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.

Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Intensive rice breeding over the past 50 y has dramatically increased productivity especially in the indica subspecies, but our knowledge of the genomic changes associated with such improvement has been limited. In this study, we analyzed low-coverage sequencing data of 1,479 rice accessions from 73 countries, including landraces and modern cultivars. We identified two major subpopulations, indica I (IndI) and indica II (IndII), in the indica subspecies, which corresponded to the two putative heterotic groups resulting from independent breeding efforts. We detected 200 regions spanning 7.8% of the rice genome that had been differentially selected between IndI and IndII, and thus referred to as breeding signatures. These regions included large numbers of known functional genes and loci associated with important agronomic traits revealed by genome-wide association studies. Grain yield was positively correlated with the number of breeding signatures in a variety, suggesting that the number of breeding signatures in a line may be useful for predicting agronomic potential and the selected loci may provide targets for rice improvement.

OsNRAMP5 contributes to manganese translocation and distribution in rice shoots.

Manganese (Mn) is an essential micronutrient for plants playing an important role in many physiological functions. OsNRAMP5 is a major transporter responsible for Mn and cadmium uptake in rice, but whether it is involved in the root-to-shoot translocation and distribution of these metals is unknown. In this work, OsNRAMP5 was found to be highly expressed in hulls. It was also expressed in leaves but the expression level decreased with leaf age. High-magnification observations revealed that OsNRAMP5 was enriched in the vascular bundles of roots and shoots especially in the parenchyma cells surrounding the xylem. The osnramp5 mutant accumulated significantly less Mn in shoots than the wild-type plants even at high levels of Mn supply. Furthermore, a high supply of Mn could compensate for the loss in the root uptake ability in the mutant, but not in the root-to-shoot translocation of Mn, suggesting that the absence of OsNRAMP5 reduces the transport of Mn from roots to shoots. The results suggest that OsNRAMP5 plays an important role in the translocation and distribution of Mn in rice plants in addition to its role in Mn uptake.

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.

Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism.

Plant metabolites are important to world food security in terms of maintaining sustainable yield and providing food with enriched phytonutrients. Here we report comprehensive profiling of 840 metabolites and a further metabolic genome-wide association study based on ∼6.4 million SNPs obtained from 529 diverse accessions of Oryza sativa. We identified hundreds of common variants influencing numerous secondary metabolites with large effects at high resolution. We observed substantial heterogeneity in the natural variation of metabolites and their underlying genetic architectures among different subspecies of rice. Data mining identified 36 candidate genes modulating levels of metabolites that are of potential physiological and nutritional importance. As a proof of concept, we functionally identified or annotated five candidate genes influencing metabolic traits. Our study provides insights into the genetic and biochemical bases of rice metabolome variation and can be used as a powerful complementary tool to classical phenotypic trait mapping for rice improvement.

OsNRAMP3 is a vascular bundles-specific manganese transporter that is responsible for manganese distribution in rice.

Manganese (Mn) is an essential trace element for plants. Recently, the genes responsible for uptake of Mn in plants were identified in Arabidopsis 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, OsNRAMP3, involved in Mn distribution. OsNRAMP3 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 OsNRAMP3 was absent, rice plants showed high sensitivity to Mn deficiency. Serious necrosis appeared on young leaves and root tips of the OsNRAMP3 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 osnramp3 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.