Genome-Wide Association Studies Reveal the Genetic Basis of Ionomic Variation in Rice

Rice (Oryza sativa) is an important dietary source of both essential micronutrients and toxic trace elements for humans. The genetic basis underlying the variations in the mineral composition, the ionome, in rice remains largely unknown. Here, we describe a comprehensive study of the genetic architecture of the variation in the rice ionome performed using genome-wide association studies (GWAS) of the concentrations of 17 mineral elements in rice grain from a diverse panel of 529 accessions, each genotyped at ∼6.4 million single nucleotide polymorphism loci. We identified 72 loci associated with natural ionomic variations, 32 that are common across locations and 40 that are common within a single location. We identified candidate genes for 42 loci and provide evidence for the causal nature of three genes, the sodium transporter gene Os-HKT1;5 for sodium, Os-MOLYBDATE TRANSPORTER1;1 for molybdenum, and Grain number, plant height, and heading date7 for nitrogen. Comparison of GWAS data from rice versus Arabidopsis (Arabidopsis thaliana) also identified well-known as well as new candidates with potential for further characterization. Our study provides crucial insights into the genetic basis of ionomic variations in rice and serves as an important foundation for further studies on the genetic and molecular mechanisms controlling the rice ionome

Preparation and Laboratory Testing of Polymeric Scale Inhibitor Colloidal Materials for Oilfield Mineral Scale Control

Mineral scale refers to the hard crystalline inorganic solid deposit from the water phase. Although scale formation is very common in the natural environment, deposited scale particles can seriously threaten the integrity and safety of various industries, particularly oilfield productions. Scale deposition is one of the three most serious water-related production chemistry threats in the petroleum industry. The most commonly adopted engineering approach to control the scale threat is chemical inhibition by applying scale inhibitor chemicals. Aminophosphonates and polymeric inhibitors are the two major groups of scale inhibitors. To address the drawbacks of conventional inhibitors, scale inhibitor colloidal materials have been prepared as an alternative delivery vehicle of inhibitors for scale control. Quite a few studies have reported on the laboratory synthesis and testing of scale inhibitor colloidal materials composed mainly of pre-precipitated metal-aminophosphonate solids. However, limited research has been conducted on the preparation of polymeric inhibitor-based colloidal materials. This study reports the synthesis approach and laboratory testing of novel polystyrene sulfonate (PSS) based inhibitor colloidal material. PSS was selected in this study due to its high thermal stability and calcium tolerance with no phosphorus in its molecule. Both precipitation and surfactant surface modification methods were employed to prepare a barium-PSS colloidal inhibitor (BaPCI) material with an average diameter of several hundred nanometers. Experimental results indicate that the prepared BaPCI material has a decent migration capacity in the formation medium, and this material is superior to the conventional PSS inhibitor in terms of inhibitor return performance. The prepared novel BaPCI material has a great potential to be adopted for field scale control where environmentally friendly, thermal stable, and/or calcium tolerating requirements should be satisfied. This study further expands and promotes our capacity to fabricate and utilize functional colloidal materials for mineral scale control

Seawater carbonate chemistry and carbon and nitrogen fixation in the hermatypic coral Galaxea fascicularis

The supply of metabolites from symbionts to scleractinian corals is crucial to coral health. Members of the Symbiodiniaceae can enhance coral calcification by providing photosynthetically fixed carbon (PFC) and energy, whereas dinitrogen (N2)-fixing bacteria can provide additional nutrients such as diazotrophically-derived nitrogen (DDN) that sustain coral productivity especially when alternative external nitrogen sources are scarce. How these mutualistic associations benefit corals in the future acidifying ocean is not well understood. In this study, we investigated the possible effects of ocean acidification (OA; pHs 7.7 and 7.4 vs. 8.1) on calcification in the hermatypic coral Galaxea fascicularis with respect to PFC and DDN assimilation. Our measurements based on isotopic tracing showed no significant differences in the assimilation of PFC among different pH treatments, but the assimilation of DDN decreased significantly after 28 days of stress at pH 7.4. The decreased DDN assimilation suggests a nitrogenous nutrient deficiency in the coral holotiont, potentially leading to reduced coral calcification and resilience to bleaching and other stressful events. This contrasting impact of OA on carbon and N flux demonstrates the flexibility of G. fascicularis in coping with OA, apparently by sustaining a largely undamaged photosystem at the expense of N2 fixation machinery, which competes with coral calcification for energy from photosynthesis. These findings shed new light on the critically important but more vulnerable N cycling in hospite, and on the trade-off between coral hosts and symbionts in response to future climate change

OsNRAMP3 Is a Vascular Bundles-Specific Manganese Transporter That Is Responsible for Manganese Distribution in Rice

<div><p>Manganese (Mn) is an essential trace element for plants. Recently, the genes responsible for uptake of Mn in plants were identified in <i>Arabidopsis</i> and rice. However, the mechanism of Mn distribution in plants has not been clarified. In the present study we identified a natural resistance-associated macrophage protein (NRAMP) family gene in rice, <i>OsNRAMP3</i>, involved in Mn distribution. <i>OsNRAMP3</i> encodes a plasma membrane-localized protein and was specifically expressed in vascular bundles, especially in phloem cells. Yeast complementation assay showed that OsNRAMP3 is a functional Mn-influx transporter. When <i>OsNRAMP3</i> was absent, rice plants showed high sensitivity to Mn deficiency. Serious necrosis appeared on young leaves and root tips of the <i>OsNRAMP3</i> knockout line cultivated under low Mn conditions, and high Mn supplies could rescue this phenotype. However, the necrotic young leaves of the knockout line possessed similar levels of Mn to the wild type, suggesting that the necrotic appearance was caused by disturbed distribution of Mn but not a general Mn shortage. Additionally, compared with wild type, leaf Mn content in <i>osnramp3</i> plants was mostly in older leaves. We conclude that OsNRAMP3 is a vascular bundle-localized Mn-influx transporter involved in Mn distribution and contributes to remobilization of Mn from old to young leaves.</p></div

Subcellular localization of OsNRAMP3 protein.

<p>Subcellular localization of OsNRAMP3 protein was determined in <i>Arabidopsis</i> protoplasts. The confocal images were acquired using a confocal laser scanning microscope (TCS SP2; Leica).</p

Complementation assay of <i>OsNRAMP3</i> on Mn-uptake deficient yeast mutant strain.

<p>(A) Yeast mutant <i>Δsmf1</i> and its wild type (WT) cells containing <i>pYES2</i> (vector), <i>OsNRAMP3</i> or <i>AtNRAMP1</i> (positive control) grown on synthetic defined (SD)-Ura plates with different EGTA supplies and 2% galactose. (B) Metal determination in <i>Δsmf1</i> and its wild-type cells containing <i>pYES2</i>, <i>OsNRAMP3</i> or <i>AtNRAMP1</i> grown in liquid SD-Ura culture with 0.2 µM Mn supplies and 2% galactose. Data are means ± SD (n = 4).</p

Expression analysis of <i>OsNRAMP3</i> by real-time RT-PCR.

<p>(A) The relative expression level of <i>OsNRAMP3</i> in different rice tissues. C1: first culm; CII: second culm; CIII: third culm; B: leaf blade; P: panicle; SH: leaf sheath; R: root. (B) Transcripts of <i>OsNRAMP3</i> of different leaves under different Mn conditions. The leaves detected here were sampled from the same tiller of rice plants – with the first leaf the oldest and the fourth leaf the youngest and partly wrapped in the leaf sheath. The plants were cultivated hydroponically under normal conditions for two weeks and then shifted to Mn-replete or Mn-free conditions for an additional one week. ZH11: cv. Zhonghua 11. (C) Expression analysis of <i>OsNRAMP3</i> in different regions of the fourth leaf. (D and E) Kinetics of the response of <i>OsNRAMP3</i> to Mn or Fe deficiency in shoot (D) and root (E) of rice plants. The plants were cultivated hydroponically under normal conditions for two weeks and then shifted to different conditions for treatment. Data are means ± SD (n = 3).</p

Histochemical staining of GUS activity in rice plants transformed with the construct <i>OsNRAMP3</i>-promoter:<i>GUS</i>.

<p>(A) Root tip; (B) mature root at 2 cm from tip; (C) lateral root; (D) leaf sheath, ligule and auricle; (E) leaf blade; (F) partly enlarged view of E; (G) hull at heading stage; (H) endosperm and hull at 25 d after heading; (I) transverse section of root, as described in B; (J) high-magnification of I; (K) transverse section of leaf blade, as described in E; (L) detail of a large vascular bundle from K; (M) enlarged view of phloem region of L; and (N) high-magnification of a small vascular bundle from K. All samples except hulls and endosperm were harvested from rice plants grown hydroponically for three weeks under normal conditions. CV: commissural vein; SV: small vascular bundle; LV: large vascular bundle; xy: xylem; ph: phloem; cc: companion cells.</p

Determination of Mn concentration in wild type and <i>osnramp3</i> plants.

<p>Elemental analysis was performed by ICP-MS on roots (A) and shoots (B) of wild type or <i>osnramp3</i> plants grown for two weeks at three different Mn supplies after two weeks of normal conditional cultivation by hydroponics. Data are means ± SD (n = 3). One and two asterisks indicate values that are significantly different from wild type at P<0.05 and P<0.01, respectively (by <i>t</i>-test).</p

Identification of the knockout line of <i>OsNRAMP3</i>.

<p>(A) The structure of <i>OsNRAMP3</i>. <i>OsNRAMP3</i> contains 13 exons and 12 introns, and a T-DNA inserted into the 12^th exon of osnramp3 mutant plants. (B) The determination of accumulation of <i>OsNRAMP3</i> in <i>osnramp3</i> plants by RT-PCR. (C) Phenotypic analysis of knockout line of <i>OsNRAMP3</i>. The plants were cultivated hydroponically under normal conditions for two weeks and then shifted to different Mn supplies for an additional two weeks. Three levels of Mn were applied: 0.08 µM (a), 8 µM (b) and 800 µM (c). The general condition for growth of plants in the three Mn treatments was photographed (d). Careful observations were performed on roots (e) and leaves (f) of wild type and <i>osnramp3</i> plants at 0.08 µM Mn supply. The red arrow indicates the necrotic area that appeared in <i>osnramp3</i> roots. In (f), the left leaves are from wild type and the right leaves from <i>osnramp3</i>; 1–4 leaves were from the same tillers, with 1-leaf the oldest and 4-leaf the youngest.</p