Harnessing genotype × environment interactions and multi-trait selection indices to identify nutritionally superior pearl millet accessions from global PMiGAP germplasm

Background Pearl millet is a climate-resilient and nutrient-dense cereal with immense potential to alleviate micronutrient malnutrition. However, the development of nutritionally superior and stable cultivars is challenged by the complex inheritance of nutritional traits and their strong genotype × environment interactions. Results In the present study, 218 pearl millet genotypes were evaluated across four environments for grain nutritional quality, anti-nutritional factors, and seed yield per plant. Multi-trait genotype selection was performed using the MTSI, followed by stability assessment using AMMI, ASV, GSI, WAASB, BLUP, and GGE biplot analysis. Factor analysis grouped the seven traits into five latent factors and predicted favourable selection gains for Fe (26.38%), Zn (9.81%), P (4.94%), and seed yield per plant (1.38%), while reducing the anti-nutritional traits, total tannin content (TTC; -16.36%) and phytic acid content (PAC; -0.78%). A modest negative response was observed for Mn (-6.89%), reflecting a trade-off under simultaneous multi-trait selection. Broad-sense heritability was high for all traits (0.83–0.99). Combined ANOVA revealed highly significant effects of genotype, environment, and G×E interaction for all traits. Based on MTSI values, 33 superior genotypes were shortlisted for detailed stability analysis. BLUP analysis identified G158 as the best genotype for low TTC (0.55 mg g⁻¹) and PAC (2.47 mg g⁻¹), whereas G88, G179, G175, G113, and G20 recorded the highest predicted values for P (9233.50 mg kg⁻¹), Fe (111.39 mg kg⁻¹), Zn (56.41 mg kg⁻¹), Mn (34.60 mg kg⁻¹), and seed yield per plant (22.65 g), respectively. The first two principal components of the GGE biplot explained 98.48–99.94% of the total G + GE variation across traits. Across the seven approaches, G113 (TTC), G62 (PAC), G129 (P), G109 (Fe), G175 (Zn), G1 (Mn), and G88 (SYP) were among the most frequently selected genotypes for the respective traits. Ranking multi-trait donors within each approach placed G169 first in AMMI-1, ASV and GSI, G110 in AMMI-2, G198 in WAASB, G108 in BLUP and G88 in the which-won-where analysis. In the integrated ranking, ten genotypes were supported by at least six of the seven approaches and were also selected by BLUP for at least one trait, and G88, G20, G132, G110, and G175 ranked highest. Conclusions Overall, G88 (IP 17690), G20 (ICTP 8203), G132 (IP 3757), G110 (IP 2058), and G175 (IP 7922) emerged as the top-ranked multi-trait donor genotypes, supported by at least six of the seven approaches and together representing mineral concentration, reduced anti-nutritional traits, seed yield, and stable performance across environments. These genotypes constitute valuable genetic resources for pearl millet biofortification and provide promising parental lines for developing nutrient-dense and environmentally stable, cultivars.