Balanced gene retention, transcription and methylation levels between subgenomes produced by soybean-specific paleo-tetraploidization

Abstract

BackgroundPolyploidization creates duplicated sets of genomes in a plant. Dominance by a subgenome is often observed in a polyploid species. Here, we studied the duplicated genomic regions in soybean, which was affected by a tetraploidization 13 million years ago.ResultsBy referring to eudicot relatives, we detailed that duplicated genes are retained in a balanced manner among homoeologs. Moreover, we found that duplicated genes in colinearity in extant genome are expressed at balance. Notably, the DNA methylation patterns of duplicated genes shared similar methylation levels among three different soybean lines (W931A, WR016, and ZAYOU1), suggesting that either the epigenetic information could be maintained transgenerationally for millions of years or homoeologs in this paleo-autopolyploid species have similar methylation patterns under similar environment.ConclusionsThese findings support the paleo-autotetraploidy of soybean. We proposed that, if taking maize as a model plant for studying paleo-allotetraploids, soybean is a model plant for studying paleo-autotetraploids.