Characterizing genetic & soil induced variation in arsenic uptake translocation & metabolism in rice to mitigate arsenic contamination in Asia

Lead Research Organisation: Rothamsted Research
Department Name: Sustainable Soils and Grassland Systems

Abstract

Rice is the dietary staple of South East Asia. Rice assimilates much more arsenic from soils that other grain crops as it is cultivated anaerobically, rather than aerobically. Anaerobic cultivation leads to much greater arsenic mobilization, and thus greater plant availability. Even at background levels of arsenic in rice, rice contributes considerably to human dietary exposure of this carcinogenic element. Unfortunately, extensive areas of land in rice producing regions have been contaminated through irrigation of paddy fields with groundwaters elevated in arsenic and through contamination from wastewater from base and precious metal activities. For example, irrigation water contamination has resulted in the contamination of rice of around 40 million Bangladeshis, whilst 20 million Chinese are dependent on arsenic contaminated paddies as a result of pollution from mining. On these contaminated soils, levels of arsenic can rise considerably in rice grain, greatly increasing dietary exposure to arsenic. The extent and nature of the soil contamination mean that it is not possible to remove arsenic from these soils, and also, given the high population densities supported by these agroecosystems, the contaminated soils must still be kept in rice production. Through initial trials we have revealed that there is considerable genetic variation in arsenic uptake, transport and metabolism in rice. This project will identify the genes responsible for this variation and locate them on the rice genome to enable rice to be bred that has low grain arsenic levels, with a high proportion of this grain arsenic being present as less toxic organic species. Field experiments will be conducted in Bangladesh, West Bengal and China to determine the variation in arsenic grain uptake and metabolism that exists in locally adapted species for plants grown both on groundwater and mine contaminated soils, to enable selection for further breeding. These trials will include mapping populations whose parents differ in arsenic uptake and metabolism, and through genetic analysis, the genes responsible for traits leading to low grain arsenic with more desirable metabolites will be identified and characterised. This genetic information will also enable breeding of rice with characteristics that make it suitable for use on arsenic contaminated soils. Soil factors affecting arsenic uptake by rice will also be investigated to determine if management practices can also lower the arsenic accumulation into rice grain.

Technical Summary

Widespread arsenic contamination of paddy fields in South East Asia has led to elevated rice grain levels of this carcinogenic element. In arsenic affected regions, dietary exposure from arsenic from rice is above World Health Organization limits. Our scoping studies where we grew a range of cultivars on one soil type and, also, where we have looked at variation in arsenic tolerance in mapping populations, have shown that there is considerable genetic variation in arsenic uptake, metabolism and export to the grain. We propose to conduct field trials to determine which currently grown local cultivars are most suitable for arsenic contaminated soils. These cultivars may be used in future low-arsenic breeding programs. We will also study the genetics of arsenic accumulation and speciation by conducting both quantitative trait loci (QTL) analysis on mapping populations and association genetic mapping using a collection of diverse rice cultivars. This will locate the genes responsible for the traits, and provide a list of candidate genes based on position on the genome. Gene expression studies, including the Affymetrix whole genome array, will be used to identify strong candidate genes within these lists, and when combined with the study of available mutants we may even prove the identity of the genes responsible. The project will also ascertain the soil factors that determine the bioavailability of arsenic in soils polluted from irrigation water or via mine waste to determine if different strategies are required for these contrastingly contaminated soils in order to deliver grain low in arsenic.
 
Description 1) Identification of rice cultivars which may be used in rice breeding programmes to reduce the concentration of arsenic in rice.



2)Identified that rice land races in the Bay of Bengal have higher grain arsenic content that high yielding locally improved cultivars. This has direct implications for what cultivars to use for low arsenic (about 30% lower) in the field, and research that has been directly fed back into rice breeders and those implementing rice breeding policy in the Bay of Bengal. A molecular breeding programme has been initiated in West Bengal under EU funding in which a local landrace with generally high grain arsenic has been crossed with tropical japonica cultivars with generally low grain arsenic. Genetic mapping of grain arsenic and further breeding are being conducted now.



3)The work has directly contributed to the WHO convening a meeting to set arsenic standards in food stuffs, a step that will have global implications for the health of the poor. The WHO has already suspended it Maximum Tolerable Daily Intake (MTDI) following our findings, and is now under obligation to replace this. This will provide an impetus and a framework for breeding and changes in paddy field management globally.



4)Besides finding that arsenic was a problem in rice per se, we have shown that it also has major impacts on grain nutrition, and this has had a major impact on how rice must be managed, leading for it being a reason raison d'etre in new field based approaches such as Alternate Wetting and Drying (AWD).



5)The rice Genome-Wide Association Studies (GWAS) analysis, as well as illuminating plant arsenic regulation, also yielded quantitative trait loci (QTLs) for yield and key mineral nutrients. We have also linked up with an American study who had independently being using the same rice GWAS panel at an number of US locations. The information to be mined from these data sets is considerable (we have concentrated on arsenic issues to date) and will provide impetus to improving the quality and productivity of rice across a range of key traits. For example, QTLs have been detected for grain element composition including grain arsenic using existing mapping populations. In addition, grain element composition has been assessed in an association mapping population (developed by Cornell University) and the data are being analysed now for grain arsenic and other grain element QTLs thought collaboration with Cornell. The cultivar Azucena, which is one of the parents of one of the mapping population used has been sequenced and the information is being compiled in advance of publication in open access depositories.



6)Our research has shown that the paddy soils in the Bengal delta irrigated with contaminated groundwater have a higher arsenic bioavailability than soils contaminated by other sources of arsenic. We have identified anaerobic arsenic mobilisation in flooded paddy soils as the main reason for excessive arsenic accumulation in rice grain.



7)We have identified a major uptake pathway of arsenic (arsenite and methylated arsenic species) by rice through silicon transporter proteins. This work has shown that silicon availability in paddy soil is an important factor controlling arsenic accumulation by rice and silicon fertilisation may be an effective way to reduce arsenic accumulation by rice.
Exploitation Route 1) This work has led to the idea of using practical water management, such as AWD, to reduce arsenic accumulation by rice, in addition to the benefit of saving water

2) Identification of rice cultivars which may be used in rice breeding programmes to reduce the concentration of arsenic in rice.


The rice Genome-Wide Association Studies (GWAS) analysis, as well as illuminating plant arsenic regulation, also yielded quantitative trait loci (QTLs) for yield and key mineral nutrients. We have also linked up with an American study who had independently being using the same rice GWAS panel at an number of US locations. The information to be mined from these data sets is considerable (we have concentrated on arsenic issues to date) and will provide impetus to improving the quality and productivity of rice across a range of key traits. For example, QTLs have been detected for grain element composition including grain arsenic using existing mapping populations. In addition, grain element composition has been assessed in an association mapping population (developed by Cornell University) and the data are being analysed now for grain arsenic and other grain element QTLs thought collaboration with Cornell. The cultivar Azucena, which is one of the parents of one of the mapping population used has been sequenced and the information is being compiled in advance of publication in open access depositories.
Sectors Agriculture, Food and Drink,Environment
 
Description Characterizing genetic & soil induced variation in arsenic uptake translocation & metabolism in rice to mitigate arsenic contamination in Asia
Geographic Reach Multiple continents/international 
Policy Influence Type Participation in advisory committee
Impact The work has directly contributed to the WHO convening a meeting to set arsenic standards in food stuffs, a step that will have global implications for the health of the poor. The WHO has already suspended it Maximum Tolerable Daily Intake (MTDI) following our findings, and is now under obligation to replace this. This will provide an impetus and a framework for breeding and changes in paddy field management globally.
 
Description Arsenic Speciation in Phloem and Xylem Exudates 
Organisation University of Science and Technology of China USTC
Country China, People's Republic of 
Sector Academic/University 
PI Contribution How arsenic (As) is transported in phloem was unknown. To help answer this question, we quantified the chemical species of As in phloem and xylem exudates of castor bean. As(V) was the main species in xylem exudate (55%?83%) whereas As(III) predominated in phloem exudate (70%?94%). Analyses of phloem exudate identified high concentrations of reduced and oxidized glutathione and some oxidized phytochelatin,but no As(III)-thiol complexes. It is thought that As(III)-thiol complexes would not be stable in the alkaline conditions of phloem sap. Small concentrations of oxidized glutathione and oxidized phytochelatin were found in xylem exudate, where there was also no evidence of As(III)-thiol complexes. MMA(V) was partially reduced to MMA(III) in roots, but only MMA(V) was found in xylem and phloem exudate. Despite the smallest uptake among the four As species supplied to plants, dimethylarsinic acid was most efficiently transported in both xylem and phloem, and its phloem concentration was 3.2 times that in xylem. Our results show that free inorganic As, mainly As(III), was transported in the phloem of castor bean.
Start Year 2008
 
Description Aspects of arsenic in rice 
Organisation University of Science and Technology of China USTC
Country China, People's Republic of 
Sector Academic/University 
PI Contribution PhD training
Start Year 2008
 
Description Aspects of arsenic in rice 
Organisation Xinjiang University
Country China, People's Republic of 
Sector Academic/University 
PI Contribution 12 months PhD training
Start Year 2008
 
Description Bioavailability of arsenic in soils from Bangladesh 
Organisation Sher-e-Bangla Agricultural University
Country Bangladesh, People's Republic of 
Sector Academic/University 
PI Contribution Rothamsted International Fellowship for 1 year
Start Year 2008
 
Description Bioavailability of arsenic in soils from Bangladesh 
Organisation Sher-e-Bangla Agricultural University
Country Bangladesh, People's Republic of 
Sector Academic/University 
PI Contribution Rothamsted International Fellowship
Start Year 2008
 
Description Investigating the sources and uptake of methylated arsenic in rice. 
Organisation Agricultural University of Hebei
Country China, People's Republic of 
Sector Academic/University 
PI Contribution 1 year Rothamsted International Fellowship
Start Year 2008
 
Description Rapid reduction of arsenate in the medium mediated by plant roots 
Organisation University of Science and Technology of China USTC
Country China, People's Republic of 
Sector Academic/University 
PI Contribution Tomato and rice roots rapidly reduce arsenate to arsenite, some of which is actively effluxed to the medium. The study reveals a new aspect of As metabolism in plants.
Start Year 2008
 
Description Rapid reduction of arsenate in the medium mediated by plant roots 
Organisation University of Science and Technology of China USTC
Country China, People's Republic of 
Sector Academic/University 
PI Contribution ? Microbes detoxify arsenate by reduction and efflux of arsenite. Plants have a high capacity to reduce arsenate, but arsenic efflux has not been reported. ? Arsenite remained stable in the nutrient solution, whereas arsenate was rapidly reduced to arsenite. Microbes and root exudates contributed little to the reduction of external arsenate. Arsenite was the predominant species in roots and xylem sap. Phosphate inhibited arsenate uptake and the appearance of arsenite in the nutrient solution, but the reduction was near complete in 24 h in both ?P- and +P-treated tomato. Phosphate had a greater effect in rice than tomato. Efflux of both arsenite and arsenate was observed; the former was inhibited and the latter enhanced by the metabolic inhibitor carbonylcyanide chlorophenylhydrazone. ? Tomato and rice roots rapidly reduce arsenate to arsenite, some of which is actively effluxed to the medium. The study reveals a new aspect of As metabolism
Start Year 2008
 
Description Rice is more efficient in arsenite uptake and translocation than wheat or barley 
Organisation Xinjiang University
Country China, People's Republic of 
Sector Academic/University 
PI Contribution The results show that rice is more efficient than wheat or barley in arsenite uptake and translocation, probably through the highly efficient pathway for silicon.
Start Year 2008
 
Description The Rice Aquaporin Lsi1 Mediates Uptake of Methylated As species 
Organisation Nanjing University of Information Science and Technology (NUIST)
Country China, People's Republic of 
Sector Academic/University 
PI Contribution The results demonstrate that Lsi1 mediates the uptake of undissociated methylated As in rice roots.
Start Year 2008
 
Description The Rice Aquaporin Lsi1 Mediates Uptake of Methylated arsenic species 
Organisation Nanjing University of Information Science and Technology (NUIST)
Country China, People's Republic of 
Sector Academic/University 
PI Contribution publciation of research in International journals
Start Year 2008
 
Description ARSENIC 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Participants in your research and patient groups
Results and Impact A dissemination workshop was held in Dhaka October 2010 which had a large training and knowledge transfer component, including creation of a dedicated website.

no actual impacts realised to date
Year(s) Of Engagement Activity 2008
 
Description Arsenic in Rice 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Interview

no actual impacts realised to date
Year(s) Of Engagement Activity 2011
 
Description Arsenic in rice 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact Tak sparked questions an ddiscussions

None to date
Year(s) Of Engagement Activity 2011
 
Description Arsenic in rice paddy 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Interview

no actual impacts realised to date
Year(s) Of Engagement Activity 2011
 
Description Aspects of arsenic in rice 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Interview

no actual impacts realised to date
Year(s) Of Engagement Activity 2011
 
Description BBC Three Counties Radio, Rothamsted Impact in Environment and Ecology Research, August. 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Media (as a channel to the public)
Results and Impact NA
Year(s) Of Engagement Activity 2010
 
Description Cancer rates attributable to As in rice vary globally 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Arsenic Crisis Newsletter & Discussion

no actual impacts realised to date
Year(s) Of Engagement Activity 2009
 
Description Cancer rates attributable to As in rice vary globally 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Participants in your research or patient groups
Results and Impact News article

no actual impacts realised to date
Year(s) Of Engagement Activity 2009
URL http://tech.dir.groups.yahoo.com/group/arsenic-crisis/message/766
 
Description Characterising genetic and soil induced variation in arsenic uptake, translocation and metabolism in rice to mitigate arsenic contamination in Asia 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Participants in your research and patient groups
Results and Impact A dissemination workshop was held in Dhaka October 2010 which had a large training and knowledge transfer component, including creation of a dedicated website

no actual impacts realised to date
Year(s) Of Engagement Activity 2010
URL http://www.abdn.ac.uk/arsenic/HomePage.html
 
Description Foods Matter, Coeliacs Matter, Free From Foods Matter and Free From Recipes Matter 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Newsletter:

no actual impacts realised to date
Year(s) Of Engagement Activity 2010
URL http://www.foodsmatter.com/allergy_intolerance/cow_milk_all_management/articles/rice
 
Description In flooded paddies, rice with high arsenic 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Newspaper report

no actual impacts realised to date
Year(s) Of Engagement Activity 2008
 
Description In flooded paddies, rice with high arsenic 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Article in Newspaper Article

no actual impacts realised to date
Year(s) Of Engagement Activity 2008
 
Description Molecular and physiological approaches to reduce accumulation of non-nutritive elements in grain for improved human health. Inaugural meeting of EU COST 0905 . Antlya, Turkey 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? Yes
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact The main objective of this Action is to evaluate and substantiate the scientific knowledge relevant for GMT biosafety protocols by putting together already existing information generated in various European countries as basis for future EU policy and regulation for the environmental impact assessment and the safe development and practical use of GMTs.

Memorandum of Understanding for the implementation of a European Concerted Research Action designated as COST Action FP0905: Biosafety of forest transgenic trees: improving the scientific basis for safe tree development and implementation of EU policy directives
Delegations
Year(s) Of Engagement Activity 2010
 
Description Open Day- Selenium in our diet and Arsenic in our rice 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Members of the public were very interested in finding out more about where to find essential elements for their health

NA
Year(s) Of Engagement Activity 2010
 
Description Rice and arsenic - what it do about it 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Article

no actual impacts realised to date
Year(s) Of Engagement Activity 2010
URL http://www.foodsmatter.com/allergy_intolerance/cow_milk_all_management/articles/rice_arsenic_2_03.10...
 
Description Silicon reduces arsenic accumulation in rice 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact Article in Chemistry and Industry Chemistry and Industry issue 15

no actual impacts realised to date
Year(s) Of Engagement Activity 2008
 
Description The problem of arsenic in rice 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Interview

no actual impacts realised to date
Year(s) Of Engagement Activity 2012
 
Description Water-stingy Agriculture reduces arsenic in rice markedly 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Participants in your research or patient groups
Results and Impact Newspaper article

no actual impacts realised to date
Year(s) Of Engagement Activity 2008
 
Description Water-stingy Agriculture reduces arsenic in rice markedly 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact Article

no actual impacts realised to date
Year(s) Of Engagement Activity 2008
 
Description http://irri.org/news-events/irri-news/bangladesh-international-workshop-on-arsenic-held 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact The event was inaugurated by Imamul Haque, chair of the Bangladesh Council of Scientific and Industrial Research and who has a long experience on arsenic research.
The following papers were presented: (1) arsenic and rice research in Bangladesh, by Rafiqul Islam; (2) arsenic bioavailability in paddy soil, by Jacqueline Stroud; (3) genetics of arsenic uptake and accumulation of arsenic in rice, by Gareth Norton; (4) straight head disease in rice, by Hesham Agrama; (5) arsenic in rice research in China, by Yongguan Zhu; (6) arsenic in rice research in India, R.D. Tripathi; and (7) IRRI's arsenic in rice research, by Ismail Abdelbagi.



A keynote paper was also presented by Dr. Islam, senior manager of the project Reducing risks of Arsenic contamination for poor people. The project is managed by M.A. Hamid Miah, IRRI Liaison Scientist for Bangladesh, and is funded by IFAD. The paper, which highlighted the status of arsenic research in Bangladesh, indicated that arsenic accumulation in irrigated rice soil is increasing and 15% of land in the country is affected by arsenic.



The work under the IFAD-funded arsenic project has gone on for about 22 months and is implemented in collaboration with Bangladesh Rice Research Institute. One of its findings is that arsenic uptake in rice plants varied with variety and location.



The workshop concluded with the statement that if a less arsenic-loving rice variety, such as BRRI dhan 47, is cultivated after harvesting mustard and irrigation using AWD technology, ingestion of arsenic by rice consumers in arsenic-prone areas may be reduced considerably.




webcast of the workshop

no actual impacts realised to date
Year(s) Of Engagement Activity 2010
URL http://irri.org/news-events/irri-news/bangladesh-international-workshop-on-arsenic-held