Figure 1
From: Patterns of homoeologous gene expression shown by RNA sequencing in hexaploid bread wheat
Analysis of hexaploid bread wheat homoeologous gene expression using nullisomic-tetrasomic lines. (A) Schematic illustrating the group 1 homoeologous chromosomes in hexaploid bread wheat, the derived nullisomic-tetrasomic lines and the A and D genome diploids. A single homoeologue-specific variant (HSV) diagnostic for each of A (red), B (blue) and D (green) homoeologous chromosomes is shown. (B) Two sets of three homoeologue-specific haplotypes of BE497595, a gene encoding a chloroplast thylakoidal peptidase-like protein and which has 24 HSVs (inverted triangles) diagnostic for either 5A (red), 5B (blue) or 5D (green) homoeologues. RNA-Seq reads are aligned to a degenerate reference sequence shown in grey containing genetic ambiguity codes at HSV locations. Double ended arrows illustrate candidate sequence regions for haplotype quantification. (C,D) RNA-Seq read frequencies from roots for the nullitetras and A and D genome diploids (C) and in two biological replicates of euploid wheat (D) for each homoeologue-specific haplotype given in the boxed region shown in (B). The homoeologous expression pattern in euploid wheat roots is indicated below the pie chart.