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BMC Plant Biol. 2019 Feb 18;19(1):78. doi: 10.1186/s12870-019-1679-0.

Inferring the regulatory network of the miRNA-mediated response to biotic and abiotic stress in melon.

Author information

1
Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC) - Universitat de València (UV), Parc Científic, Cat. Agustín Escardino 9, 46980, Paterna, Spain.
2
Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universidad Politécnica de Valencia (UPV), CPI 8E, Av. de los Naranjos s/n, 46022, Valencia, Spain.
3
Instituto Nacional de Investigaciones Agropecuarias (INIAP), Estación Experimental Pichilingue, Km5 vía Quevedo El Empalme, Mocache, Ecuador.
4
Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC) - Universitat de València (UV), Parc Científic, Cat. Agustín Escardino 9, 46980, Paterna, Spain. gustavo.gomez@csic.es.
5
Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universidad Politécnica de Valencia (UPV), CPI 8E, Av. de los Naranjos s/n, 46022, Valencia, Spain. gustavo.gomez@csic.es.

Abstract

BACKGROUND:

MiRNAs have emerged as key regulators of stress response in plants, suggesting their potential as candidates for knock-in/out to improve stress tolerance in agricultural crops. Although diverse assays have been performed, systematic and detailed studies of miRNA expression and function during exposure to multiple environments in crops are limited.

RESULTS:

Here, we present such pioneering analysis in melon plants in response to seven biotic and abiotic stress conditions. Deep-sequencing and computational approaches have identified twenty-four known miRNAs whose expression was significantly altered under at least one stress condition, observing that down-regulation was preponderant. Additionally, miRNA function was characterized by high scale degradome assays and quantitative RNA measurements over the intended target mRNAs, providing mechanistic insight. Clustering analysis provided evidence that eight miRNAs showed a broad response range under the stress conditions analyzed, whereas another eight miRNAs displayed a narrow response range. Transcription factors were predominantly targeted by stress-responsive miRNAs in melon. Furthermore, our results show that the miRNAs that are down-regulated upon stress predominantly have as targets genes that are known to participate in the stress response by the plant, whereas the miRNAs that are up-regulated control genes linked to development.

CONCLUSION:

Altogether, this high-resolution analysis of miRNA-target interactions, combining experimental and computational work, Illustrates the close interplay between miRNAs and the response to diverse environmental conditions, in melon.

KEYWORDS:

Agriculture; Climatic change; Cucurbits; Non-coding RNAs; RNA silencing; Stress tolerance

PMID:
30777009
PMCID:
PMC6379984
DOI:
10.1186/s12870-019-1679-0
[Indexed for MEDLINE]
Free PMC Article

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