Extended Data Fig. 3: F1 hybrid (ERBxHO40_23; EH23a and EH23b) between two phenotypically and genetically divergent parents clarifies features of the genome missed in other studies to-date.

A) Inheritance of alleles across the genome from the F2 population. The upper panel presents the frequency of each allele and the lower panel shows FIS or the deviation from our evolutionarily neutral expectation of heterozygosity. B) Haplotype specific expression for all tissue types from EH23, grouped by chromosome. Haplotype gene pairs were either syntenic or reciprocal best hits. Balanced and biased gene expression was assigned according to TPM difference. A difference threshold of 5 TPM was required for gene pairs to be assigned as biased, otherwise gene pairs were assigned as balanced (see also Supplemental Table 2 for counts by tissue type). C) LATE ELONGATED HYPOCOTYL (LHY) showed biased gene expression in EH23b foliage under 12 h of light (12/12 h). D) The copy of LHY with biased expression also belonged to an orthogroup with high entropy in different populations, with the largest difference in entropy separating feral and MJ. E) GO term enrichment of biased gene expression for all tissues in EH23a; and F) GO term enrichment of biased gene expression for all tissues in EH23b. See also Supplemental Note 2.