Biomass and elemental concentrations of 22 rice cultivars grown under alternate wetting and drying conditions at three field sites in Bangladesh.

As the global population grows, demand on food production will also rise. For rice, one limiting factor effecting production could be availability of fresh water, hence adoption of techniques that decrease water usage while maintaining or increasing crop yield are needed. Alternative wetting and drying (AWD) is one of these techniques. AWD is a method by which the level of water within a rice field cycles between being flooded and nonflooded during the growth period of the rice crop. The degree to which AWD affects cultivars differently has not been adequately addressed to date. In this study, 22 rice cultivars, mostly landraces of the aus subpopulation, plus some popular improved indica cultivars from Bangladesh, were tested for their response to AWD across three different field sites in Bangladesh. Grain and shoot elemental concentrations were determined at harvest. Overall, AWD slightly increased grain mass and harvest index compared to plants grown under continually flooded (CF) conditions. Plants grown under AWD had decreased concentrations of nitrogen in their straw compared to plants grown under CF. The concentration of elements in the grain were also affected when plants were grown under AWD compared to CF: Nickel, copper, cadmium and iron increased, but sodium, potassium, calcium, cobalt, phosphorus, molybdenum and arsenic decreased in the grains of plants grown under AWD. However, there was some variation in these patterns across different sites. Analysis of variance revealed no significant cultivar × treatment interaction, or site × cultivar × treatment interaction, for any of the plant mass traits. Of the elements analyzed, only grain cadmium concentrations were significantly affected by treatment × cultivar interactions. These data suggest that there is no genetic adaptation amongst the cultivars screened for response to AWD, except for grain cadmium concentration and imply that breeding specifically for AWD is not needed.

Role of LOTR1 in Nutrient Transport through Organization of Spatial Distribution of Root Endodermal Barriers.

The formation of Casparian strips and suberin lamellae at the endodermis limits the free diffusion of nutrients and harmful substances via the apoplastic space between the soil solution and the stele in roots [1-3]. Casparian strips are ring-like lignin polymers deposited in the middle of anticlinal cell walls between endodermal cells and fill the gap between them [4-6]. Suberin lamellae are glycerolipid polymers covering the endodermal cells and likely function as a barrier to limit transmembrane movement of apoplastic solutes into the endodermal cells [7, 8]. However, the current knowledge on the formation of these two distinct endodermal barriers and their regulatory role in nutrient transport is still limited. Here, we identify an uncharacterized gene, LOTR1, essential for Casparian strip formation in Arabidopsis thaliana. The lotr1 mutants display altered localization of CASP1, an essential protein for Casparian strip formation [9], disrupted Casparian strips, ectopic suberization of endodermal cells, and low accumulation of shoot calcium (Ca). Degradation by expression of a suberin-degrading enzyme in the mutants revealed that the ectopic suberization at the endodermal cells limits Ca transport through the transmembrane pathway, thereby causing reduced Ca delivery to the shoot. Moreover, analysis of the mutants showed that suberin lamellae function as an apoplastic diffusion barrier to the stele at sites of lateral root emergence where Casparian strips are disrupted. Our findings suggest that the transmembrane pathway through unsuberized endodermal cells, rather than the sites of lateral root emergence, mediates the transport of apoplastic substances such as Ca into the xylem.

The MYB36 transcription factor orchestrates Casparian strip formation.

The endodermis in roots acts as a selectivity filter for nutrient and water transport essential for growth and development. This selectivity is enabled by the formation of lignin-based Casparian strips. Casparian strip formation is initiated by the localization of the Casparian strip domain proteins (CASPs) in the plasma membrane, at the site where the Casparian strip will form. Localized CASPs recruit Peroxidase 64 (PER64), a Respiratory Burst Oxidase Homolog F, and Enhanced Suberin 1 (ESB1), a dirigent-like protein, to assemble the lignin polymerization machinery. However, the factors that control both expression of the genes encoding this biosynthetic machinery and its localization to the Casparian strip formation site remain unknown. Here, we identify the transcription factor, MYB36, essential for Casparian strip formation. MYB36 directly and positively regulates the expression of the Casparian strip genes CASP1, PER64, and ESB1. Casparian strips are absent in plants lacking a functional MYB36 and are replaced by ectopic lignin-like material in the corners of endodermal cells. The barrier function of Casparian strips in these plants is also disrupted. Significantly, ectopic expression of MYB36 in the cortex is sufficient to reprogram these cells to start expressing CASP1-GFP, correctly localize the CASP1-GFP protein to form a Casparian strip domain, and deposit a Casparian strip-like structure in the cell wall at this location. These results demonstrate that MYB36 is controlling expression of the machinery required to locally polymerize lignin in a fine band in the cell wall for the formation of the Casparian strip.

Large-scale plant ionomics.

Large-scale phenotyping methods are at the heart of efficiently deciphering the functions of genes and gene networks in the postgenomic era. In order to obtain meaningful results when comparing natural variants, and mutants and wild-types during large-scale quantitative analyses, necessary precautions must be employed throughout the whole process. Here, we describe large-scale elemental profiling in Arabidopsis thaliana and other genetic model organisms using high-throughput analytical methodologies. We also include a description of workflow management and data storage systems.

High-resolution genome-wide scan of genes, gene-networks and cellular systems impacting the yeast ionome.

BACKGROUND: To balance the demand for uptake of essential elements with their potential toxicity living cells have complex regulatory mechanisms. Here, we describe a genome-wide screen to identify genes that impact the elemental composition ('ionome') of yeast Saccharomyces cerevisiae. Using inductively coupled plasma - mass spectrometry (ICP-MS) we quantify Ca, Cd, Co, Cu, Fe, K, Mg, Mn, Mo, Na, Ni, P, S and Zn in 11890 mutant strains, including 4940 haploid and 1127 diploid deletion strains, and 5798 over expression strains. RESULTS: We identified 1065 strains with an altered ionome, including 584 haploid and 35 diploid deletion strains, and 446 over expression strains. Disruption of protein metabolism or trafficking has the highest likelihood of causing large ionomic changes, with gene dosage also being important. Gene over expression produced more extreme ionomic changes, but over expression and loss of function phenotypes are generally not related. Ionomic clustering revealed the existence of only a small number of possible ionomic profiles suggesting fitness tradeoffs that constrain the ionome. Clustering also identified important roles for the mitochondria, vacuole and ESCRT pathway in regulation of the ionome. Network analysis identified hub genes such as PMR1 in Mn homeostasis, novel members of ionomic networks such as SMF3 in vacuolar retrieval of Mn, and cross-talk between the mitochondria and the vacuole. All yeast ionomic data can be searched and downloaded at http://www.ionomicshub.org. CONCLUSIONS: Here, we demonstrate the power of high-throughput ICP-MS analysis to functionally dissect the ionome on a genome-wide scale. The information this reveals has the potential to benefit both human health and agriculture.

Bioavailability of arsenic in soil: pilot study results and design considerations.

Bioavailability of arsenic (As) from ingested soil is estimated in a two-period experimental study involving 11 subjects/period. In the first period, a 7-day mass-balance study measured As in food/beverages, urine, and stool to estimate bioavailability of As in food and beverages. Food/beverage As bioavailability (percentage ingested that is not in stool samples) is estimated as 91.0% with a 95% confidence interval given by (84.1%, 97.9%). In the second 7-day study period, subjects were placed on an As suppression diet. In the evening of day 2, each subject ingested a capsule containing 0.63 g of soil, including approximately 111.7 µg of soil-As. The bioavailability estimate of As from food and beverage ingestion during the first 2 days of the second period was 89.7%. Bioavailability of soil-As was estimated over the 5-day period following capsule ingestion, accounting for estimated bioavailability of food/beverage As. Assuming analytic recovery rates of As from combined soil and food/beverage samples are equal, soil-As bioavailability is estimated as 48.7% (95% CI [36.2%, 61.3%]). Relative to bioavailability of As from food/beverage sources, soil-As is estimated to be 54.3% (95% CI [40.3%, 68.4%]) as bioavailable.