Homoeolog Expression Is Modulated Differently by Different Subgenomes in Brassica napus Hybrids and Allotetraploids

Synthetic and natural allotetraploid Brassica napus (2n = 38, AACC) have been widely used as a model to study the genetic changes associated with allopolyploidization; however, there has been little research on the homoeolog expression patterns and the roles of cis and trans regulation. Herein, homoeolog expression patterns were assessed by using RNA-seq for two interspecific hybrids (A(n)C(o) with the extracted A subgenome from natural B. napus, and A(r)C(o) with the A subgenome from extant B. rapa), synthetic and natural allopolyploids (C(o)C(o)A(r)A(r) and A(n)A(n)C(n)C(n)), and the diploid parents. The ranges of homoeolog expression bias decreased after hybridization, whereas the extents of homoeolog expression bias and non-conserved expression, especially transgressive expression, increased over evolutionary time. Despite sharing the same C subgenome parent, these two hybrids showed different homolog expression patterns in many respects. In A(n)C(o), the trans-regulatory factors from C-o subgenome tended to cause downregulation of A(n) subgenome homoeologs, but trans-regulatory factors from the A(n) subgenome acted as both activators and repressors, and such asymmetric effects of trans-regulatory factors might explain why the homoeolog expression was biased toward the C subgenome after genome merger. No significant asymmetric effects of trans-regulatory factors were found in A(r)C(o), which was consistent with the overall balanced expression of homoeologs. These results suggested that A subgenomes with different regulatory systems might act differently in modulating homoeolog expression after merger with the C subgenome, resulting in either balanced or unbalanced homoeolog expression biases.