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

ABSTRACT: we found the expression levels of 76 known miRNAs were highly variable between the reciprocal hybrids through the high-throughput sequencing of small RNAs

ORGANISM(S): Solanum lycopersicum x Solanum pimpinellifolium Solanum lycopersicum Solanum pimpinellifolium

PROVIDER: GSE62196 | GEO | 2014/10/10

SECONDARY ACCESSION(S): PRJNA263443

REPOSITORIES: GEO

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

Project description:we found the expression levels of 76 known miRNAs were highly variable between the reciprocal hybrids through the high-throughput sequencing of small RNAs small RNA sequencing were performed in Solanum lycopersicum, S. pimpinellifolium and their reciprocal hybrids

2014-10-10 | E-GEOD-62196 | biostudies-arrayexpress

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

Project description: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.

| S-EPMC4232637 | biostudies-literature

Differential DNA methylation and gene expression in reciprocal hybrids between Solanum lycopersicum and S. pimpinellifolium.

Project description:Wide hybridization is a common and efficient breeding strategy for enhancing crop yield and quality. An interesting phenomenon is that the reciprocal hybrids usually show different phenotypes, and its underlying mechanism is not well understood. Here, we reported our comparative analysis of the DNA methylation patterns in Solanum lycopersicum, Solanum pimpinellifolium and their reciprocal hybrids by methylated DNA immunoprecipitation sequencing. The reciprocal hybrids had lower levels of DNA methylation in CpG islands and LTR retroelements when compared with those of their parents. Importantly, remarkable differences in DNA methylation patterns, mainly in introns and CDS regions, were revealed between the reciprocal hybrids. These different methylated regions were mapped to 79 genes, 14 of which were selected for analysis of gene expression levels. While there was an inverse correlation between DNA methylation and gene expression in promoter regions, the relationship was complicated in gene body regions. Further association analysis revealed that there were 15 differentially methylated genes associated with siRNAs, and that the methylation levels of these genes were inversely correlated with respective siRNAs. All these data raised the possibility that the direction of hybridization induced the divergent epigenomes leading to changes in the transcription levels of reciprocal hybrids.

| S-EPMC5726463 | biostudies-literature

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

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

| PRJNA263443 | ENA

Gene expression of Col, Van and reciprocal hybrids

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Transcriptomic profile of two tomato cultivars and their reciprocal hybrids

Project description:The tomato cultivars Querubín FCA (Q) and Gema FCA (G) as parental genotypes and the hybrids Q x G and G x Q were selected to perform and investigation of the gene actions involved in gene expression profile. In this work, we aimed to study the differences between parental lines and the presence of heterosis and reciprocal effects in the reciprocal hybrids.

2022-12-31 | GSE199011 | GEO

Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids.

Project description:The behavior of transcriptomes and epigenomes in hybrids of heterotic parents is of fundamental interest. Here we report highly integrated maps of the epigenome, mRNA and small RNA transcriptomes of two rice subspecies and their reciprocal hybrids. We found that gene activity was correlated with DNA methylation and both active and repressive histone modifications in transcribed regions. Differential epigenetic modifications correlated with changes in transcript levels among hybrids and parental lines. Distinct patterns in gene expression and epigenetic modifications in reciprocal hybrids were observed. Through analyses of single nucleotide polymorphisms from our sequence data, we observed a high correlation of allelic bias of epigenetic modifications or gene expression in reciprocal hybrids with their differences in the parental lines. The abundance of distinct small RNA size classes differed between the parents and more small RNAs were down-regulated than up-regulated in the reciprocal hybrids. Together, our data reveals a comprehensive overview of transcriptional and epigenetic trends in heterotic rice crosses, and provides a very useful resource for the rice community.

2010-01-20 | GSE19602 | GEO

CG Methylation of Col, Van and reciprocal hybrids using HpaII and MspI digestion

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Genome-wide profiling of DNA methylation in two Arabidopsis ecotypes and their reciprocal hybrids

Project description:This SuperSeries is composed of the following subset Series: GSE34655: Genome-wide profiling of DNA methylation in two Arabidopsis ecotypes and their reciprocal hybrids - mRNA-seq GSE34656: Genome-wide profiling of DNA methylation in two Arabidopsis ecotypes and their reciprocal hybrids - small RNA-seq GSE34657: Genome-wide profiling of DNA methylation in two Arabidopsis ecotypes and their reciprocal hybrids - Bisulfite-seq Refer to individual Series

2011-12-22 | E-GEOD-34658 | biostudies-arrayexpress

Genomic hybridization of Col, Van and reciprocal hybrids

Project description:Genomic DNA of Col, Van and reciprocal hybrids, bioprime random labeling, and hybridization to AtTILE1 forward array. Study on genetic ploymorphic between arabidopsis thaliana accessions Col-0 and Van-0, and set the scale of F1 hybrid intensity for SFPs.

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