Fig. 1

Gene expression analysis of lyc homozygous transcribed regions in hybrids. a Parental lines (S. lycopersicum and S. pennellii) and offspring (from F1 to F4), each column being a separate F1 lineage. For F2–F4, each plant keeps the number of the parental plant adding one digit. The number of digits indicates the generation (i.e., P4042 is F4 generation, progeny of plant P404). b Percentage of homozygous transcribed regions for S. lycopersicum (orange), S. pennellii (blue), or heterozygous transcribed (gray) in each of the F4 plants and parental lines. c Volcano plot showing the fold change (FC) in genes upregulated (+ DEG, red), downregulated (− DEG, blue), “in-between” (lilac), and not differentially expressed (non-DEG, yellow) in lyc homozygous transcribed regions for P4042. Thresholds: DEG, FDR < 0.05; “in-between” genes, 0.05 < FDR < 0.9; non-DEG, FDR > 0.9. d Percentage of genes in each category calculated from the total of genes in the lyc homozygous transcribed region, being each bar an individual F4 plant compared to lyc parent. The right-hand panel shows an expanded view of the + DEG (red) and − DEG (blue). e Overlap matrix showing the number of lyc DEG genes shared among the F4 hybrids. The color scale shows the ratio of observed over expected genes shared in a pairwise combination