Genomic expression dominance in the natural allopolyploid Coffea arabica is massively affected by growth temperature

Polyploidy occurs throughout the evolutionary history of many plants and considerably impacts species diversity, giving rise to novel phenotypes and leading to ecological diversification and colonization of new niches. Recent studies have documented dynamic changes in plant polyploid gene expression, which reflect the genomic and functional plasticity of duplicate genes and genomes. The aim of the present study was to describe genomic expression dominance between a relatively recently formed natural allopolyploid (Coffea arabica) and its ancestral parents (Coffea canephora and Coffea eugenioides) and to determine if the divergence was environment-dependent. Employing a microarray platform designed against 15 522 unigenes, we assayed unigene expression levels in the allopolyploid and its two parental diploids. For each unigene, we measured expression variations among the three species grown under two temperature conditions (26-22 degrees C (day-night temperatures) and 30-26 degrees C (day-night temperatures)). More than 35% of unigenes were differentially expressed in each comparison at both temperatures, except for C. arabica vs C. canephora in the 30-26 degrees C range, where an unexpectedly low unigene expression divergence (< 9%) was observed. Our data revealed evidence of transcription profile divergence between the allopolyploid and its parental species, greatly affected by environmental conditions, and provide clues to the plasticity phenomenon in allopolyploids.