Genome-Wide Gene Expressions Respond Differently to A-subgenome Origins in Brassica napus Synthetic Hybrids and Natural Allotetraploid

Dawei Zhang,Xianhong Ge,Zaiyun Li,Qi Pan,Yujiao Shao,Chen Tan,Bin Zhu

doi:10.3389/fpls.2016.01508

Abstract

The young allotetraploid Brassica napus (2n = 38, AACC) is one of models to study genomic responses to allopolyploidization. The extraction of AA component from natural B. napus and then restitution of progenitor B. rapa should provide a unique opportunity to reveal the genome interplay for gene expressions during the evolution. Herein, B. napus hybrids (2n = 19, AC) between the extracted and extant B. rapa (2n = 20, AA) and the same B. oleracea genotype (2n = 18, CC) were studied by RNA-seq and compared with natural B. napus donor, to reveal the gene expression changes from hybridization and domestication and the effects of A genome with different origins. Upon the initial merger of two diploid genomes, additive gene expression was prevalent in these two hybrids, for non-additively expressed genes only represented a small portion of total expressed genes. A high proportion of genes exhibited expression level dominance, with no preference to either of the parental genomes. Comparison of homoeolog expressions also showed no bias toward any genomes and the parental expression patterns were often maintained in the hybrids and natural allotetraploids. Although, the overall patterns of gene expression were highly conserved between two hybrids, the extracted B. rapa responded less and appeared more compatible for hybridization than the extant B. rapa. Our results suggested that expression level dominance and homoeolog expressions bias were balanced at the initial stage of genome merger, and such balance were largely maintained during the domestication of B. napus, despite the increased extent over time.

Highlights

Allopolyploidization, through the merger and duplication of two or more sets of divergent parental genomes, is an ancient and ongoing evolutionary process (Otto, 2007; Doyle et al, 2008)
An array of investigations in recent or synthetic allopolyploids have demonstrated that the initial stage of allopolyploidization is accompanied by various changes at genetic (Song et al, 1995; Xiong et al, 2011), epigenetic (Adams et al, 2003; Cui et al, 2013; Ge et al, 2013) as well as gene expression level (Wang et al, 2006; Chelaifa et al, 2010; Yoo et al, 2013)
To study the gene expression patterns after the genome merger, we first performed pairwise comparisons between the two progenitors involved in each cross to identify pre-existing divergence in gene expression (Figure 2)

Summary

Introduction

Allopolyploidization, through the merger and duplication of two or more sets of divergent parental genomes, is an ancient and ongoing evolutionary process (Otto, 2007; Doyle et al, 2008). An array of investigations in recent or synthetic allopolyploids have demonstrated that the initial stage of allopolyploidization is accompanied by various changes at genetic (Song et al, 1995; Xiong et al, 2011), epigenetic (Adams et al, 2003; Cui et al, 2013; Ge et al, 2013) as well as gene expression level (Wang et al, 2006; Chelaifa et al, 2010; Yoo et al, 2013). Both homoeolog expression bias and expression level dominance are quantitative, meaning that they may be balanced, or unbalanced, alternatively (Grover et al, 2012)

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Conclusion