The lack of negative association between TE load and subgenome dominance in synthesized Brassica allotetraploids

Polyploidization is important to the evolution of plants. Subgenome dominance is a distinct phenomenon associated with most allopolyploids. A gene on the dominant subgenome tends to express to higher RNA levels in all organs as compared to the expression of its syntenic paralogue (homoeolog). The mechanism that underlies the formation of subgenome dominance remains unknown, but there is evidence for the involvement of transposon/DNA methylation density differences nearby the genes of parents as being causal. The subgenome with lower density of transposon and methylation near genes is positively associated with subgenome dominance. Here, we generated eight generations of allotetraploid progenies from the merging of parental genomes Brassica rapa and Brassica oleracea. We found that transposon/methylation density differ near genes between the parental (rapa:oleracea) existed in the wide hybrid, persisted in the neotetraploids (the synthetic Brassica napus), but these neotetraploids expressed no expected subgenome dominance. This absence of B. rapa vs. B. oleracea subgenome dominance is particularly significant because, while there is no negative relationship between transposon/methylation level and subgenome dominance in the neotetraploids, the more ancient parental subgenomes for all Brassica did show differences in transposon/methylation densities near genes and did express, in the same samples of cells, biased gene expression diagnostic of subgenome dominance. We conclude that subgenome differences in methylated transposon near genes are not sufficient to initiate the biased gene expressions defining subgenome dominance. Our result was unexpected, and we suggest a nuclear chimera model to explain our data.

Automated summary

Polyploidization plays a crucial role in plant evolution. Subgenome dominance, characterized by higher expression levels of genes on the dominant subgenome, is a common phenomenon in allopolyploids. The underlying mechanism of subgenome dominance remains unclear, but it is suggested that differences in transposon and DNA methylation density near genes may be involved. In this study, eight generations of allotetraploid progenies were generated from the fusion of parental genomes Brassica rapa and Brassica oleracea. Despite the differences in transposon/methylation density between the parental genomes being maintained in the neotetraploids (synthetic Brassica napus), no subgenome dominance was observed. These findings challenge the idea that differences in methylated transposon near genes alone are sufficient to initiate subgenome dominance.