The transcriptional and splicing changes caused by hybridization can be globally recovered by genome doubling during allopolyploidization

Allopolyploidization, which involves hybridization and genome doubling, is a key driving force in higher plant evolution. The transcriptome reprogramming that accompanies allopolyploidization can cause extensive phenotypic variations, and thus confers allopolyploids higher evolutionary potential than their diploid progenitors. Despite many studies, little is known about the interplay between hybridization and genome doubling in transcriptome reprogramming during allopolyploidization. Here, we performed genome-wide analyses of gene expression and splicing changes during allopolyploidization in wheat and brassica lineages. Our results indicated that both hybridization and genome doubling can induce genome-wide transcriptional and splicing changes. Notably, the gene transcriptional and splicing changes caused by hybridization can be largely recovered to parental levels by genome doubling in allopolyploids. Since transcriptome reprogramming is an important contributor to heterosis, our results revealed that only part of the heterosis in hybrids can be fixed in allopolyploids through genome doubling. Therefore, our findings update the current understanding of the permanent fixation of heterosis in hybrids through genome doubling. In addition, our results indicated that a large proportion of the transcriptome reprogramming in interspecific hybrids was not caused by the merging of two parental genomes, providing novel insights into the mechanism of heterosis.