Apomixis refers to plant asexual reproduction through seeds that give rise to progeny which are genotypically
identical to the maternal parent. It has evolved from many different sexual taxa although the underlying genetic factors
remain unknown. Previous analyses of the over-representation of transcription factors, in a comparison of microdissected
ovules from apomictic and sexual Boechera, showed that many transcription factor mRNAs possessed microRNA
(miRNAs) binding sites, thus pointing to miRNAs as potentially important factors that may be involved in the regulatory
switch from sexual to apomictic reproduction. A microarray-based approach was used to identify (1) 673 microsatellitelike
small RNAs (misRNAs) containing predominantly 2-7 repeats of (GAA)n/(CUU)n, (GCA)n/(CGU)n, (GGA)n/(CCU)n,
(GGU)n/(CCA)n and (UGA)n/(ACU)n, and (2) 166 more typical non-repeat small RNAs. In total, 87 small RNAs were
found to be located in cDNAs that could fold into stem-loop structures and thus represent miRNA molecules. In addition,
109 Boechera small RNAs including both misRNAs and non-repeat small RNAs, showed significant homology to 407
Arabidopsis thaliana small RNAs including the A. thaliana pollen-specific ath-miR5021. This indicates that only a fraction
of the identified small RNAs are unique to Boechera. Ten small RNAs were validated using a Northern blot assay on
flower and leaf tissues, eight of which showed flower-specific expression with varying abundance. The potential binding
sites of many of the misRNAs and non-repeat small RNAs occur predominantly in exonic regions. This feature coupled
with their flower-specific pattern of expression is suggestive of their probable role in post-transcriptional gene regulation.
We propose that quantitative variation for misRNA target binding (and hence post-transcriptional gene regulation) could
arise via microsatellite length polymorphisms occurring either in misRNA precursors or in their gene targets.
Keywords: Apomixis, Boechera, flower, microsatellites, sex, small RNAs.
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