Integrating morphological and molecular diversity to develop high-biomass fodder pearl millet composites

Pearl millet (<i>Pennisetum glaucum</i> L. R. Br., syn. <i>Cenchrus americanus</i> [L.] Morrone) is a climate-resilient cereal and a vital fodder source in arid and semi-arid regions. Identification and characterization of diverse inbred lines are essential for developing superior forage composites and hybrids with enhanced yield and stress resilience. In this study, 96 fodder pearl millet inbreds along with four checks were evaluated during rainy season 2024 and summer seasons 2025 for 29 morpho-physiological and root architectural traits, complemented by molecular characterization using 46 polymorphic SSR markers. Significant genotypic variation and strong genotype × season interactions were observed for key yield and physiological traits, indicating substantial environmental responsiveness. Correlation analyses identified stem girth, plant height, dry matter yield, and major root traits as major determinants of green fodder yield. Morphological clustering grouped genotypes into five clusters, with maximum divergence between Clusters II and V. SSR analysis detected 203 alleles across 46 loci (average: 5.28 alleles per locus; PIC = 0.62), and population structure analysis resolved six genetic groups highlighting their potential use as heterotic parents. Based on combined phenotypic and molecular diversity, selected inbreds were randomly intermated to develop eight fodder composites. Two composites exhibited 17-20% higher green fodder yield than the best check cultivar. These results demonstrate that integrating morphological and molecular diversity enables effective parental selection and rapid development of superior high-biomass fodder pearl millet composites.