Shao Deyi, Yin Lixin, Zhao Jian, Luo Zhengliang, Li Weiguo, Wang Yongka, Liu Xiangjie, Tian Bingchuan, Long Xiaobo, Yin Hexing, Zhou Kun
Huazhi Biotechnology Co., LTD., Changsha, 410125 China.
Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Science, Changsha, 410125 China.
Mol Breed. 2025 Aug 2;45(8):66. doi: 10.1007/s11032-025-01575-z. eCollection 2025 Aug.
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.
The online version contains supplementary material available at 10.1007/s11032-025-01575-z.
水稻中镉（Cd）的存在对消费者构成了重大健康风险，凸显了培育低镉积累水稻品种的紧迫性。为了鉴定用于培育此类水稻品种的遗传资源和潜在基因，对158个水稻品种进行了全面的全基因组关联研究（GWAS），这些品种在2021年至2023年期间在低镉积累测试框架中进行了测试，以鉴定与糙米镉含量相关的候选基因。根据它们的亲本来源和遗传群体结构分析，我们将这158个品种分为四个亚组：珞红、、中间型和早籼系列。具体而言，低镉品种的这四个亚组分别基于突变体珞红3A/4A、、莲1S和绍香100培育而成。GWAS分析鉴定出16个与镉含量显著相关的位点，其中12个在多个环境中表现出一致的关联，这些位点被定位到染色体1、2、5、7、11和12上，表明它们具有进一步精细定位和功能验证的潜力。通过基因功能注释分析，鉴定出这些位点中与镉含量相关的候选基因，包括、（）、（）、（）、（）、、、和。这些基因与重金属，特别是镉的吸收、运输和积累有关。对关键基因、、、和的单倍型分析鉴定出了特定的低镉显性单倍型。值得注意的是，-Hap2（GC）、-Hap1（DEL）和-Hap1（DEL）与珞红起源的品种相关，而-Hap1（AC）、-Hap2（AA）和-Hap2（GGG）与起源的品种相关。总体而言，本研究阐明了培育低镉水稻品种的遗传基础，并提供了候选位点以开发分子标记，通过降低重金属含量来提高食品安全。
在线版本包含可在10.1007/s11032-025-01575-z获取的补充材料。
