Plant growth is inseparable from the presence of mineral nutrients such as nitrogen (N), phosphorus (P), and potassium (K), but the mechanism by which horticultural plants such as tomatoes respond to mineral elements is poorly understood. Here, we collected 28 phenotypic datasets, including 5 agronomic traits and 4 pigment accumulation traits, under full nutrition and nitrogen/phosphorus/potassium-deficiency conditions, most of which showed abundant variation. Phenotyping analysis suggested that the yellowing of leaves under low-nitrogen treatment was caused by an increase in the carotenoid content and a decrease in the chlorophyll b content. A genome-wide association study identified a total of 138 suggestive loci (including 23 significant loci) corresponding to 116 loci, including many reported and new candidate genes related to mineral element response and absorption. Transcriptome analysis of tomato seedlings under full nutrient and N/P/K-deficiency conditions revealed 1108 and 1507 common differentially expressed genes in above-ground and below-ground tissues, respectively, with 103 overlapping genes. Gene Ontology term enrichment analysis revealed that tomato plants resist low nutrient stress by increasing photosynthesis in the above-ground parts and ion transport capacity in the below-ground parts. Through the combined analysis of GWAS and RNA-Seq, we identified 28 mineral element response genes with high confidence, corresponding to 17 loci, which may be closely related to the response and utilization of N, P, and K in tomato. Two candidate genes, auxin-repressed protein (Solyc02g077880), which responds to carotenoid and chlorophyll b accumulation, and guanine nucleotide exchange factor-like protein (Solyc04g005560), which responds to low-phosphorus conditions, were further validated via haplotype analysis. This study provides new insights into the nitrogen, phosphorus, and potassium response mechanisms of tomato and offers valuable genetic resources for future improvements in tomato breeding.

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