Small Non-Coding RNAs in the Regulatory Network of Wheat Dwarf Virus-Infected Wheat

ABSTRACT: Wheat dwarf virus (WDV) is a major constraint to global wheat production, causing severe yield losses and economic disruption. Understanding the molecular basis of wheat–WDV interactions is essential for developing resistant cultivars. Non-coding RNAs (ncRNAs), including long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), are key regulators of gene expression and defence. This study identified ncRNAs involved in wheat responses to WDV, including host lncRNAs, miRNAs, and viral small interfering RNAs (siRNAs) targeting WDV genomic regions. High-throughput sequencing revealed extensive ncRNA reprogramming under WDV infection. A total of 437 differentially expressed lncRNAs (DElncRNAs) and 58 miRNAs (DEmiRNAs) were detected. Resistant genotypes displayed more DElncRNAs (204 in Svitava; 163 in Fengyou 3) than the susceptible Akteur (141). In Akteur, 66.7% of DElncRNAs were downregulated, whereas in Svitava, 56.9% were upregulated. Akteur also exhibited more DEmiRNAs (28) than resistant genotypes (15), with predominant downregulation. A co-expression network analysis revealed 391 significant DElncRNA–mRNA interactions mediated by 16 miRNAs. The lncRNA XLOC_058282 was linked to 298 transcripts in resistant genotypes, suggesting a central role in the host defence. Functional annotation showed enrichment in signalling, metabolic, and defence-related pathways. Small RNA profiling identified 1166 differentially expressed sRNAs targeting WDV, including conserved hotspots and 408 genotype-specific sites in Akteur versus Fengyou 3. Infected plants displayed longer sRNAs, a sense-strand bias, and a 5′ uridine preference, but lacked typical 21–24 nt phasing. These findings highlight the central roles of ncRNAs in orchestrating wheat antiviral defence and provide a molecular framework for breeding virus-resistant wheat.

ORGANISM(S): Triticum aestivum

PROVIDER: GSE230156 | GEO | 2026/04/17

REPOSITORIES: GEO