Fig. 5

An example showing that inserting a transposon suppressed gene expression by destroying the tissue-specific TF binding element. A Manhattan plot of an eQTL (Chr10:2344288-2356500) of Zm00001d023299 expression in drought-stressed leaves. Note that the eQTL has no associated SNPs that passed the Bonferroni-corrected P-value cut-off, the leading variant had a large effect size (BETA), and the highest probability for the cause (fine-mapping) was an insertion (PZ00001aSV02097079INS) located 2269 bp upstream the target gene. B The influence of PZ00001aSV02097079INS on the Zm00001d023299 expression related to different levels of drought stress. WW, well-watered; WS1, 70% relative leaf water content (RLWC); WS2, 50% RLWC; 0/0, the reference allele; 1/1, the alternative allele. The significant differences were evaluated using the Kruskal-Wallis test. C The influence of PZ00001aSV02097079INS on the drought resistance-related trait (survival rate under drought stress). The significant differences were evaluated using the Wilcoxon-Mann-Whitney test. D The validation of PZ00001aSV02097079INS alleles by multiple genome alignment of the maize reference-level genomes. The genomes with reference and alternative alleles are blue and red, respectively. E Comparison of the Zm00001d023299 expression patterns in different tissues of four CUBIC parents with (red) or without (blue) the PZ00001aSV02097079INS insertion. The expression difference in the tenth leaf at the V9 stage is highlighted by the black rectangle. F The epigenetic patterns and TF binding sites of maize leaves, and the predicted cis-regulatory elements in the targeted eQTL region. Only items showing distinct peaks near the PZ00001aSV02097079INS were plotted for the epigenetic patterns and TF binding sites. Only the elements located in the positive strand and 4 Kb upstream of the target gene were plotted for the predicted CREs. G An illustration showing that the PZ00001aSV02097079INS inserted in a predicted cis-acting element involved in the abscisic acid responsive element (ABRE). H The relative promoter activities represented by the ratio of luciferase (LUC) to Renilla luciferase (REN) activity (LUC/REN in Y-axis) for the treatments (X-axis), including pGreenII 0800-LUC without a minimal promoter (CK), with ABRE (ABRE+) and without ABRE (ABRE−), see also Additional file 1: Fig. S23. The P-values were calculated from 10,000 permutations of the t-test