Genetic loci regulating cadmium content in rice grains

Gareth Norton, Anthony Travis, Panthita Ruangareerate, Graeme W Nicol, Ayotunde Abiodun Adeosun, Mahmud Hossain, Rafiq Islam, Alex Douglas, Adam H Price* (Corresponding Author)

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

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It has been estimated that up to 90% of human exposure to cadmium is through food, and that cadmium within rice grains can be a major contributor to that dietary source. In this study genome wide association (GWA) mapping was conducted on the Bengal and Assam Aus Panel (BAAP) of rice to identify quantitative trait loci and candidate genes for lowering grain cadmium. Field experiments were conducted over two years under two different irrigation systems: continually flooded (CF) and alternate wetting and drying (AWD). There was significant effects of water treatment, genotype, and genotype by water treatment interaction. Importantly, AWD increased grain cadmium, on average, by 49.6% and 108.8 % in year 1 and 2 respectively. There was between 4.6 to 28 fold variation in cadmium concentration. A total of 58 QTLs were detected but no loci are clearly specific to one water regime despite approximately 20% of variation attributable to genotype by water regime interaction. A number of QTLs were consistent across most water treatments and years. These included QTLs on chromosome 7 (7.23 – 7.61, 8.93 – 9.04, and 29.12 – 29.14 Mbp), chromosome 5 (8.66 – 8.72 Mbp), and chromosome 9 (11.46 – 11.64 Mbp). Further analysis of the loci on chromosome 7 (8.93 – 9.04 Mbp), identified the candidate gene OsNRAMP1 , where cultivars with a deletion upstream of the gene had higher concentrations of cadmium compared to the cultivars that did not have the deletion. The distribution of alleles within the BAAP suggest this QTL is easily detected in this population because it is composed of aus
cultivars. Local genome cluster analysis suggest high Cd alleles are uncommon, but should be avoided in breeding.
Original languageEnglish
Article number35
Number of pages16
Issue number3
Early online date10 Feb 2021
Publication statusPublished - 10 Feb 2021

Bibliographical note

Open Access via the Springer Compact Agreement

Plant material was imported into the UK under import licence IMP/SOIL/19/2014.
The authors would like to thank reviewers of the manuscript who helped improve the presentation.
The bulk of this work was supported by the Biotechnology and Biological Sciences Research Council, mostly from project BB/J003336/1. A small part of the work by AJT was supported by project BB/N013492/1 (NEWS-India-UK). PR was financially supported by a Royal Thai Government Scholarship and National Science and Technology Development Agency (NSTDA), Thailand and AAA supported by the Elphinstone Scholarship Scheme (University of Aberdeen).


  • Rice
  • cadmiun
  • genome wide association genetics
  • alternate wetting and drying
  • Cadmium
  • Alternate wetting and drying
  • Genome wide association genetics


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