Total RNA transcript analysis to identify regulatory non-coding RNAs and their targets in response to drought stress in wheat (Triticum aestivum L.)

Zare, Mohammad Ali; Zarinpanjeh, Nasim; Khalaj, Hamideh; Rafiepour, Mostafa; Mir Alizadeh, Syyed Reza

doi:10.22034/cmr.2025.8503.3305

Total RNA transcript analysis to identify regulatory non-coding RNAs and their targets in response to drought stress in wheat (Triticum aestivum L.)

Document Type : Research Paper

Authors

Mohammad Ali Zare ¹

Nasim Zarinpanjeh ²

Hamideh Khalaj ³

Mostafa Rafiepour ⁴

Syyed Reza Mir Alizadeh ⁵

¹ Student, Department of Biotechnology, Payeme Noor University, Tehran, Iran

² Medicinal Plants Research Center, Institute of Medicinal Plants, ACECR, Karaj, Iran

³ Assistant professor, Department of Agriculture, Payeme Noor University, Tehran, Iran

⁴ Department of Genetics, Faculty of Science, Danesh Alborz University, Qazvin, Iran

⁵ Department of Agriculture and environment, Payeme Noor University, Tehran, Iran

10.22034/cmr.2025.8503.3305

Abstract

Drought is a significant abiotic stress factor that impacts the productivity of crops, including wheat. However, drought tolerance is a complex trait involving numerous genes and cellular pathways. Understanding the molecular regulatory network of wheat in response to drought stress is crucial for molecular breeding. Non-coding RNAs affect plant growth and resistance to abiotic stresses by regulating gene expression. To help understand the complex regulatory mechanisms governing drought tolerance in wheat, we performed a total RNA transcriptome sequence analysis in a drought-tolerant wheat cultivar. A total of 20462 mRNAs and 209 miRNAs with different expressions were identified. Among 20462 genes with different expressions, 1025 were identified as genes that withstand drought stress. The target genes identified by psRNATarget were all enriched in gene ontology categories. Significant differences exist in the number of target genes regulated by differently expressed miRNAs, especially in signal transduction, stress response, and antioxidant pathways. Our results elucidate wheat's molecular mechanisms of drought tolerance and identify drought-responsive miRNAs and their target genes. These insights can be utilized to enhance wheat and related crops, providing valuable genomic resources for molecular breeding.

Keywords

Drought stress

RNA sequencing

Wheat

Non-coding RNAs

Subjects