Extended Data Fig. 5: Overview of the ZmTINY locus with allele-specific mRNA abundance and TF-binding.
a) Genome browser view of the upstream and downstream region of ZmTINY in the hybrid of B73xCML333. Green arrows mark DS-bQTL positions. Yellow blocks mark regions analyzed in (c). The black transposable elements (TE) block marks a TE that is present in B73, A188, Ki3, and Mo18W. The scale bar applies to both tracks. b) Fold change (FC) in mRNA abundance between the NAM allele and the B73 allele under DS conditions. c) FC in MOA occupancy between the NAM allele and the B73 allele under DS conditions. Average MOA occupancy per base was calculated in the three yellow regions marked in (a). To ensure comparison of homologous regions, regions between two homologous SNPs determined by whole-genome alignment were chosen. Note that the W22 promoter contains a TE in the (A) region, adding ~5 kb compared to the syntenic W22 region. Two additional regions in W22 were compared to the B73 (A) region: the region up to the TE (FC 0.36) and a region of similar length to the B73 (A) region (FC 0.21). The downstream regions of A188 and Mo18W do not differ from B73, and thus, no FC could be detected. d: CG methylation in 40 bp surrounding SNP B73-chr3:4729798 (just after the TE sequence downstream of ZmTINY).
