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Background <p>Long non-coding RNAs (lncRNAs) have emerged as crucial regulators in plant responses to abiotic stresses, including salinity, drought, heavy metals, and temperature fluctuations. The functional characterization of drought-responsive lncRNAs in <i>Solanum lycopersicum</i> remains incomplete and poorly understood. In this study, we performed transcriptome-wide identification and functional analysis of lncRNAs in two tomato cultivars, drought-tolerant variety Falcon, and drought-susceptible SC2121, when subjected to drought stress.</p> Methods and Results <p>Physiological parameters—such as shoot height, root length, soluble protein, and water content- were measured to evaluate drought-induced changes in the tomato varieties. In addition, five lncRNAs were selected for reverse transcription quantitative PCR (RT-qPCR) analysis. Using high-throughput RNA sequencing, we identified 269 drought-responsive lncRNAs, including 124 upregulated and 145 downregulated transcripts. Interestingly, in tomato, predicted lncRNA–mRNA interactions suggest that XR_003244833.1, XR_003247168.1, and XR_743350.3 may be associated with the sorbitol (polyol) pathway, the ABC-2 type transporter protein, and the U11/U12 small nuclear ribonucleoprotein involved in the spliceosome complex, respectively.</p> Conclusions <p>Using high-throughput RNA sequencing, we identified 269 drought-responsive lncRNAs, including 124 upregulated and 145 downregulated transcripts. Interestingly, in tomato, predicted lncRNA–mRNA interactions suggest that XR_003244833.1, XR_003247168.1, and XR_743350.3 may be associated with the sorbitol (polyol) pathway, the ABC-2 type transporter protein, and the U11/U12 small nuclear ribonucleoprotein involved in the spliceosome complex, respectively. Accordingly, lncRNAs may be actively involved in the drought stress response and regulate key adaptive pathways through interactions with protein-coding genes. These findings provide new insights into the molecular mechanisms of drought tolerance in tomato and offer potential targets for the genetic improvement of stress-resilient cultivars.</p>

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Differential expression of long-noncoding RNAs under drought stress in tomato (Solanum lycopersicum)

  • 期刊论文

  • 发表日期：

    2026年5月16日

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  • Mehtap Aydın,
  • Elif Karlık Urhan,
  • Fikrettin Şahin,
  • Andrew John Harvey

摘要

Background

Long non-coding RNAs (lncRNAs) have emerged as crucial regulators in plant responses to abiotic stresses, including salinity, drought, heavy metals, and temperature fluctuations. The functional characterization of drought-responsive lncRNAs in Solanum lycopersicum remains incomplete and poorly understood. In this study, we performed transcriptome-wide identification and functional analysis of lncRNAs in two tomato cultivars, drought-tolerant variety Falcon, and drought-susceptible SC2121, when subjected to drought stress.

Methods and Results

Physiological parameters—such as shoot height, root length, soluble protein, and water content- were measured to evaluate drought-induced changes in the tomato varieties. In addition, five lncRNAs were selected for reverse transcription quantitative PCR (RT-qPCR) analysis. Using high-throughput RNA sequencing, we identified 269 drought-responsive lncRNAs, including 124 upregulated and 145 downregulated transcripts. Interestingly, in tomato, predicted lncRNA–mRNA interactions suggest that XR_003244833.1, XR_003247168.1, and XR_743350.3 may be associated with the sorbitol (polyol) pathway, the ABC-2 type transporter protein, and the U11/U12 small nuclear ribonucleoprotein involved in the spliceosome complex, respectively.

Conclusions

Using high-throughput RNA sequencing, we identified 269 drought-responsive lncRNAs, including 124 upregulated and 145 downregulated transcripts. Interestingly, in tomato, predicted lncRNA–mRNA interactions suggest that XR_003244833.1, XR_003247168.1, and XR_743350.3 may be associated with the sorbitol (polyol) pathway, the ABC-2 type transporter protein, and the U11/U12 small nuclear ribonucleoprotein involved in the spliceosome complex, respectively. Accordingly, lncRNAs may be actively involved in the drought stress response and regulate key adaptive pathways through interactions with protein-coding genes. These findings provide new insights into the molecular mechanisms of drought tolerance in tomato and offer potential targets for the genetic improvement of stress-resilient cultivars.