Figure 6.

AS-Coupled NMD.

(A) An example of an AS-coupled NMD mechanism. GRMZM2G021742 was detected with a significant cis-sQTL. For the transcript model, UTRs are shown in gray boxes on the two sides, and CDSs are shown in black boxes in the middle. Lines indicate introns. Transcripts named “T” stand for known transcript. Red arrow indicates the position of cis-sQTL SNP, and gray arrows indicate the position of other less significant SNPs. TC, termination codon; PTC, premature termination codon. The positions of primers used for RT-qPCR were indicated by dotted lines with arrows. For the upper panel, the average rate at each base on the gene is plotted, where individuals were stratified according to their genotype (AA and GG) at sQTL SNP rs#chr1.S_298434582. Brown dotted box shows where transcript structures differ. Relative to T01, T02 has a PTC located 79 bp upstream of the exon-exon junction.

(B) Significant changes in splicing ratio at sQTL SNP rs#chr1.S_298434582 but no difference in overall gene expression level.

(C) RT-qPCR results. For each genotype at the sQTL, four inbred lines were randomly selected from the maize association panel for the RT-qPCR assay of kernels at 15 DAP. Values represent the mean ± sd of the measurements (n = 4).