Genome doubling affects pre-miRNA expression in plants

Genome doubling, which results in polyploidy, is common in plants and causes genetic and epigenetic alterations. Several researches are in progress to ascertain the effects of polyploidization at the molecular, physiological, and phenotypic level. Although extensive studies are available in synthetic allopolyploids, less is known about the consequences of autopolyploidization. Here, we present a comprehensive analysis of pre-miRNA expression in diploids vs. tetraploids of five different plant species, including the par excellence model Arabidopsis thaliana. Three conserved pre-miRNAs (pre-miR414, pre-miR5538 and pre-miR5141) abounded in all diploids, although their expression was not detected in the tetraploids. Each miRNA target more than one mRNA transcript, many of them belonging to transcription factors (TF) family, DNA repair mechanisms, and related to stress. By contrast, sixteen pre-miRNAs were found in common in all 2x and 4x. Among them, pre-miRNA482, pre-miRNA2916, and pre-miRNA167 significantly changed their expression, being induced or repressed in tetraploids. Based on our results, a microRNA-target regulation network following polyploidization is proposed, which involves DNA repair, ATP-synthesis, terpenoid biosynthesis, and many transcripts responsive to stress. Overall, the results outlined the critical role of microRNAs mediated responses following autopolyploidization in plants.