Integrated genome-wide association and RNA sequencing analyses reveal key long noncoding RNAs and target genes for drought tolerance in wheat

Drought poses a major threat to global crop productivity, necessitating the identification of genetic components and regulatory networks underlying drought tolerance in wheat. Here, we integrated genome-wide association studies (GWAS) of 334 diverse wheat accessions with comparative transcriptomic analysis of drought-sensitive and drought-tolerant genotypes. GWAS identified 45 significant SNPs (−log10(p) > 3.5) and 281 candidate genes linked to seedling dry weight loss under drought stress. Transcriptome profiling revealed 821 differentially expressed genes, with co-expression network analysis uncovering 21 drought-responsive long noncoding RNAs (lncRNAs) and their target genes. These targets were enriched in ubiquitin-mediated protein degradation and transcriptional regulation pathways. Notably, lncRNA XR_006461531 was predicted to interact with TaFBX361—a gene co-identified by GWAS and RNA-seq—via a lncRNA-miRNA-mRNA interaction. Functional validation through virus-induced gene silencing (VIGS) demonstrated that knockdown of TaFBX361 significantly impaired plant growth and increased oxidative damage under drought, confirming its positive role in stress adaptation. Our findings reveal coordinated coding and noncoding regulatory modules governing drought responses in wheat, with TaFBX361 emerging as a promising genetic target for enhancing drought resilience. This study advances the molecular breeding toolkit by integrating multi-omics approaches to dissect complex traits, offering novel insights into lncRNA-mediated regulatory networks in crop abiotic stress tolerance.