Fig. 2

Expression partitioning of duplicate genes in newly synthetic allotetraploid rice. a Tissue-specific relative expression levels of gene copies derived from japonica (cv. Nipponbare, labelled as “N”) and indica (cv. 9311, labelled as “9”) rice in in vitro “hybrids (2X),” F1 hybrids (2X) and reciprocal synthetic allotetraploids (S3 generation, NN99 and 99NN). Reciprocal hybrids and allotetraploids were constructed from japonica and indica rice subspecies. 99NN and NN99 had cv. 9311 and cv. Nipponbare as maternal parents, respectively. In all four plant groups, the biased expression categories corresponded to the percentage contribution of japonica rice homeolog (N) to total transcripts [N/(9 + N) × 100%]: completely N-biased (95–100% N expression, 9-silence); strongly N-biased (80–95% N expression); N-biased (60–80% N expression); equivalent (40–60% N expression); completely 9-biased (0–5% N expression, N-silenced); strongly 9-biased (5–20% N expression); 9-biased (20–40% N expression). Silencing of both copies was considered as “No expression”. b Distribution of homeolog-specific expression states within different tissue types and among plant groups. L1, R1 represent expression of the mature leaf and root, respectively, at the tillering stage; L2, R2, F and S represent the expression of the mature leaf, root, flag leaf and young spike, respectively, at the booting stage