Navigating the genetic basis of cadmium accumulation: a comprehensive analysis of low-cadmium accumulation rice.

Unlabelled: The presence of cadmium (Cd) in rice poses a significant health risk to consumers, highlighting the urgency of breeding rice varieties with low Cd accumulation. To identify genetic resources and potential genes for developing such rice varieties, a comprehensive genome-wide association study (GWAS) was conducted on 158 rice varieties, which tested between 2021 and 2023 in low cadmium accumulation testing framework, to identify candidate genes associated with cadmium content in brown rice. Based on their parental origin and genetic population structure analysis, we categorized these 158 varieties into four subgroups: Luohong, , intermediate and early indica series. Specifically, the four subgroups of low cadmium varieties were breeded based on mutants Luohong 3A/4A, , Lian 1S and Shaoxiang 100, respectively. GWAS analysis identified sixteen loci significantly associated with cadmium content, twelve of which showed consistent associations across multiple environments, these loci were mapped to chromosomes 1, 2, 5, 7, 11, and 12, suggesting their potential for further fine mapping and functional validation. Through gene function annotation analysis, candidate genes related to cadmium content in these loci were identified, including , (), (), (), (), , , and . These genes are implicated in the absorption, transport, and accumulation of heavy metals, particularly cadmium. Haplotype analysis of key genes , , , and identified specific low-cadmium dominant haplotypes. Notably, -Hap2 (GC), -Hap1 (DEL), and -Hap1 (DEL) were associated with Luohong-origin varieties, while -Hap1 (AC), -Hap2 (AA), and -Hap2 (GGG) were linked to -origin varieties. Overall, this study illustrated the genetic basis for breeding low-cadmium rice varieties and provided candidate loci to develop molecular markers to enhance food safety through reduced heavy metal content.

Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-025-01575-z.