Fig. 3: Association mapping and DNA methylation assay.

a Associations of 433 DNA polymorphisms at the KNR6 locus with KNR in 224 diverse maize inbred lines. Each dot represents a polymorphic site. Black dots, polymorphic sites within 10_kb flanking sequences of KNR6; purple dot, the Harbinger-like TE PAV; green dot, the LTR-TE PAV; gray dots, others. Black rectangles, exons; white rectangles, UTRs. The significance level of the associated site, p = 0.05/the number of polymorphic sites. b The pattern of linkage disequilibrium for polymorphic sites. Asterisks, two PAV sites in the LD block. c Pearson correlation between KNR6 expression levels and KNR. The p value is determined by the two-tailed Student’s t test. d Expression levels of KNR6 in 20 Hap1 lines and 85 Hap2 lines using qPCR, with three biological replicates in each case. e, f Box-and-whisker plots of KNR (e) and EL (f) for 48 Hap1 lines and 176 Hap2 lines. Each box represents the median and interquartile range. Whiskers extend to maximum and minimum values. Significance of difference is estimated by the one-way ANOVA. g A diagram of the constructs. TE⁺ construct includes a 5570_bp fragment containing the Harbinger-like TE; TE⁻ construct represents the 567_bp sequence lacking the TE. h Luciferase activity in maize leaf protoplasts. Luciferase activity is measured with three biological replicates, each with two technical replicates. Data are normalized with respect to the average value of the empty construct, and are shown as means ± s.d. p Value is estimated by the one-way ANOVA. i Visualization of the DNA methylation regions. DNA methylation levels were measured by bisulfite sequencing, and the methylation status was illustrated using the Integrated Genome Viewer. The upper and lower panels show the sense and antisense strands, respectively. j DNA methylation level of the three contexts in the long terminal repeat (LTR) retrotransposon and the Harbinger-like TE. k Methylation patterns of the flanking regions of the Harbinger-like TE in both parent lines. The methylation levels of CG, CHG, and CHH were scanned using a window size of 200 bp and a step size of 100 bp. Source data underlying Fig. 3e–h are provided in a Source Data file.