Molecular mapping and application of quantitative trait loci (QTL) associated with a higher level of grain Zinc is a viable option to enhance zinc content in rice through breeding. An F₂ population derived from a cross between a high yielding variety, BRRI dhan28, and a locally adapted Zn enriched cultivar, Kalobokri was used to map QTLs associated with higher levels of Zn in rice grain. The F_2:3 progenies varied significantly (P < 0.0001) in Zinc contents with a mean value remarkably higher than those in the superior parent. Through marker by trait analysis using IciMapping, we detected a large-effect QTL, qGZn3 on chromosome 3 between RM5419 and RM1164 spanning 1.83 Mb interval at the 0.05 level of significance with a threshold LOD of 10.61. This QTL showed a 21.1% (R² value) contribution to the total phenotypic variation for zinc content in the unpolished rice grains with 4.68 μg/g additive effect of Kalobokri alleles. We also detected 11 metal homeostasis related genes within the interval of qGZn3. In-silico analysis showed that four expressed sequence tags of one candidate gene (LOC_Os03g22810) encoding Cu/Zn superoxide dismutase, a metal-binding protein, are highly active in the endosperm as well as in the embryonic tissue of rice grain. Taken together, our results suggest that qGZn3 is a major QTL associated with high grain Zn content in the F₂ progenies of rice. Our findings offer valuable genetic resources to facilitate breeding for high yielding and Zinc-enriched rice variety.

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