A two-phase evaluation system integrating hydroponic and field screening identifies nutrient-efficient sweetpotato (Ipomoea batatas (L.) Lam.) germplasm

(L.) Lam.) is a crucial crop for global food security. However, its sustainable production is hindered by low nutrient use efficiency. Reliable screening protocols that accurately identify nutrient-efficient germplasm of this crop across developmental stages are still lacking. To bridge this gap, we established a novel two-phase evaluation system integrating hydroponic seedling screening with multi-nutrient field validation. We conducted principal component and regression analyses of 35 germplasms lines under controlled deficiencies of nitrogen (N), phosphorus (P), and potassium (K). Five conserved seedling traits were identified, including leaf number per plant, shoot fresh weight, root fresh weight, shoot dry weight, and net photosynthetic rate (Pn). These traits consistently correlated with tolerance to N, P, or K deficiency, thereby supporting their utility as reliable early indicators of nutrient stress. Field validation further confirmed that storage root fresh and dry weight, nutrient content, accumulation, and use efficiency varied significantly among nutrient treatments and genotypes, serving as key indicators of field performance. This integrated approach successfully identified elite germplasm with specific nutrient use efficiency: XN1985-7 as a low-N-tolerant and N-efficient utilization genotype, XN17104-132 as low-K-tolerant and K-efficient utilization, XN2141-3 as low-P-tolerant and P-efficient utilization, and notably XN2153-5, which exhibited concurrent tolerance to low N, P, and K with broad-spectrum efficiency. Our integrated two-phase framework provides a scalable model for screening nutrient-efficient germplasm in root crops, thereby contributing to sustainable breeding programs.