Abstract
BackgroundReciprocal hybrids showing different phenotypes have been well documented in previous studies, and many factors accounting for different phenotypes have been extensively investigated. However, less is known about whether the profiles of small RNAs differ between reciprocal hybrids and how these small RNAs affect gene expression and phenotypes. To better understand this mechanism, the role of small RNAs on phenotypes in reciprocal hybrids was analysed.ResultsReciprocal hybrids between Solanum lycopersicum cv. Micro-Tom and S. pimpinellifolium line WVa700 were generated. Significantly different phenotypes between the reciprocal hybrids were observed, including fruit shape index, single fruit weight and plant height. Then, through the high-throughput sequencing of small RNAs, we found that the expression levels of 76 known miRNAs were highly variable between the reciprocal hybrids. Subsequently, a total of 410 target genes were predicted to correspond with these differentially expressed miRNAs. Furthermore, gene ontology (GO) annotation indicated that those target genes are primarily involved in metabolic processes. Finally, differentially expressed miRNAs, such as miR156f and 171a, and their target genes were analysed by qRT-PCR, and their expression levels were well correlated with the different phenotypes.ConclusionsThis study showed that the profiles of small RNAs differed between the reciprocal hybrids, and differentially expressed genes were also observed based on the different phenotypes. The qRT-PCR results of target genes showed that differentially expressed miRNAs negatively regulated their target genes. Moreover, the expression of target genes was well correlated with the observations of different phenotypes. These findings may aid in elucidating small RNAs contribute significantly to different phenotypes through epigenetic modification during reciprocal crossing.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0296-1) contains supplementary material, which is available to authorized users.
Highlights
Reciprocal hybrids showing different phenotypes have been well documented in previous studies, and many factors accounting for different phenotypes have been extensively investigated
The results showed that Micro-Tom × WVa700 exhibited significantly larger fruit shape index and smaller single fruit weight and plant height compared with WVa700 × Micro-Tom (Figure 1E; F; Additional file 1)
Small RNAs sequencing in reciprocal hybrids and their progenitors Mature small RNAs are generated in the cytoplasm; small RNAs in reciprocal hybrids with different cytoplasms were analysed by high-throughput sequencing to determine whether there are differences between them and explore the relationship of small RNAs with gene expression and phenotypes in the reciprocal hybrids
Summary
Reciprocal hybrids showing different phenotypes have been well documented in previous studies, and many factors accounting for different phenotypes have been extensively investigated. Less is known about whether the profiles of small RNAs differ between reciprocal hybrids and how these small RNAs affect gene expression and phenotypes. To better understand this mechanism, the role of small RNAs on phenotypes in reciprocal hybrids was analysed. Previous studies have shown that epigenetic modifications, especially those involving small RNAs, are a main factor for the development and growth of plants. Small RNAs including miRNAs and siRNAs, which function as mediators and regulators, play an extensive role in epigenetic processes and gene expression. Finding the differences in small RNAs after hybridization and how these small RNAs regulate gene expression and subsequent phenotypes between reciprocal hybrids is worth exploring
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