plant genotype and average site effects; F8,257=4.53, P=0.00011. Bars depict one standard error of the mean. (c) Least-squares mean leaf Shannon diversity is plotted for each genotype and each site, revealing site-dependent differences in the relative leaf community richness among host genotypes; F8,261=2.33, P=0.04. Bars show 1 s.e.m. (d) The total relative abundance of OTUs that were predicted by site-specific genotype effects in NBMs is shown for leaves and roots in each site (Wald test, P<0.05 after Benjamini–Hochberg correction for multiple comparisons).