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

IF 3 3区农林科学 Q1 AGRONOMY

Molecular Breeding Pub Date : 2025-08-02 eCollection Date: 2025-08-01 DOI:10.1007/s11032-025-01575-z

Deyi Shao, Lixin Yin, Jian Zhao, Zhengliang Luo, Weiguo Li, Yongka Wang, Xiangjie Liu, Bingchuan Tian, Xiaobo Long, Hexing Yin, Kun Zhou

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Abstract

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, lcd1, intermediate and early indica series. Specifically, the four subgroups of low cadmium varieties were breeded based on OsNramp5 mutants Luohong 3A/4A, lcd1, 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 Os05 g0382200, Os07 g0232800 (OsZIP8), Os07 g0232900 (OsHMA3), Os07 g0257200 (OsNramp5), Os07 g0258400 (OsNramp1), Os12 g0512100, Os12 g0512700, and Os12 g0514000. These genes are implicated in the absorption, transport, and accumulation of heavy metals, particularly cadmium. Haplotype analysis of key genes OsZIP8, OsHMA3, OsNramp5, and OsNramp1 identified specific low-cadmium dominant haplotypes. Notably, OsHMA3-Hap2 (GC), OsNramp5-Hap1 (DEL), and OsNramp1-Hap1 (DEL) were associated with Luohong-origin varieties, while OsHMA3-Hap1 (AC), OsNramp5-Hap2 (AA), and OsNramp1-Hap2 (GGG) were linked to lcd1-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.

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镉积累的遗传基础导航：低镉积累水稻的综合分析。

水稻中镉（Cd）的存在对消费者构成重大健康风险，突出了培育低镉积累水稻品种的紧迫性。为寻找糙米镉含量的遗传资源和潜在基因，在2021 - 2023年对158个水稻品种进行了全基因组关联研究（GWAS），并在低镉积累测试框架下进行了测试，以确定糙米镉含量的候选基因。根据亲本来源和遗传群体结构分析，将158个品种划分为4个亚群：罗红、lcd1、中籼和早籼。其中，以OsNramp5突变体罗红3A/4A、lcd1、连1S和少香100为基础，分别选育了4个低镉品种亚群。GWAS分析鉴定出16个与镉含量显著相关的位点，其中12个位点在多个环境中表现出一致的相关性，这些位点被定位到染色体1、2、5、7、11和12上，表明它们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，在这些基因座中鉴定出与镉含量相关的候选基因，包括Os05 g0382200、Os07 g0232800 （OsZIP8）、Os07 g0232900 （OsHMA3）、Os07 g0257200 （OsNramp5）、Os07 g0258400 （OsNramp1）、Os12 g0512100、Os12 g0512700和Os12 g0514000。这些基因与重金属，特别是镉的吸收、运输和积累有关。关键基因OsZIP8、OsHMA3、OsNramp5和OsNramp1的单倍型分析鉴定出特定的低镉优势单倍型。值得注意的是，OsHMA3-Hap2 （GC）、OsNramp5-Hap1 （DEL）和OsNramp1-Hap1 （DEL）与罗红源品种相关，而OsHMA3-Hap1 （AC）、OsNramp5-Hap2 （AA）和OsNramp1-Hap2 （GGG）与lcd1源品种相关。总体而言，本研究为培育低镉水稻品种提供了遗传基础，并为开发通过降低重金属含量来提高食品安全的分子标记提供了候选位点。补充信息：在线版本包含补充资料，提供地址为10.1007/s11032-025-01575-z。

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来源期刊

Molecular Breeding 农林科学-农艺学

CiteScore

5.60

自引率

6.50%

发文量

审稿时长

1.5 months

期刊介绍： Molecular Breeding is an international journal publishing papers on applications of plant molecular biology, i.e., research most likely leading to practical applications. The practical applications might relate to the Developing as well as the industrialised World and have demonstrable benefits for the seed industry, farmers, processing industry, the environment and the consumer. All papers published should contribute to the understanding and progress of modern plant breeding, encompassing the scientific disciplines of molecular biology, biochemistry, genetics, physiology, pathology, plant breeding, and ecology among others. Molecular Breeding welcomes the following categories of papers: full papers, short communications, papers describing novel methods and review papers. All submission will be subject to peer review ensuring the highest possible scientific quality standards. Molecular Breeding core areas: Molecular Breeding will consider manuscripts describing contemporary methods of molecular genetics and genomic analysis, structural and functional genomics in crops, proteomics and metabolic profiling, abiotic stress and field evaluation of transgenic crops containing particular traits. Manuscripts on marker assisted breeding are also of major interest, in particular novel approaches and new results of marker assisted breeding, QTL cloning, integration of conventional and marker assisted breeding, and QTL studies in crop plants.