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MicroRNAs (miRNAs) and small interfering RNAs are important regulators of plant development and seed formation, yet their population and abundance in the oil crop Brassica napus are still not well understood, especially at different developmental stages and among cultivars with varied seed oil contents. Here, we systematically analyzed the small RNA expression profiles of Brassica napus seeds at early embryonic developmental stages in high-oil-content and low-oil-content B. napus cultivars, both cultured in two environments. A total of 50 conserved miRNAs and 9 new miRNAs were identified, together with some new miRNA targets. Expression analysis revealed some miRNAs with varied expression levels in different seed oil content cultivars or at different embryonic developmental stages. A large number of 23-nucleotide small RNAs with specific nucleotide composition preferences were also identified, which may present new classes of functional small RNAs.
Increasing numbers of small RNAs have been identified as regulatory RNAs that modulate gene expression at both the transcriptional and posttranscriptional levels. Currently, two major classes of endogenous small RNAs have been identified in plants, namely microRNAs (miRNAs) and small interfering RNAs (siRNAs; Brodersen and Voinnet, 2006; Jones-Rhoades et al., 2006; Mallory and Vaucheret, 2006; Chen, 2009; Voinnet, 2009). They are approximately 20 to 24 nucleotides long and have crucial regulatory functions in diverse biological processes. Plant miRNAs are produced from hairpin-shaped precursors and mostly 21 nucleotides long, whereas the majority of plant siRNAs are 24 nucleotides in length and generated from long double-stranded RNA duplexes or transcripts derived from inverted repeat regions (Chen, 2009; Voinnet, 2009). Endogenous plant siRNAs can be divided into several classes, including miRNAinduced transacting siRNAs (ta-siRNAs), heterochromatic siRNAs, natural antisense siRNAs, and millions of unclassified small RNA sequences (Choudhuri, 2009). Ta-siRNAs are in-phase-generated small RNAs whose production depends on the cleavage of nonprotein- coding transcripts of ta-siRNA genes by miRNAs (Vazquez et al., 2004; Allen et al., 2005; Yoshikawa et al., 2005; Montgomery et al., 2008a, 2008b). Both miRNAs and ta-siRNAs can induce the cleavage of mRNAs with partially or fully complementary sequences to them. Heterochromatic siRNAs are usually produced from repeats and transposable elements (Xie et al., 2004; Lu et al., 2005; Kasschau et al., 2007; Zhang et al., 2007; Mosher et al., 2008) and inhibit gene expression at the...