Figure 2

Genotype-specific alternative acceptor site associated with cis -sQTL (a2016). A cryptic acceptor site activation and removal of a 206 bp segment that is associated with four cis-sQTL. All plots are shown for the most significant cis-sQTL. a-b: Exon/intron coverage plots of the genotype-specific splicing event are shown for the F1-hybrids that carried derived (a) and ancestral (b) variants of cis-sQTL on natural alleles. Tester alleles of all F1-hybrids carried ancestral variant of cis-sQTL. The coverage for each genomic positions is shown separately for exonic (blue) and intronic (yellow) parts of reads. The coverage from multiple genotypes that carry the same allele is merged. Exon/intron boundaries are marked by vertical dashed lines. The position of cis-sQTL is shown by the red arrow. The alternative gene models are shown under the coverage plots: blue rectangles and yellow lines correspond to exons and introns, respectively. c: The distributions of Ψ-values for alleles of this cis-sQTL. d: The Manhattan plot of association test log-p-values for all tested cis-SNPs. e: Q-Q plot for the observed (y-axis) and expected (x-axis) distributions of association p-values for the tested cis-SNPs (red dots) and 10000 random SNPs from other chromosomes (black dots). f: RT-PCR validation of gene models. The predicted lengths of PCR-products corresponding to the long and short isoforms were 337 bp and 131 bp, respectively. A/A: inbred line carrying only ancestral alleles (tester line); A/D: F1-hybrid carrying both ancestral and derived alleles; D/D: inbred line carrying only derived alleles (natural line).