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The role of small RNAs on phenotypes in reciprocal hybrids between Solanum lycopersicum and S. pimpinellifolium.

Li J, Sun Q, Yu N, Zhu J, Zou X, Qi Z, Ghani MA, Chen L - BMC Plant Biol. (2014)

Bottom Line: 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.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Reciprocal 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.

Results: Reciprocal 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.

Conclusions: This 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.

No MeSH data available.


The different expression of miRNAs in the leaves between the reciprocal hybrids and the parents displayed with hierarchical cluster analysis.
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Fig2: The different expression of miRNAs in the leaves between the reciprocal hybrids and the parents displayed with hierarchical cluster analysis.

Mentions: To explore the different influences of miRNAs on phenotypes between reciprocal hybrids, differentially expressed known miRNAs were analysed by the approach of hierarchical cluster (Figure 2). The expression levels of 76 miRNAs including 13 conserved and 63 non-conserved miRNAs were highly variable between the reciprocal hybrids, and a total of 63 miRNAs displayed a greater than four-fold change (Additional file 9). Among them, the expression of 40 miRNAs in Micro-Tom × WVa700 were higher than those of WVa700 × Micro-Tom, such as conserved miRNAs (miR156f-3p, miR171a-3p, miR535a and miR169a) and non-conserved miR5081 that showed similar expression levels between Micro-Tom and WVa700. The expression levels of the other 36 miRNAs, including miR482c, miR394a, miR535b, miR169b, miR170, miR393a, miR160a and miR165a, were obviously lower in Micro-Tom × WVa700. Hence, the differentially expressed miRNAs may be relevant to significantly different phenotypes between reciprocal hybrids.Figure 2


The role of small RNAs on phenotypes in reciprocal hybrids between Solanum lycopersicum and S. pimpinellifolium.

Li J, Sun Q, Yu N, Zhu J, Zou X, Qi Z, Ghani MA, Chen L - BMC Plant Biol. (2014)

The different expression of miRNAs in the leaves between the reciprocal hybrids and the parents displayed with hierarchical cluster analysis.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4232637&req=5

Fig2: The different expression of miRNAs in the leaves between the reciprocal hybrids and the parents displayed with hierarchical cluster analysis.
Mentions: To explore the different influences of miRNAs on phenotypes between reciprocal hybrids, differentially expressed known miRNAs were analysed by the approach of hierarchical cluster (Figure 2). The expression levels of 76 miRNAs including 13 conserved and 63 non-conserved miRNAs were highly variable between the reciprocal hybrids, and a total of 63 miRNAs displayed a greater than four-fold change (Additional file 9). Among them, the expression of 40 miRNAs in Micro-Tom × WVa700 were higher than those of WVa700 × Micro-Tom, such as conserved miRNAs (miR156f-3p, miR171a-3p, miR535a and miR169a) and non-conserved miR5081 that showed similar expression levels between Micro-Tom and WVa700. The expression levels of the other 36 miRNAs, including miR482c, miR394a, miR535b, miR169b, miR170, miR393a, miR160a and miR165a, were obviously lower in Micro-Tom × WVa700. Hence, the differentially expressed miRNAs may be relevant to significantly different phenotypes between reciprocal hybrids.Figure 2

Bottom Line: 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.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Reciprocal 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.

Results: Reciprocal 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.

Conclusions: This 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.

No MeSH data available.