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Genomic interactions in allopolyploids create expression variation of homoeologous alleles through protein-protein and protein-DNA interactions. However, the molecular basis for this is largely unknown. Here we investigated the protein-protein and protein-DNA interactions among homoeologous transcription factors in the circadian-clock feedback loop, consisting of CCA1 HIKING EXPEDITION (CHE), CIRCADIAN CLOCK ASSOCIATED1 (CCA1), and TIMING OF CAB EXPRESSION1 (TOC1), plus the interaction with a chromatin factor, HISTONE DEACETYLASE1 (HD1). In the allotetraploids formed between  A. thaliana  (At) and  Arabidopsis arenosa  (Aa),  AtCCA1  is expressed at lower levels than  AaCCA1 , which could alter clock output traits. The reduced  AtCCA1  expressions in the allotetraploids are consistent with the biochemical data that AaCHE showed preferential binding to the  AtCCA1  promoter, in which AaCHE interacts with a higher affinity to AtHD1 than AtCHE. AaCHE also showed a higher affinity to TOC1 than AtCHE, consistent with the effect of TOC1 on repressing  CCA1 . Thus, stronger AaCHE-TOC1 and AaCHE-AtHD1 interactions reduce  AtCC1  allelic expression. Our current data suggest a biochemical basis for protein interactions  in trans  with a preference to the  cis -acting elements in heterologous combinations to reduce  AtCCA1  expression, while altered  CCA1  expression has been shown to affect metabolic and biomass heterosis in interspecific hybrids or allotetraploids.

Heterologous protein-DNA interactions lead to biased allelic expression of circadian clock genes in interspecific hybrids