Journal of Agronomy and Field Innovations

Zinc (Zn) deficiency is a major global public health problem, particularly in developing countries where rice (Oryza sativa L.) serves as the primary staple food. Modern elite rice cultivars are typically poor sources of essential micronutrients, especially after the milling process. Genetic biofortification via molecular breeding presents a sustainable approach to enhance grain Zn concentration without compromising agronomic yields. In this study, a Recombinant Inbred Line (RIL) population (F_{7:8}), derived from a cross between an elite indica variety (IR64, low grain Zn) and a wild-derived landrace donor (Madukar, high grain Zn), was evaluated across two consecutive environments to identify stable Quantitative Trait Loci (QTLs) for grain zinc concentration (GZnC) and related agronomic traits, including grain yield per plant (GY) and days to 50% flowering (DTF). A high-density genetic linkage map consisting of 1,245 Single Nucleotide Polymorphism (SNP) markers spanning 1,542.3 cM across the 12 rice chromosomes was used. Composite Interval Mapping (CIM) identified a total of nine QTLs for GZnC across both environments. Notably, two major, stable QTLs—qGZnC1.1 and qGZnC7.1—were identified on chromosomes 1 and 7, explaining 18.4% and 14.2% of the phenotypic variance, respectively. Co-localization analysis revealed that qGZnC7.1 overlaps with QTLs for grain iron concentration, suggesting a shared transport mechanism. In silico analysis within the stable QTL intervals revealed promising candidate genes, including members of the ZIP (ZRT/IRT-like Protein) transporter family and Nicotianamine Synthase (OsNAS2). These stable QTLs and flanking SNP markers provide robust tools for marker-assisted selection (MAS) to accelerate the development of zinc-dense, high-yielding rice varieties.