Integrating multi-trait selection indices and molecular marker-based diversity analysis for identification of yield and nutritional quality traits in pearl millet ( Pennisetum glaucum L.)

Abstract

Background : Pearl millet ( Pennisetum glaucum L.) is a resilient C ₄ cereal adapted to arid and semiarid regions and is recognized as a climate-smart crop with considerable nutritional potential. Germplasm characterization provides a foundation for genetic improvement and marker-assisted breeding. This study investigated morpho-biochemical and molecular diversity among pearl millet genotypes of Indian origin. Methods : Forty-eight pearl millet genotypes were evaluated using integrated morphological, biochemical and molecular approaches. Variability and associations among agro-morphological and biochemical traits were assessed. The comparative efficiency of the genotype by yield*trait (GYT) biplot and multi-trait genotype-ideotype distance index (MGIDI) was evaluated for multi-trait genotype selection. Population structure was also examined using simple sequence repeat (SSR) and sequence-related amplified polymorphism (SRAP) markers to aid molecular breeding and germplasm characterization. Results : Considerable genetic variability was observed for most traits, with high heritability and genetic advance except for days to maturity, phosphorus and total phenolic acids. Grain yield per plant was positively associated with plant height, thousand-seed weight, manganese and potassium, while path analysis revealed positive direct effects of plant height, protein content and days to maturity on yield. The first seven principal components, with eigenvalues greater than 1, explained 63.4% of the total variation and cluster analysis grouped the genotypes into four distinct clusters. GYT identified G47, G15, G12, G24, G13, G28 and G7 as superior for desirable yield-trait combinations, whereas MGIDI selected G7, G8, G25, G33, G34, G37 and G48 for balanced multi-trait performance. Molecular diversity analysis revealed 83% of the total variation within populations and STRUCTURE analysis classified the genotypes into two subpopulations with limited admixture. Conclusion : The GYT biplot and MGIDI provided complementary approaches for multi-trait selection by combining visual interpretation of yield-trait relationships with ideotype-based genotype ranking. Integrating phenotypic, biochemical and molecular diversity analyses provided a comprehensive framework for identifying promising and genetically diverse pearl millet genotypes for yield and nutritional quality improvement.