Rice (Oryza sativa L.) is a major dietary source of cadmium (Cd). Developing rice varieties with reduced Cd levels in the grain is a cost-effective and practical approach to enhance food safety, particularly in regions with high Cd contamination. However, the genetic mechanisms underlying Cd accumulation in rice grains are not fully understood. In this study, we identified eight quantitative trait loci (QTLs) associated with Cd accumulation in rice grains through substitution mapping using single segment substitution lines (SSSLs). These QTLs, named qCd‐2‐1, qCd‐3‐1, qCd‐3‐2, qCd‐5‐1, qCd‐6‐1, qCd‐7‐1, qCd‐8‐1, and qCd‐11‐1, are distributed across seven chromosomes. Notably, the qCd‐5‐1 and qCd‐6‐1 loci are reported for the first time. We performed a detailed haplotype analysis of candidate genes related to heavy metal metabolism, specifically focusing on Cd accumulation. All SSSLs carrying alleles from donor parents exhibited a significant reduction in Cd accumulation, with additive effects ranging from −0.061 to −0.105. To further develop rice varieties with lower Cd accumulation in the grain, we developed six pyramided lines through crossing and marker-assisted selection. These pyramided lines showed significantly reduced Cd content in the grain compared to the elite indica recurrent parent, Huajingxian74 (HJX74). Importantly, most agronomic characteristics of the pyramided lines were similar to those of HJX74. In conclusion, this study demonstrates that identifying and pyramiding QTLs associated with reduced Cd accumulation is an effective strategy for developing rice varieties with lower Cd content in the grain.

Design of rice with low cadmium accumulation in grain using single segment substitution line