Genetic and epigenetic changes in a genomic region containing MIR172 in Arabidopsis allopolyploids and their progenitors

Combination of divergent genomes in allopolyploids creates genome-wide gene expression changes including many miRNA targets in Arabidopsis allotetraploids relative to the parents Arabidopsis thaliana and Arabidopsis arenosa. Here we report expression and epigenetic changes in a chromosomal region containing the MIR172b locus in the allotetraploids. Although mature miRNA sequences are conserved, A. thaliana and A. arenosa miRNA loci diverge rapidly in sequence and expression. Among four MIR172 loci in Arabidopsis, the level of nucleotide sequence divergence between A. thaliana and A. arenosa MIR172 loci is 15-25%, which is higher than that of protein-coding genes (similar to 5%). MIR172b locus and its flanking genes in A. arenosa were expressed at low levels relative to that in A. thaliana, which is associated with hypermethylation of this region in the allotetraploids. Consistently with this notion, pri-miR172 transcripts in the allotetraploids were primarily derived from the A. thaliana MIR172b locus. Expression of homoeologous alleles in miR172 target loci is associated with allelic loss, allelic changes in outcrossing A. arenosa or repression of A. thaliana alleles. These data suggest that gene expression changes in this homoeologous region are associated with genetic diversity and epigenetic variation of miRNA genes and their targets in allopolyploids.