Cereal grains are the dominant source of cadmium in the human diet, with rice being to the fore. Here we explore the effect of geographic, genetic, and processing (milling) factors on rice grain cadmium and rice consumption rates that lead to dietary variance in cadmium intake. From a survey of 12 countries on four continents, cadmium levels in rice grain were the highest in Bangladesh and Sri Lanka, with both these countries also having high per capita rice intakes. For Bangladesh and Sri Lanka, there was high weekly intake of cadmium from rice, leading to intakes deemed unsafe by international and national regulators. While genetic variance, and to a lesser extent milling, provide strategies for reducing cadmium in rice, caution has to be used, as there is environmental regulation as well as genetic regulation of cadmium accumulation within rice grains. For countries that import rice, grain cadmium can be controlled by where that rice is sourced, but for countries with subsistence rice economies that have high levels of cadmium in rice grain, agronomic and breeding strategies are required to lower grain cadmium.

The concentration of arsenic (As) in rice grains has been identified as a risk to human health. The high proportion of inorganic species of As (As i ) is of particular concern as it is a nonthreshold, class 1 human carcinogen. To be able to breed rice with low grain As, an understanding of genetic variation and the effect of different environments on genetic variation is needed. In this study, 13 cultivars grown at two field sites each in Bangladesh, India, and China are evaluated for grain As. There was a significant site, genotype, and site by genotype interaction for total grain As. Correlations were observed only between sites in Bangladesh and India, not between countries or within the Chinese sites. For seven cultivars the As was speciated which revealed significant effects of site, genotype, and site by genotype interaction for percentage As i . Breeding low grain As cultivars that will have consistently low grain As and low As i , over multiple environments using traditional breeding approaches may be difficult, although CT9993-5-10-1-M, Lemont, Azucena, and Te-qing in general had low grain As across the field sites.

BackgroundGenetic diversity among rice cultivars from Bangladesh and North East India was assessed using a custom 384-SNP microarray assay. A total of 511 cultivars were obtained from several sources, choosing landraces likely to be from the aus subpopulation and modern improved cultivars from Bangladesh. Cultivars from the OryzaSNP set and Rice Diversity Panel 1 (RDP1) were also included for reference.ResultsThe population analysis program STRUCTURE was used to infer putative population groups in the panel, revealing four groups: indica (76 cultivars), japonica (55) and two distinct groups within the aus subpopulation (aus-1 = 99, aus-2 = 151). Principal Component Analysis was used to confirm the four population groups identified by STRUCTURE. The analysis revealed cultivars that belonged to neither aus-1 nor aus-2 but which are clearly aus based on the combined probabilities of their membership of the two aus groups which have been termed aus-admix (96). Information obtained from the panel of 511 cultivars was used to assign rice groups to 74 additional landraces obtained from Assam and West Bengal. While both the aus-1 and aus-2 groups were represented approximately equally in India, aus-2 (which includes cultivar N 22) was more common in Bangladesh, but was not found at all in West Bengal.ConclusionsExamining the distribution of landrace names within theaus-1 and aus-2 groups suggests that aus-1 is associated with the term “boro”, a word used to describe a winter growing season in Bangladesh and Assam. The information described here has been used to select a population of 300 cultivars for Genome Wide Association studies of the aus rice subpopulation.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-015-0068-z) contains supplementary material, which is available to authorized users.

Summary• The genetics of arsenic tolerance in plants has not been extensively studied and no arsenic tolerance gene has been genetically mapped.• Screening 20 diverse genotypes of rice for reduced root growth in 13.3 µ M arsenate identified marked differences in tolerance. The most sensitive variety, Dawn, is known to be highly susceptible to straighthead, a condition linked to arsenic contamination of soil.• Screening 108 recombinant inbred lines of the Bala × Azucena mapping population revealed the presence of a major gene, AsTol , which mapped between markers RZ516 and RG213 on chromosome 6.• This gene is a good target for further characterisation. It should prove valuable for investigations into the physiological and molecular mechanism behind arsenic tolerance in plants and may lead to strategies aimed at breeding for arsenic contaminated regions. © New Phytologist (2004) 163 : 45 -49

The crop management practice of alternate wetting and drying (AWD) is being promoted by IRRI and the national research and extension program in Bangladesh and other parts of the world as a water‐saving irrigation practice that reduces the environmental impact of dry season rice production through decreased water usage, and potentially increases yield. Evidence is growing that AWD will dramatically reduce the concentration of arsenic in harvested rice grains conferring a third major advantage over permanently flooded dry season rice production. AWD may also increase the concentration of essential dietary micronutrients in the grain. However, three crucial aspects of AWD irrigation require further investigation. First, why is yield generally altered in AWD? Second, is AWD sustainable economically (viability of farmers' livelihoods) and environmentally (aquifer water table heights) over long‐term use? Third, are current cultivars optimized for this irrigation system? This paper describes a multidisciplinary research project that could be conceived which would answer these questions by combining advanced soil biogeochemistry with crop physiology, genomics, and systems biology. The description attempts to show how the breakthroughs in next generation sequencing could be exploited to better utilize local collections of germplasm and identify the molecular mechanisms underlying biological adaptation to the environment within the context of soil chemistry and plant physiology.

Arsenic (As) contamination of paddy soils threatens rice cultivation and the health of populations relying on rice as a staple crop. In the present study, isotopic dilution techniques were used to determine the chemically labile (E value) and phytoavailable (L value) pools of As in a range of paddy soils from Bangladesh, India, and China and two arable soils from the UK varying in the degree and sources of As contamination. The E value accounted for 6.2-21.4% of the total As, suggesting that a large proportion of soil As is chemically nonlabile. L values measured with rice grown under anaerobic conditions were generally larger than those under aerobic conditions, indicating increased potentially phytoavailable pool of As in flooded soils. In an incubation study, As was mobilized into soil pore water mainly as arsenite under flooded conditions, with Bangladeshi soils contaminated by irrigation of groundwater showing a greater potential of As mobilization than other soils. Arsenic mobilization was best predicted by phosphate-extractable As in the soils.

Sesame is an important ancient oilseed crop of high medicinal value. In the present study, 37 characters including both quantitative and qualitative traits of sixty genotypes were characterized following IPGRI morphological descriptors for sesame. Multivariate analysis was computed to distinguish the varieties into different groups. Though thirty six microsatellite markers including genomic and Est-SSR markers were initially selected, but, finally, the accessions were genotyped by eight polymorphic primers. Altogether, 27 alleles were detected among the 60 genotypes, with an average of 3.37 alleles per locus. The number of alleles ranged from 2 to 6 alleles. From data of microsatellite markers, dissimilarity coefficients between varieties were computed following Jaccard's coefficient method. Principal co-ordinate analysis was used to represent the varieties in bi-directional space. Dendrogram was constructed using NJ method based on dissimilarity matrix. Cluster analysis based on morphological and molecular marker classified sesame genotypes into two major groups. Mantel test showed an insignificant correlation between phenotypic and molecular marker information. The genotypes belonging to the same geographical area did not always occupy the same cluster. The results confirmed that both genetic and phenotypic diversity in a combined way could efficiently evaluate the variation present in different sesame accessions in any breeding program.

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