ArticleBMC genomics2014
Identification of chilling stress-responsive tomato microRNAs and their target genes by high-throughput sequencing and degradome analysis.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed, 113 citations in OpenAlex.
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- Transcription start site aware catalogue of microRNA encoded peptides in tomato (Solanum lycopersicum).Discover plants · 2026Article
- Long Non-Coding RNAs in the Cold-Stress Response of Horticultural Plants: Molecular Mechanisms and Potential Applications.International journal of molecular sciences · 2025Review
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- Research progress on plant noncoding RNAs in response to low-temperature stress.Plant signaling & behavior · 2022Review
- Application of RNAi technology: a novel approach to navigate abiotic stresses.Molecular biology reports · 2022Review
- Identification and profiling of conserved microRNAs in different developmental stages of crown imperial (Fritillaria imperialis L.) using high-throughput sequencing.Molecular biology reports · 2022Article
- ASRmiRNA: Abiotic Stress-Responsive miRNA Prediction in Plants by Using Machine Learning Algorithms with PseudoInternational journal of molecular sciences · 2022Article
- miRNAs and lncRNAs in tomato: Roles in biotic and abiotic stress responses.Frontiers in plant science · 2022Review
- Integrative analysis of microRNAs and mRNAs reveals the regulatory networks of triterpenoid saponin metabolism in Soapberry (Frontiers in plant science · 2022Article
- MicroRNA-mediated bioengineering for climate-resilience in crops.Bioengineered · 2021Review
- Genome-wide identification, phylogeny, and expression analysis of the bHLH gene family in tobacco (Physiology and molecular biology of plants : an international journal of functional plant biology · 2021Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMicroRNAs (miRNAs) are a class of noncoding small RNAs (sRNAs) that are 20-24 nucleotides (nt) in length. Extensive studies have indicated that miRNAs play versatile roles in plants, functioning in processes such as growth, development and stress responses. Chilling is a common abiotic stress that seriously affects plants growth and development. Recently, chilling-responsive miRNAs have been detected in several plant species. However, little is known about the miRNAs in the model plant tomato. 'LA1777' (Solanum habrochaites) has been shown to survive chilling stress due to its various characteristics.
resultsHere, two small RNA libraries and two degradome libraries were produced from chilling-treated (CT) and non-chilling-treated (NT) leaves of S. habrochaites seedlings. Following high-throughput sequencing and filtering, 161 conserved and 236 novel miRNAs were identified in the two libraries. Of these miRNAs, 192 increased in the response to chilling stress while 205 decreased. Furthermore, the target genes of the miRNAs were predicted using a degradome sequencing approach. It was found that 62 target genes were cleaved by 42 conserved miRNAs, while nine target genes were cleaved by nine novel miRNAs. Additionally, nine miRNAs and six target genes were validated by quantitative real-time PCR (qRT-PCR). Target gene functional analysis showed that most target genes played positive roles in the chilling response, primarily by regulating the expression of anti-stress proteins, antioxidant enzyme and genes involved in cell wall formation.
conclusionsTomato is an important model plant for basic biological research. In this study, numerous conserved and novel miRNAs involved in the chilling response were identified using high-throughput sequencing, and the target genes were analyzed by degradome sequencing. The work helps identify chilling-responsive miRNAs in tomato and increases the number of identified miRNAs involved in chilling stress. Furthermore, the work provides a foundation for further study of the regulation of miRNAs in the plant response to chilling stress.
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