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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 GO (Gene ontology) annotation of target genes. A. biological process, B. cellular component, C. molecular function.
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Fig4: The GO (Gene ontology) annotation of target genes. A. biological process, B. cellular component, C. molecular function.

Mentions: A total of 410 target genes for 76 differentially expressed miRNAs were predicted. The gene functions of these targets were determined by gene ontology (GO) annotation and involved biological processes, cellular components and molecular functions (FigureĀ 4). The top three biological processes were metabolic processes (20%), cellular processes (18%) and response to stimuli (12%). Moreover, those target genes were primarily located within the cell, cell parts and organelles at 29%, 29% and 23%, respectively. In addition, 50% of target genes for molecular function were attributed to binding and 39% were attributed to catalytic activity, indicating that those targets may be involved in many metabolic processes and that there may be complicated relationships between those targets and different phenotypes.Figure 4


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 GO (Gene ontology) annotation of target genes. A. biological process, B. cellular component, C. molecular function.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: The GO (Gene ontology) annotation of target genes. A. biological process, B. cellular component, C. molecular function.
Mentions: A total of 410 target genes for 76 differentially expressed miRNAs were predicted. The gene functions of these targets were determined by gene ontology (GO) annotation and involved biological processes, cellular components and molecular functions (FigureĀ 4). The top three biological processes were metabolic processes (20%), cellular processes (18%) and response to stimuli (12%). Moreover, those target genes were primarily located within the cell, cell parts and organelles at 29%, 29% and 23%, respectively. In addition, 50% of target genes for molecular function were attributed to binding and 39% were attributed to catalytic activity, indicating that those targets may be involved in many metabolic processes and that there may be complicated relationships between those targets and different phenotypes.Figure 4

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.