Genome-specific differential gene expressions in resynthesized Brassica allotetraploids from pair-wise crosses of three cultivated diploids revealed by RNA-seq.

Dawei Zhang,Chen Tan,Zaiyun Li,Xianhong Ge,Cheng Cui,Qi Pan,Yujiao Shao

doi:10.3389/fpls.2015.00957

Abstract

Polyploidy is popular for the speciation of angiosperms but the initial stage of allopolyploidization resulting from interspecific hybridization and genome duplication is associated with different extents of changes in genome structure and gene expressions. Herein, the transcriptomes detected by RNA-seq in resynthesized Brassica allotetraploids (Brassica juncea, AABB; B. napus, AACC; B. carinata, BBCC) from the pair-wise crosses of the same three diploids (B. rapa, AA; B. nigra, BB; B. oleracea, CC) were compared to reveal the patterns of gene expressions from progenitor genomes and the effects of different types of genome combinations and cytoplasm, upon the genome merger and duplication. From transcriptomic analyses for leaves and silique walls, extensive expression alterations were revealed in these resynthesized allotetraploids relative to their diploid progenitors, as well as during the transition from vegetative to reproductive development, for differential and transgressive gene expressions were variable in numbers and functions. Genes involved in glucosinolates and DNA methylation were transgressively up-regulated among most samples, suggesting that gene expression regulation was immediately established after allopolyploidization. The expression of ribosomal protein genes was also tissue-specific and showed a similar expression hierarchy of rRNA genes. The balance between the co-up and co-down regulation was observed between reciprocal B. napus with different types of the cytoplasm. Our results suggested that gene expression changes occurred after initial genome merger and such profound alterations might enhance the growth vigor and adaptability of Brassica allotetraploids.

Highlights

Allopolyploidization which is realized through the merger and duplication of distinct parental genomes following interspecific hybridizations of two or more related species results in the origin of new allopolyploid species (Otto, 2007; Doyle et al, 2008)
Widespread changes of gene expression during allopolyploidization have been revealed in different aspects, including homoeolog expression bias, novel gene expression, or silencing, transgressive up or down-regulation, expression level dominance, and altered expression times and locations (Doyle et al, 2008)
Global transcriptome analyses through RNA-Seq were made for serial synthetic Brassica allotetraploids derived from the same three diploid parents (Figure 1; Cui et al, 2012)

Summary

Introduction

Allopolyploidization which is realized through the merger and duplication of distinct parental genomes following interspecific hybridizations of two or more related species results in the origin of new allopolyploid species (Otto, 2007; Doyle et al, 2008). This pattern of speciation occurs widely in angiosperms, largely because the allopolyploids relative to their progenitors show the enhanced growth vigor (the phenomenon of heterosis) and the advantage in ecological adaptation (Chen, 2007; Leitch and Leitch, 2008). As to the crucial gene expression in hybrids and new allopolyploids, widespread changes are revealed by transcriptomic analysis and extensive gene expression changes are non-additive in allopolyploids relative to their parents, including expression level dominance and transgression (outside the range of either parent), such profound changes to gene expression may enable new hybrids to survive in novel environments not accessible to their parent species (Wang et al, 2006; Chen, 2007; Rapp et al, 2009; Flagel and Wendel, 2010; Yoo et al, 2013; Li et al, 2014)

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Results

Conclusion