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Genome-wide analysis has documented differential gene expression between closely related species in plants and animals and nonadditive gene expression in hybrids and allopolyploids compared to the parents. In  Arabidopsis , 15–43% of genes are expressed differently between the related species,  Arabidopsis thaliana  and  Arabidopsis arenosa , the majority of which are nonadditively expressed (differently from mid-parent value) in allotetraploids. Nonadditive gene expression can be caused by transcriptional regulation through chromatin modifications, but the role of posttranscriptional regulation in nonadditive gene expression is largely unknown. Here we reported genome-wide analysis of mRNA decay in resynthesized  Arabidopsis  allotetraploids. Among ∼26,000 annotated genes, over 1% of gene transcripts showed rapid decay with an estimated half-life of less than 60 minutes, and they are called allotetraploid genes with unstable transcripts ( AlloGUTs ). Remarkably, 30% of  alloGUTs  matched the nonadditively expressed genes, and their expression levels were negatively correlated with the decay rate. Compared to all genes, these nonadditively expressed  alloGUTs  were overrepresented 2-6-fold in the Gene Ontology (GOSlim) classifications in response to abiotic and biotic stresses, signal transduction, and transcription. Interestingly, the  AlloGUTs  include transcription factor genes that are highly inducible under stress conditions and circadian clock regulators that regulate growth in  A. thaliana . These data suggest a role of mRNA stability in homoeologous gene expression in  Arabidopsis  allopolyploids. The enrichment of nonadditively expressed genes in stress-related pathways were commonly observed in  Arabidopsis  and other allopolyploids such as wheat and cotton, which may suggest a role for stress-mediated growth vigor in hybrids and allopolyploids.

Unstable Transcripts in Arabidopsis Allotetraploids Are Associated with Nonadditive Gene Expression in Response to Abiotic and Biotic Stresses