TY - JOUR
T1 - Characterizing small RNA profiles in allotetraploid poa annua L. And its diploid parents
AU - Mao, Qing
AU - Huff, David R.
N1 - Funding Information:
This research was financially supported by the Huck Institute of Life Sciences, Pennsylvania State University, the Pennsylvania Turfgrass Council (PTC), and USDA National Institute of Food and Agriculture, Hatch Projects 0222520, 1006804, and PA 4442.
Publisher Copyright:
© Crop Science Society of America. All rights reserved.
PY - 2017/7/1
Y1 - 2017/7/1
N2 - 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.
AB - 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.
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U2 - 10.2135/cropsci2016.06.0462
DO - 10.2135/cropsci2016.06.0462
M3 - Article
AN - SCOPUS:85028661197
SN - 0011-183X
VL - 57
SP - S-13-S-25
JO - Crop Science
JF - Crop Science
ER -