Homoeolog Expression Is Modulated Differently by Different Subgenomes in Brassica napus Hybrids and Allotetraploids
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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 (AnCo with the extracted A subgenome from natural B. napus, and ArCo with the A subgenome from extant B. rapa), synthetic and natural allopolyploids (CoCoArAr and AnAnCnCn), 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 AnCo, the trans-regulatory factors from Co subgenome tended to cause downregulation of An subgenome homoeologs, but trans-regulatory factors from the An 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 ArCo, 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.
KeywordsBrassica napus Synthetic hybrids Homoeolog expression bias cis and trans regulation Allopolyploidization
This work was funded by National Key Research and Development Program of China (Grant No. 2016YFD0100202), National Natural Science Foundation of China (Grant No. 31701462), The Hunan Provincial Natural Science Foundation of China (Grant No. 2016JJ1010), and Foundation of Hunan University of Science and Technology (Grant No. E51760).
ZYL and YML conceived the study. CT, XHG, and LLL participated in sample preparations for RNA-seq. DWZ and QP analyzed the data and wrote the manuscript. All the authors have read and approved the final manuscript.
Compliance with Ethical Standards
Conflict of Interest
The authors declare that they have no competing interests.
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