Integration of multi-trait stability indices for selection of nutrient-dense and yield-stable pearl millet genotypes across environments

Addressing micronutrient malnutrition through pearl millet biofortification remains challenging because of complex trait interactions, anti-nutritional factors, and genotype × environment interactions. This study comparatively evaluated four multi-trait selection indices—SHI, FAI-BLUP, MTSI, and MGIDI for identifying pearl millet genotypes with improved nutritional composition, reduced anti-nutritional factors, and desirable yield-related performance. A diverse PMiGAP panel of 218 genotypes was evaluated across four contrasting environments representing the A, A₁, and B pearl millet-growing zones of India. The traits comprised iron, zinc, manganese, and phosphorus, total tannin content, phytic acid content, grain filling duration, tiller productivity, spike size, sink capacity, thousand-seed weight, and seed yield per plant. Combined analysis of variance revealed highly significant effects of genotype, environment, and genotype × environment interaction for all evaluated traits, indicating substantial genetic variability and differential environmental responses. Correlation analysis revealed positive associations among nutritional and yield-related traits, whereas anti-nutritional traits showed antagonistic relationships. At 15% selection intensity, MGIDI produced gains of 8.78% for Fe, 3.85% for Zn, and 3.01% for Mn, while reducing PAC and TTC by 6.31% and 10.70%, respectively. MTSI produced the greatest gains for several yield-related traits, including tiller productivity (21.55%), seed yield per plant (14.63%), spike size (11.98%), and sink capacity (16.51%). SHI achieved the largest reductions in PAC (17.90%) and TTC (13.40%), whereas FAI-BLUP showed substantial gains for several yield traits but increased PAC (8.96%) and TTC (13.40%). Four genotypes—IP 15,872, IP 19,584, IP 3757, and IP 6310—were consistently selected by all four indices, demonstrating strong concordance among selection approaches. These consensus genotypes represent promising genetic resources for the development of pearl millet with improved nutritional quality, reduced anti-nutritional factors, and desirable yield-related attributes.