Figure 1

Genotype-specific transcriptomes. a: Common reference design. 81 inbred lines, which were derived from natural populations (natural lines), were crossed with one common line (tester line). Each heterozygous F1-hybrid had the same tester allele (green bars) and variable natural allele (dark blue bars). Transcriptomes of these F1-hybrids were sequenced and used to annotate and quantify genotype-specific splicing patterns. b: Annotation and quantification of alternative splicing events. We focused on two most common types of alternative splicing events, namely, alternative donor/acceptor sites and cassette exons. The counts of inclusion ( i ) and exclusion ( e ) junction reads were used to quantify each alternative splicing event in each F1-hybrid. Ψ-value represented fraction of the longer isoform among two alternate transcripts.