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

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.

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.