Comprehensive GWAS and omics profiling identify key genetic factors and metabolic pathways for oat's low-phosphorus tolerance

• 180 oat accessions were evaluated for five traits under normal and low phosphorus conditions. • GWAS identified 32 QTLs and 206 candidate genes related to stress signaling, metabolic regulation, and nutrient acquisition. • Two contrasting genotypes were selected and the tolerant accession showed enhanced root growth and higher PUE under LP stress. • Integrated transcriptomic and metabolomic profiling revealed LP-responsive pathways. Phosphorus deficiency is a major constraint to crop productivity, particularly in cereals like oat ( Avena sativa L.). In this study, 180 diverse oat accessions were evaluated under normal phosphorus (NP) and low phosphorus (LP) hydroponic conditions to investigate the genetic basis of early seedling responses to LP stress. High broad-sense heritability ( H ² > 0.8) for shoot length (SL) and phosphorus use efficiency (PUE) suggested strong genetic effects. A composite LP tolerance index was applied to classify genotypes along a continuum from tolerant to sensitive, and two contrasting accessions were selected for further molecular analysis. The relatively tolerant accession exhibited greater root development and higher PUE compared to the sensitive one under LP conditions. A genome-wide association study (GWAS) using the FarmCPU model identified 37 significant marker–trait associations (MTAs) across five traits, explaining up to 44.6% of the phenotypic variance. These MTAs clustered into 32 QTL intervals containing 1087 annotated genes, with 206 prioritized as candidate genes based on sequence variation, expression patterns, and differential expression analysis. Several candidate genes were related to stress signaling, metabolic regulation, and nutrient acquisition. In addition, some were involved in aromatic amino acid metabolism, phenylpropanoid biosynthesis, and glutathione metabolism. Integration of transcriptomic and metabolomic data highlighted putative pathways contributing to genotype-specific responses under LP stress. This study provides a set of loci and candidate genes that may serve as promising targets for further functional validation and future breeding efforts aimed at improving phosphorus efficiency in oat.