Figure 3

Expression of up to three homoeoloci for wheat genes on chromosomes 1 and 5. (A) Genes may be expressed from one, two or three homoeologous chromosomes of group 1 or 5, inferred using nullitetra analysis of RNA-Seq data to detect homoeologue-specific variants (HSVs) or haplotypes in shoots or roots. Genes expressed from 3 homoeologous chromosomes (yellow) have diagnostic sequences for all 3 homoeoloci (A, B and D). Genes expressed from at least two homoeologous chromosomes either have diagnostic sequences for a single homoeolocus, leaving the identity of the second expressed homoeolocus uncertain (light green) or diagnostic sequences for two homoeoloci (dark green). Genes expressed from at least one homoeolocus (orange) have no diagnostic sequences. Genes without evidence for expression from all three homoeoloci are classified as expressed from at least one (≥1) or at least two (≥2) homoeoloci, since they may also be expressed from additional homoeoloci with identical sequences, which cannot be identified. (B) Total expression level (RPKM) from all expressed homoeoloci for group 1 and 5 genes expressed from one (orange), two (green) or three (yellow) homoeoloci in shoots (left hand boxes) or roots (right hand boxes). P values are given for a Mann–Whitney test and significant values indicated with an asterisk. (C) The number of group 1 (upper panel) or group 5 (lower panel) genes expressed from each combination of homoeologous chromosomes in shoots (left panel) or roots (right panel). Coloured dashed circles indicate genes expressed from the corresponding homoeologous chromosome plus at least one other chromosome whose identity cannot be distinguished. Grey dashed circles indicate genes expressed from a single homoeolocus (A, B or D), whose identity cannot be distinguished. Grey filled circles represent ‘unassigned’ genes whose expressed homoeoloci remained uncertain (see Additional file 15: Table S6).