Extended Data Fig. 5: Trans genetic variation explains a minor fraction of gbM.

(a) Percentage of eQTL^gbM/teM retained (R) genes that have trans genetic QTLs associated with the variation of gbM or teM. (b) Average effects ( ± standard error) of trans polymorphism on mCG variation in all retained eQTL^gbM/teM genes, with number of QTLs indicated. (c) Effect sizes of trans polymorphism on mCG variation of retained eQTL^gbM/teM genes having trans QTLs. Center lines represent sample medians, box limits indicate the 25th and 75th percentiles, whiskers extend to 1.5 times the interquartile range. The number of QTLs corresponding to each class is indicated above the plots. (d) Percentage of retained eQTL^gbM having trans QTLs in the entire worldwide population, a published Swedish population⁵⁰, and a random population of equal size to the Swedish population. Numbers of accessions in each panel are indicated. (e) Effect sizes of trans genetic polymorphisms on gbM variation of retained eQTL^gbM genes having trans QTLs in worldwide, Swedish, and random populations. Box plots as in c. Different letters signify P < 0.05, one-way ANOVA, Tukey’s test. (f) Average effects ( ± standard error) of trans genetic variation on gbM variation of all retained eQTL^gbM genes in worldwide, Swedish, and random populations, with number of genes indicated. Note the inflation of estimated trans effects in the smaller populations, a phenomenon known as the Beavis effect^119,120.