Soil has available spaces between two grains Seedling emergence Seedlings are irregular in size Seedlings of each cluster are even in size Almost all seedlings are even in size Crop coverage and leaf color Poor crop growth, yellow/purple/light green in color Moderate crop growth, green in color Healthy crop growth, dark green in color.
Here we analyze small RNA populations from mature rice grain and seedlings by pyrosequencing.
In contrast, among sparse hotspots from grain and seedlings only five loci were found to contain miRNA-like foldback structures.
In this study, we have initiated the sequencing of the small RNA population from rice grain and seedlings to determine the abundance and role of miRNAs and other small RNAs in both dormant and growing tissues.
Grain and seedling libraries showed distinct, tissue-specific expression patterns, with more miRNA-associated hotspots in seedlings.
Grain and seedling small RNAs were similar in size distributions with distinct peaks at 21- and 24-nt (Figure S1).
Using a cutoff of P<E-50 for hotspots resulted in a combined total of 498 small RNA clusters in <span class="lh">grain and seedling (Table S2).
Small RNA hotspot clusters accounted for over 53% and 49% of the total small RNA abundance in grain and seedling, respectively.
We hypothesize that alternative regulatory siRNAs, including ta-siRNAs and naturally occurring antisense siRNAs, (nat-siRNA) might account for the discrepancy in miRNA abundance between grain and seedling 21-nt siRNAs [31], [32].
The unique small RNA sequences from grain and seedling were significantly different, which could reflect either lack of sequence coverage to fully capture the complexity of the small RNA population, or regions of small RNA expression unique to each tissue.
While our efforts in deep sequencing of rice grain and seedling tissue have revealed a number of unique elements in the regulatory small RNA family of rice, the functions of many of these remain to be elucidated.
