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

Abstract Rice (Oryza sativa L.) is a major source of dietary cadmium (Cd). Developing rice varieties with lower levels of Cd in the grain offers an economical and practical way to improve food safety, especially in areas with high Cd contamination. However, the genetic mechanism of Cd accumulation in rice grain is not fully understood. Here, we identified eight QTLs for Cd accumulation in rice grain based on substitution mapping using single segment substitution lines (SSSLs). The QTLs were located on 7 chromosomes, and 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 accordingly. Two of them, qCd-5-1 and qCd-6-1 are reported here for the first time. The haplotypes of candidate genes associated with heavy metal metabolism, especially Cd accumulation, were analyzed in detail. All SSSLs harbouring alleles from donor parents significantly decreased Cd accumulation with additive effects ranging from − 0.061 to -0.105. Six pyramided lines were developed based on crossing and maker-assisted selection, and these six pyramided lines showed significantly decreased Cd content in grain compared with that of the elite, indica recurrent parent, HJX74, while most of agronomic characteristics of the pyramided lines were similar to HJX74. Taken together, this study demonstrates that identifying and pyramiding QTLs for lower Cd accumulation is an effective strategy for developing rice varieties with lower grain Cd accumulation.