The deletions (orange) and duplications (blue) detected in Van. (a) The density distribution of median probe log intensity difference between Col and Van for deletions, duplications, and all analyzed probes (black). For each probe the absolute difference of mean probe log intensity between four Col replicates and four Van replicates was calculated. The medians were then obtained across deleted or duplicated regions. (b) The length distribution of deleted and duplicated regions. (c) The chromosome distribution of deleted and duplicated regions. Each chromosome was divided into 100 kb bins. Within each bin the length of deletions or duplications was divided by the bin size (y-axis). The black ticks along each chromosome mark the position of centromeres.

Detection of ASE in F1 hybrids. (a) Col ASE for gene AT4G29950. After correction of overall gene expression level, the relative log intensity (y-axis) for Col (red), Van (blue), F1 hybrids (orange), and mid-parent (black) were plotted along chromosomal positions (x-axis), with standard deviation indicated. Solid dots, non-SFP probes; crossed circles, SFP probes. (b) Fold enrichments of significant ASE genes within the differential genes between Col and Van. The numbers of significant calls were selected according to permutation-based FDRs.

The effect of SFP probes on expression estimation. F statistics of genotype × SFP effects (y-axis) and that of genotype effects (x-axis) were obtained from the ANOVA model, Gene/exon/intron intensity = Genotype + SFP + Genotype × SFP + Error, for (a) gene expression, (b) exonic splicing, and (c) intronic splicing analysis.

The additive, dominant and maternal effects of gene expression. (a) The number of genes (y-axis) significant for additive (left), dominant (middle), or maternal (right) terms. From left to right, the bars represent Col > Van, Van > Col, F1s > parents, parents > F1s, Col mother F1 > Van mother F1, Van mother F1 > Col mother F1. (b) Histogram of the dominance/additive ratio (x-axis) for 1,925 genes differentially expressed between Col and Van at a 2% FDR. The red lines represent the number of genes up-regulated in Col. (c) The inheritance pattern determined by partition of gene expression means by k-means, for genes significant for dominant (left block) or maternal (right block) terms. From left to right, the bars represent the number of genes (y-axis) showing Col dominance (Col > Van, Col < Van), Van dominance (Van > Col, Van < Col), over-dominance (F1s > parents, F1s < parents), Col mother F1 separated from the other three strains (Col mother F1 > others, Col mother F1 < others), Van mother F1 separated from the other three strains (Van mother F1 > others, Van mother F1 < others), maternal effect (Col > Van, Col < Van), and paternal effect (Col >Van, Col < Van).

The additive, dominant and maternal effects of splicing. (a) Quantile-quantile plots of additive (left), dominant (middle) and maternal (right) terms for exonic splicing. The real d scores (y-axis) were plotted against the null d scores (x-axis) obtained by 1,000 permutations. (b) Experimental validation for AT1G51350 intron 8. The relative log intensity (y-axis) of Col (red) and Van (blue) was plotted along chromosomal positions (x-axis), with standard deviation indicated. Annotated exons and introns are indicated as thick and thin black horizontal bars, respectively, at y = 0. The arrows point to the start positions (along the forward strand) of the pair of flanking primers. Gel patterns show from left to right: Van (V) and Col (C) genomic DNA (gDNA), and three replicates of Van and Col cDNA.

De novo transcriptome variation. (a) The generalized HMM procedure for a chromosome region. Upper panel: the relative log intensity for four Col replicates (red) and four Van replicates (black) along chromosome positions. Blue bars, annotated genes. Middle panel: probe level p-value was obtained by one-sided two sample t-test between Col and Van. Emission and transition probability was estimated by the Baum-Welch algorithm. Lower panel: posterior probabilities of no difference (blue), greater Van expression (green), and greater Col expression (orange) were determined using the Forward-Backward algorithm. Black line: 0.99 posterior probability cutoff. (b) The distribution of the length of differential segment (white bars) and probes per differential segment (grey bars) for state 2 (upper panel) and state 3 (lower panel) segments.