The causes and consequences of subgenome dominance in hybrids and recent polyploids

Abstract

Contents Summary 87 I. Introduction 87 II. Evolution in action: subgenome dominance within newly formed hybrids and polyploids 88 III. Summary and future directions 90 Acknowledgements 92 References 92 SUMMARY: The merger of divergent genomes, via hybridization or allopolyploidization, frequently results in a 'genomic shock' that induces a series of rapid genetic and epigenetic modifications as a result of conflicts between parental genomes. This conflict among the subgenomes routinely leads one subgenome to become dominant over the other subgenome(s), resulting in subgenome biases in gene content and expression. Recent advances in methods to analyze hybrid and polyploid genomes with comparisons to extant parental progenitors have allowed for major strides in understanding the mechanistic basis for subgenome dominance. In particular, our understanding of the role that homoeologous exchange might play in subgenome dominance and genome evolution is quickly growing. Here we describe recent discoveries uncovering the underlying mechanisms and provide a framework to predict subgenome dominance in hybrids and allopolyploids with far-reaching implications for agricultural, ecological, and evolutionary research.

Replaying the evolutionary tape to investigate subgenome dominance in allopolyploid Brassica napus

“…Furthermore, a previous analysis of the B. napus reference genome identified a greater number of retained genes in the B. oleracea (C) subgenome compared to B. rapa (A) subgenome (28) . This is consistent with patterns observed in older allopolyploids that exhibit subgenome dominance -dominant subgenome retaining a greater number of genes (33) . Lastly, because the resynthesized B. napus lines were made with doubled haploids, each of the independent lines started out genetically identical (34) .…”

Current research frontiers in plant epigenetics: an introduction to a Virtual Issue

“…Building on these ideas, it has been proposed that the subgenome with a higher TE load will have more genes in proximity to TEs, therefore at greater silencing risk, causing an expression bias towards the genome with less TE load (Woodhouse et al , 2014; Gaebelein et al , 2019). Similarly, it has been shown that the dominant genome can be targeted by less silencing in comparison to the parental level, while the recessive genome retains the parental level of silencing (reviewed in Bird et al , 2018). The ‘TE model’ of subgenome‐specific bias and its influence on cis–trans interactions and homoeologue expression are discussed in a recent paper by Hu & Wendel (2019).…”

Cis–trans controls and regulatory novelty accompanying allopolyploidization

“…small RNA populations and preferential recruitment of epigenetic modifiers) on homoeolog expression. As a consequence, the homoeolog physically closer to epigenetically silenced TEs is more likely to be repressed via localized heterochromatinization, and even lost in the longer term (hence, ‘biased fractionation’; see recent reviews: Bird et al ., ; Cheng et al ., ; Wendel et al ., ).…”

“…Estimating the impact of allopolyploidization ( P r ) for different molecular traits enables hypothesis testing for ‘genome dominance’. If the parental conditions in TE adjacency and epigenetic accessibility () are predominantly inherited to explain the extent and direction of homoeolog expression bias, the TE model (Steige & Slotte, ; Bird et al ., ; Cheng et al ., ; Wendel et al ., ) is supported. Not exclusively, if the parental divergence in TF affinity is inherited () and correlates with homoeolog expression levels, the euchromatin/TF model (Bottani et al ., ) is supported.…”