Identification of conserved microRNAs and their targets from Solanum lycopersicum Mill

Zhang, Jianguang; Zeng, Rong; Jia, Qiong; Liu, Xin; Liao, Qinhong

doi:10.1016/j.gene.2008.05.023

Cited by 77 publications

(53 citation statements)

References 28 publications

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“…Ru et al (2006) find enhanced expression of microRNA167 inhibits reproductive development through degradation of auxin response factor 8 mRNA and repressing auxin response factor 6 translation. ARF6 and ARF8 have been reported in regulating gynoecium and stamen development in immature flowers and their transcripts are cleaved by miR167 (Zhang et al, 2008). These miRNAs were up-regulated in low-N sensitive rice compared with low-N tolerant rice according to our analysis.…”

Section: Discussionsupporting

confidence: 51%

Identification of MicroRNAs Associated with Nitrogen Use Efficiency and Fertility in Rice

Ouyang¹,

Li²

2015

IJAB

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To cite this paper: Ouyang, J.X. and S. B. AbstractA study was conducted to identify target genes through differential expression of microRNAs (miRNAs) under low nitrogen (low-N) level (0.01 mM NH4NO3) for tolerant and sensitive rice samples, which may provide valuable information for breeding and improving production under nitrogen stress condition. MiRNA microarray data GSE38213 were downloaded from Gene Expression Ominibus database, including 2 low-N tolerant rice samples and 2 low-N sensitive rice samples. After the data were preprocessed and normalized, limma package in R was applied to identify the differentially expressed miRNAs. Then the target genes of the most significant up-regulated miRNAs were collected by using Plant miRNA Database. In addition, the high-reliable signal nucleotide polymorphisms (SNPs) of target genes were screened out by Rice Genome Browser in TIFR (The Institute for Genomic Research). Functional analysis was performed to the genes with SNPs. As the results, total 22 differentially expressed miRNAs were identified and the most significant ones were osa-miR530-3p, and osamiR319a. Additionally, high-reliable SNPs were only discovered in 4 target genes of osa-miR530-3p. Functional analysis revealed that the 4 target genes of osa-miR530-3p were associated with plant growth, development and respiration. In conclusion, differentially expressed osa-miR530-3p and its target genes that had high-reliable SNPs were identified in present study. Besides, miR167 and miR319 were found to be associated with fertility. These miRNAs identified in the present study are potential targets for developing high yield low-N tolerant rice.

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Section: Discussionsupporting

confidence: 51%

Identification of MicroRNAs Associated with Nitrogen Use Efficiency and Fertility in Rice

Ouyang¹,

Li²

2015

IJAB

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“…Similarly to other species, several families of conserved miRNAs and targets were identified in tomato by using bioinformatic and cloning techniques (Moxon et al 2008;Mohorianu et al 2011;Zhang et al 2008;Karlova et al 2013). Some miRNA families showed differential accumulation during fruit development, suggesting a particular role in this developmental process in tomato.…”

Section: Small Rnasmentioning

confidence: 99%

Tomato Epigenetics: Deciphering the “Beyond” Genetic Information in a Vegetable Fleshy-Fruited Crop

Nogueira

2014

Epigenetics in Plants of Agronomic Importance: Fundamentals and Applications

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The first natural plant mutant for which the molecular basis was determined to be an epimutation rather than a change in DNA sequence was a peloric variant of toadflax, Linaria vulgaris. Remarkably, the second example of a natural epimutant came from the vegetable fleshy-fruited crop tomato (Solanum lycopersicum). The discovery of the molecular basis for the Colorless nonripening (Cnr) epimutation was a landmark for plant epigenetics and, importantly, linked epigenetic mechanisms with an important agronomical trait. More recently, several studies on tomato have contributed to our better understanding of epigenetic mechanisms underlying important heritable crop traits, such as ripening and stress response. Epigenetic mechanisms have also been associated with transgressive segregation in hybrids generated from crosses between cultivated tomato and close wild relatives. Therefore, we can only envision that tomato will became a model for studying the epigenetic basis of economically important phenotypes, allowing for their more efficient exploitation in plant breeding.

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“…miRNA microarrays and sequencing-bysynthesis approaches enable profiling differentially expressed miRNA genes in various organs and tissues, during certain developmental stages, among distinct mutants or under the effects of some chemicals (Zhang et al 2008;Fahlgren et al 2009;Mica et al 2010). When research on seed germination-associated miRNAs was initiated, only a small number (~28) of plant miRNA species were known.…”

Section: Hormone Sensitivitymentioning

confidence: 99%

MicroRNA Function in Seed Biology

et al. 2011

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The involvement of microRNA (miRNA) in various developmental programs in plants, such as leaf and flower development, and the response of plants to biotic and abiotic stresses, has been characterized. Information on the involvement of miRNA in seed biology is limited, but emerging. miRNAs and transcription factors or other genes that are targeted by miRNA are expressed during embryogenesis, seed maturation, imbibition, and seedling establishment, suggesting that the downregulation of target genes by miRNA may play a critical role in seed development and germination. This chapter focuses on the biological function of miRNA and miRNA-targeted genes involved in seed formation, the sensitivity of mature seeds to plant hormones, and postembryonic seedling development.

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Identification of conserved microRNAs and their targets from Solanum lycopersicum Mill

Cited by 77 publications

References 28 publications

Identification of MicroRNAs Associated with Nitrogen Use Efficiency and Fertility in Rice

Identification of MicroRNAs Associated with Nitrogen Use Efficiency and Fertility in Rice

Tomato Epigenetics: Deciphering the “Beyond” Genetic Information in a Vegetable Fleshy-Fruited Crop

MicroRNA Function in Seed Biology

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