Polyploidy has occurred throughout the evolutionary history of all eukaryotes and is extremely common in plants. Reunification of the evolutionarily divergent genomes in allopolyploids creates regulatory incompatibilities that must be reconciled. Here we report genomewide gene expression analysis of Arabidopsis synthetic allotetraploids, using spotted 70-mer oligo-gene microarrays. We detected .15% transcriptome divergence between the progenitors, and 2105 and 1818 genes were highly expressed in Arabidopsis thaliana and A. arenosa, respectively. Approximately 5.2% (1362) and 5.6% (1469) genes displayed expression divergence from the midparent value (MPV) in two independently derived synthetic allotetraploids, suggesting nonadditive gene regulation following interspecific hybridization. Remarkably, the majority of nonadditively expressed genes in the allotetraploids also display expression changes between the parents, indicating that transcriptome divergence is reconciled during allopolyploid formation. Moreover, .65% of the nonadditively expressed genes in the allotetraploids are repressed, and .94% of the repressed genes in the allotetraploids match the genes that are expressed at higher levels in A. thaliana than in A. arenosa, consistent with the silencing of A. thaliana rRNA genes subjected to nucleolar dominance and with overall suppression of the A. thaliana phenotype in the synthetic allotetraploids and natural A. suecica. The nonadditive gene regulation is involved in various biological pathways, and the changes in gene expression are developmentally regulated. In contrast to the small effects of genome doubling on gene regulation in autotetraploids, the combination of two divergent genomes in allotetraploids by interspecific hybridization induces genomewide nonadditive gene regulation, providing a molecular basis for de novo variation and allopolyploid evolution.

No abstract

The joining of different genomes in allotetraploids played a major role in plant evolution, but the molecular implications of this event are poorly understood. In synthetic allotetraploids of Arabidopsis and Cardaminopsis arenosa, we previously demonstrated the occurrence of frequent gene silencing. To explore the involvement of epigenetic phenomena, we investigated the occurrence and effects of DNA methylation changes. Changes in DNA methylation patterns were more frequent in synthetic allotetraploids than in the parents. Treatment with 5-aza-2Ј-deoxycytidine, an inhibitor of DNA methyltransferase, resulted in the development of altered morphologies in the synthetic allotetraploids, but not in the parents. We profiled mRNAs in control and 5-aza-2Ј-deoxycytidine-treated parents and allotetraploids by amplified fragment length polymorphism-cDNA. We show that DNA demethylation induced and repressed two different transcriptomes. Our results are consistent with the hypothesis that synthetic allotetraploids have compromised mechanisms of epigenetic gene regulation.Allotetraploids are formed by hybridization between two species and inherit a complete diploid set of chromosomes from each parental species. Although many established wild and cultivated allopolyploids are fertile, well adapted, and genetically stable, allopolyploids of more recent origin commonly display genomic and phenotypic instability (Soltis and Soltis, 1995;Pikaard, 1999; Comai, 2000).As a consequence of the union of two genomes, abnormal phenotypes have been reported (Comai, 2000;Schranz and Osborn, 2000). The causes of these phenotypes are largely unknown. McClintock (1984) described similar phenomena as "genomic shock," which she defined as a preprogrammed response to an unusual challenge resulting in extensive restructuring of the genome. This "unusual challenge" may involve epigenetic gene silencing, which results from homologous DNA-DNA or DNA-RNA interactions. The hybridization of redundant and diverged homeologous sets of genes in allopolyploids might trigger widespread gene silencing and changes in chromatin structure and DNA methylation patterns.Recent molecular data are consistent with the gene silencing hypothesis. Previously, we have reported about 1% changes in gene expression by comparing synthetic allotetraploids derived by hybridizing 4x Arabidopsis and 4x Cardaminopsis arenosa (also known as Arabidopsis arenosa; Comai et al., 2000). These changes can involve both normal genes and genes related to transposons. The corresponding natural allotetraploid, Arabidopsis suecica, was examined by Lee and Chen (2001), who demonstrated similar silencing levels. Furthermore, they found that silencing was related to methylation and could be reversed by treatment with the DNA demethylating agent 5-aza-2Ј-deoxycytidine (azadC). Instability can also be manifested by genomic rearrangements. Synthetic hybrids of wheat (Triticum aestivum) displayed rapid and widespread loss of DNA sequences and changes in DNA methylation Shaked et al., 2001). These...

Polyploidization is an abrupt speciation mechanism for eukaryotes and is especially common in plants. However, little is known about patterns and mechanisms of gene regulation during early stages of polyploid formation. Here we analyzed differential expression patterns of the progenitors' genes among successive selfing generations and independent lineages. The synthetic Arabidopsis allotetraploid lines were produced by a genetic cross between A. thaliana and A. arenosa autotetraploids. We found that some progenitors' genes are differentially expressed in early generations, whereas other genes are silenced in late generations or among different siblings within a selfing generation, suggesting that the silencing of progenitors' genes is rapidly and/or stochastically established. Moreover, a subset of genes is affected in autotetraploid and multiple independent allotetraploid lines and in A. suecica, a natural allotetraploid derived from A. thaliana and A. arenosa, indicating locus-specific susceptibility to ploidy-dependent gene regulation. The role of DNA methylation in silencing progenitors' genes is tested in DNA-hypomethylation transgenic lines of A. suecica using RNA interference (RNAi). Two silenced genes are reactivated in both ddm1-and met1-RNAi lines, consistent with the demethylation of centromeric repeats and gene-specific regions in the genome. A rapid and stochastic process of differential gene expression is reinforced by epigenetic regulation during polyploid formation and evolution.