Characterizing Small RNA Profiles in Allotetraploid Poa Annua L. and Its Diploid Parents

A role for small RNAs has been implicated for polyploid evolution. This study was designed to examine the small RNA profiles of Poa annua L. and its diploid parental species. Four profiles, Poa infirma Kunth., Poa supina Schrad., perennial-type Poa annua, and annual-type Poa annua, were analyzed using three biological replicates representing each profile, resulting in a total of 12 libraries, totaling 20,920,659 small (18–30 nucleotide) RNA sequences. Small RNA length distributions were compared between biological replicates within each profile, as well as between profiles. Both redundant and unique small RNA length distributions were similar among the four profiles (Cramer’s V < 0.05 for overall profile comparison). A total of 121 conserved microRNAs belonging to 27 families were identified from the four profiles, and we did not observe specific patterns in expression levels of these microRNA families when comparing between these profiles. A total of 79 novel microRNAs were predicted using reference genomes from three model plant species. It was interesting to find that the perennial-type and annual-type Poa annua displayed very similar small RNA profiles, despite their morphological and life history differences. In addition, the small RNA profiles of tetraploid Poa annua were very similar to its diploid parental species as well. The incorporation of biological replicates in our study helped to increase our confidence in the results of our data analyses.