Gene Expression Changes During the Allo-/Deallopolyploidization Process of Brassica napus.

Qi Pan,Chaobo Tong,Zaiyun Li,Dawei Zhang,Bin Zhu,Xianhong Ge,Shengyi Liu

doi:10.3389/fgene.2019.01279

Abstract

Gene expression changes due to allopolyploidization have been extensively studied in plants over the past few decades. Nearly all these studies focused on comparing the changes before and after genome merger. In this study, we used the uniquely restituted Brassica rapa (RBR, AeAe, 2n = 20) obtained from Brassica napus (AnAnCnCn, 2n = 38) to analyze the gene expression changes and its potential mechanism during the process of allo-/deallopolyploidization. RNA-seq-based transcriptome profiling identified a large number of differentially expressed genes (DEGs) between RBR and natural B. rapa (ArAr), suggesting potential effects of allopolyploidization/domestication of AA component of B. napus at the tetrapolyploid level. Meanwhile, it was revealed that up to 20% of gene expressions were immediately altered when compared with those in the An-subgenome. Interestingly, one fifth of these changes are in fact indicative of the recovery of antecedent gene expression alternations occurring since the origin of B. napus and showed association with homoeologous expression bias between An and Cn subgenomes. Enrichment of distinct gene ontology (GO) categories of the above sets of genes further indicated potential functional cooperation of the An and Cn subgenome of B. napus. Whole genome methylation analysis revealed a small number of DEGs were identified in the differentially methylated regions.

Highlights

Polyploidy is an important speciation mechanism for all eukaryotes, especially in higher plant evolution
Because we do not know the exact original progenitor B. rapa of ZS11, we compared the transcriptome of An-subgenome and RBR with those of natural B. rapa (ArAr, 2n = 20), which represented by four cultivars of two subspecies, pekinensis (Chiifu-401) and campestris (TRA1,TRA2, BY1) using RNAseq (Supplementary Figure 1)
These results were consistent with the known breeding history of ZS11 and the evolution and/or domestication histories of these B. rapa lines: (1) BY1 has been used as one of the cross parents during the breeding of ZS11 (Supplementary Figure 1); (2) Chiifu-401 is domesticated for use as a vegetable, whereas the other B. rapa are used as oilseeds

Summary

Introduction

Polyploidy (whole-genome duplication) is an important speciation mechanism for all eukaryotes, especially in higher plant evolution. Allopolyploid speciation results from interspecific hybridization and genome doubling. During the formation and evolution of allopolyploids, genome-wide genetic, epigenetic, and gene expression changes might occur, when compared with the parents (Chen, 2007; Jackson and Chen, 2010; Madlung and Wendel, 2013). On one hand, these alternations undoubtedly promote new traits formation, thereby increasing adaptability. Heterozygosity and intergenomic interactions in allopolyploids may result in heterosis, giving rise to phenotypic variations and increased growth vigor (Comai, 2005; Chen, 2010).

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Results

Conclusion