Extended Data Fig. 4: Most eQTL^gbM/teM gene expression effects are independent of local SNP variation.

(a and b) Frequency of retained (R) or lost (L) eQTL^gbM (a) and eQTL^teM (b) genes after accounting for expression GWA SNPs. (c) Loss of statistical power for association analyses in haplogroups due to decreasing population size. The -log₁₀ P values for associations between gbM/teM and gene expression exhibit an exponential increase with respect to the number of accessions in haplogroups. Indicated R² and P values correspond to exponential regression. (d and e) Frequency of eQTL^gbM (d) and eQTL^teM (e) genes with a significant association between mCG and gene expression in at least one haplogroup. Despite reduced statistical power (c) in SNP invariant haplogroups due to smaller population sizes, significant associations between gbM variation and expression are detected for a majority of eQTL^gbM genes. (f and g) Frequency of retained or lost eQTL^gbM (f) and eQTL^teM (g) genes after accounting for structural variation (SV) effects on expression.