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Molecular markers provide novel tools for linkage mapping of QTLs of target traits and can greatly enhance the efficacy of breeding programs to improve mineral (iron and zinc) density in rice. F3, F4, BC1F2 and BC1F3 populations derived from the cross between high-yielding (PAU201) and iron-rich (Palman 579) indica rice varieties displayed large variation for various physio-morphological traits including grain yield per plant and mineral (iron and zinc) contents.