Abstract
BackgroundmicroRNAs (miRNAs) are endogenous small RNAs that play important regulatory functions in plant development. Genetic variations in miRNAs sequences or their target-binding sites (microRNA-target interaction sites) can alter miRNA targets in animal and human. Whether these single nucleotide polymorphisms (SNPs) in plant are functional have not yet been determined.ResultsIn this study, we constructed leaf, root, and stem-derived small libraries of cucumber (Cucumis sativus) line 9930 (cultivated China-group cucumber) and C. sativus var. hardwickii (wild India group cucumber). A total of 22 conserved miRNA families, nine less-conserved miRNA families, and 49 cucumber-specific miRNAs were identified in both line 9930 and hardwickii. We employed cucumber resequencing data to perform a genome-wide scan for SNPs in cucumber miRNA-target interaction sites, including miRNA mature sequences and miRNA-target binding sites. As a result, we identified a total of 19 SNPs in mature miRNA sequences and 113 SNPs in miRNA-target binding sites with the potential to affect miRNA-target interactions. Furthermore, we experimentally confirmed that these SNPs produced 14 9930-unique targets mRNAs and 15 hardwickii-unique targets mRNA for cucumber miRNAs. This is the first experimental validation of SNPs in miRNA-target interaction sites affecting miRNA-target binding in plants.ConclusionsOur results indicate that SNPs can alter miRNA function and produce unique miRNA targets in cultivated and wild cucumbers. Therefore, miRNA-related SNPs may have played important in events that led to the agronomic differences between domestic and wild cucumber.
Highlights
MicroRNAs are endogenous small RNAs that play important regulatory functions in plant development
Our results showed that single nucleotide polymorphisms (SNPs) can alter miRNA function and cause unique miRNA targets for domestic and wild cucumbers
Our results showed that snp-miRNAs could interact with a total of 34 new targets compared with the cognate miRNAs (Additional file 5: Table S4), with snp-miRNAs 396d having the maximum number new targets
Summary
MicroRNAs (miRNAs) are endogenous small RNAs that play important regulatory functions in plant development. Genetic variations in miRNAs sequences or their target-binding sites (microRNA-target interaction sites) can alter miRNA targets in animal and human. Whether these single nucleotide polymorphisms (SNPs) in plant are functional have not yet been determined. MicroRNAs (miRNAs), a class of 21–24 nt small RNAs, have important roles in post-transcriptional gene regulation in plants [1]. The appearance in the database of large numbers of species-specific miRNAs (new miRNAs) suggests that miRNAs are born frequently but are lost frequently, and the foldback sequences in genomes, inverted duplication events, and transposable elements, are thought to be important sources of many new miRNAs [9]
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