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<p>Drought stress severely compromises photosynthetic efficiency and yield stability in barley, yet the genetic and regulatory networks underlying drought-responsive chlorophyll fluorescence traits remain inadequately characterized. The current study was carried out to identify the hub genes and regulatory factors associated with major QTLs under drought stress in barley. Accordingly, a genome‒wide composite interval mapping approach was utilized under the framework of multi‒locus genome‒wide association studies. A total of 25 stable lines were identified using genotype by environment interactions. Furthermore, 34 and 63 stable and closely linked QTLs associated with OJIP (O, J, I, P phases of chlorophyll fluorescence induction) test parameters were traced in control and drought conditions, respectively. Common genomic regions across both environments were mapped on chromosomes 1H, 3H, 4H, 5H, and 7H. Bioinformatics analysis included gene ontology (GO) enrichment, protein–protein interaction (PPI) network construction, transcription factor (TF) and microRNA (miRNA) target prediction, and in silico expression validation using RNA-Seq data. Moreover, 214 candidate genes related to major QTLs were identified through bioinformatics analysis. Gene ontology analysis revealed that these candidate genes were enriched in biological processes including cytoskeleton organization, stress response, proteolysis, and lipid biosynthesis. The most significant molecular functions were related to peptidase inhibitor activity and endopeptidase regulator and inhibitor activities. In addition, eight hub genes were identified in protein–protein interaction networks. Among these, four genes (HORVU.MOREX.r3.5HG0446800, HORVU.MOREX.r3.5HG0447870, HORVU.MOREX.r3.3HG0246800, and HORVU.MOREX.r3.3HG0246580) were validated through in silico RNA‑Seq analysis. Finally, 11 transcription factors (e.g., the B3 family) and protein kinases (RLK/Pelle and CAMK) emerged as key regulators, whereas 69 microRNAs (e.g., hvu‒miR5049, hvu‒miR6192, and hvu‒miR6197) were implicated in gene regulatory networks. Collectively, the validated hub genes may serve as promising candidate targets for the development of functional markers in marker-assisted selection (MAS), potentially facilitating early-stage screening and pyramiding of drought-tolerant alleles in barley breeding programs, pending experimental validation. This study provides new insights into the molecular processes underlying drought tolerance in barley.</p>

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Emerging molecular strategies to improve drought tolerance in barley Hordeum vulgare L.)

  • 期刊论文

  • 发表日期：

    2026年7月16日

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  • Hossein Sabouri,
  • Borzo Kazerani,
  • Fakhtak Taliei,
  • Shahram Ghasemi,
  • Zahra Pezeshkian

摘要

Drought stress severely compromises photosynthetic efficiency and yield stability in barley, yet the genetic and regulatory networks underlying drought-responsive chlorophyll fluorescence traits remain inadequately characterized. The current study was carried out to identify the hub genes and regulatory factors associated with major QTLs under drought stress in barley. Accordingly, a genome‒wide composite interval mapping approach was utilized under the framework of multi‒locus genome‒wide association studies. A total of 25 stable lines were identified using genotype by environment interactions. Furthermore, 34 and 63 stable and closely linked QTLs associated with OJIP (O, J, I, P phases of chlorophyll fluorescence induction) test parameters were traced in control and drought conditions, respectively. Common genomic regions across both environments were mapped on chromosomes 1H, 3H, 4H, 5H, and 7H. Bioinformatics analysis included gene ontology (GO) enrichment, protein–protein interaction (PPI) network construction, transcription factor (TF) and microRNA (miRNA) target prediction, and in silico expression validation using RNA-Seq data. Moreover, 214 candidate genes related to major QTLs were identified through bioinformatics analysis. Gene ontology analysis revealed that these candidate genes were enriched in biological processes including cytoskeleton organization, stress response, proteolysis, and lipid biosynthesis. The most significant molecular functions were related to peptidase inhibitor activity and endopeptidase regulator and inhibitor activities. In addition, eight hub genes were identified in protein–protein interaction networks. Among these, four genes (HORVU.MOREX.r3.5HG0446800, HORVU.MOREX.r3.5HG0447870, HORVU.MOREX.r3.3HG0246800, and HORVU.MOREX.r3.3HG0246580) were validated through in silico RNA‑Seq analysis. Finally, 11 transcription factors (e.g., the B3 family) and protein kinases (RLK/Pelle and CAMK) emerged as key regulators, whereas 69 microRNAs (e.g., hvu‒miR5049, hvu‒miR6192, and hvu‒miR6197) were implicated in gene regulatory networks. Collectively, the validated hub genes may serve as promising candidate targets for the development of functional markers in marker-assisted selection (MAS), potentially facilitating early-stage screening and pyramiding of drought-tolerant alleles in barley breeding programs, pending experimental validation. This study provides new insights into the molecular processes underlying drought tolerance in barley.