Lijuan Zhang

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

Wild relatives of crops are an important source of genetic diversity for agriculture, but their gene repertoire remains largely unexplored. We report the establishment and analysis of a pan-genome of Glycine soja, the wild relative of cultivated soybean Glycine max, by sequencing and de novo assembly of seven phylogenetically and geographically representative accessions. Intergenomic comparisons identified lineage-specific genes and genes with copy number variation or large-effect mutations, some of which show evidence of positive selection and may contribute to variation of agronomic traits such as biotic resistance, seed composition, flowering and maturity time, organ size and final biomass. Approximately 80% of the pan-genome was present in all seven accessions (core), whereas the rest was dispensable and exhibited greater variation than the core genome, perhaps reflecting a role in adaptation to diverse environments. This work will facilitate the harnessing of untapped genetic diversity from wild soybean for enhancement of elite cultivars.

Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing

BackgroundArtificial selection played an important role in the origin of modern Glycine max cultivars from the wild soybean Glycine soja. To elucidate the consequences of artificial selection accompanying the domestication and modern improvement of soybean, 25 new and 30 published whole-genome re-sequencing accessions, which represent wild, domesticated landrace, and Chinese elite soybean populations were analyzed.ResultsA total of 5,102,244 single nucleotide polymorphisms (SNPs) and 707,969 insertion/deletions were identified. Among the SNPs detected, 25.5% were not described previously. We found that artificial selection during domestication led to more pronounced reduction in the genetic diversity of soybean than the switch from landraces to elite cultivars. Only a small proportion (2.99%) of the whole genomic regions appear to be affected by artificial selection for preferred agricultural traits. The selection regions were not distributed randomly or uniformly throughout the genome. Instead, clusters of selection hotspots in certain genomic regions were observed. Moreover, a set of candidate genes (4.38% of the total annotated genes) significantly affected by selection underlying soybean domestication and genetic improvement were identified.ConclusionsGiven the uniqueness of the soybean germplasm sequenced, this study drew a clear picture of human-mediated evolution of the soybean genomes. The genomic resources and information provided by this study would also facilitate the discovery of genes/loci underlying agronomically important traits.

Ion sieving in graphene oxide membranes via cationic control of interlayer spacing

Graphene oxide membranes—partially oxidized, stacked sheets of graphene—can provide ultrathin, high-flux and energy-efficient membranes for precise ionic and molecular sieving in aqueous solution. These materials have shown potential in a variety of applications, including water desalination and purification, gas and ion separation, biosensors, proton conductors, lithium-based batteries and super-capacitors. Unlike the pores of carbon nanotube membranes, which have fixed sizes, the pores of graphene oxide membranes—that is, the interlayer spacing between graphene oxide sheets (a sheet is a single flake inside the membrane)—are of variable size. Furthermore, it is difficult to reduce the interlayer spacing sufficiently to exclude small ions and to maintain this spacing against the tendency of graphene oxide membranes to swell when immersed in aqueous solution. These challenges hinder the potential ion filtration applications of graphene oxide membranes. Here we demonstrate cationic control of the interlayer spacing of graphene oxide membranes with ångström precision using K+, Na+, Ca2+, Li+ or Mg2+ ions. Moreover, membrane spacings controlled by one type of cation can efficiently and selectively exclude other cations that have larger hydrated volumes. First-principles calculations and ultraviolet absorption spectroscopy reveal that the location of the most stable cation adsorption is where oxide groups and aromatic rings coexist. Previous density functional theory computations show that other cations (Fe2+, Co2+, Cu2+, Cd2+, Cr2+ and Pb2+) should have a much stronger cation–π interaction with the graphene sheet than Na+ has, suggesting that other ions could be used to produce a wider range of interlayer spacings.

Nanoscale multiple gaseous layers on a hydrophobic surface

The nanoscale gas state at the interfaces of liquids (water, acid, and salt solutions) and highly oriented pyrolytic graphite (HOPG) was investigated via tapping-mode atomic force microscopy (AFM). For the first time, we report that the interfacial gases could form bilayers and trilayers, i.e., on the top of a flat gas layer, there are one or two more gas layers. The formation of these gas layers could be induced by a local supersaturation of gases, which can be achieved by (1) temperature difference between the liquids and the HOPG substrates or (2) exchange ethanol with water. Furthermore, we found that the gas layers were less stable than spherical bubbles. They could transform to bubbles with time or under the perturbation of the AFM tip.

Mechanical mapping of nanobubbles by PeakForce atomic force microscopy

The mechanical behavior of nanobubbles represents their physical essence and has been thought to be closely related to their mysteriously long lifetimes. However, it is difficult to measure the mechanical properties of nanobubbles by conventional atomic force microscopy (AFM). In this paper, nanobubbles were investigated via a novel AFM imaging mode, PeakForce Quantitative Nano-Mechanics (PF-QNM), at the interface of water and highly oriented pyrolytic graphite (HOPG). High resolution images of the nanobubbles in true-contact were achieved by PF-QNM and compared with those obtained by tapping mode AFM (TM-AFM) in the same area. From the force curves simultaneously captured during the PF-QNM imaging processes, the stiffness of the nanobubbles was derived and mapped, ranging usually from 60 to 120 pN nm−1, indicating that the gas–water interface of nanobubbles has similar mechanical properties to those of microbubbles. Interestingly, a size dependence of the stiffness was found and the small nanobubbles had a higher stiffness.

The length scales for stable gas nanobubbles at liquid/solid surfaces

We present results focusing on whether gas bubbles are stable at all length scales at liquid/solid surfaces. Tapping mode atomic force microscopy was used to observe nanoscale bubbles of air or hydrogen produced by two methods on hydrophilic and hydrophobic solid surfaces. The observed nanobubbles of air or hydrogen always have curvature radii of less than 2.0 μm and heights of less than 100 nm, suggesting the possible instability of these nanobubbles beyond these length scales. This is further supported by the observation of blank circular areas on the electrode surface, which are interpreted as footprints of departed large bubbles with curvature radii equal to or above 2.0 μm from the surface.

The Morphology and Stability of Nanoscopic Gas States at Water/Solid Interfaces

Nanoscale gas bubbles have surprising stability at water/solid surfaces. Herein, we summarize progress made on investigating gases at the water/solid interfaces on the nanometer scale. The gas states include nanobubbles, micropancakes, multiple gas layers and their coexistence; these were investigated from experimental and theoretical aspects. The stability of nanoscale gas bubbles may be attributed to high inner density, as observed in molecular dynamic simulations and theoretical analysis. Moreover, it was found that there were maximal length scales for stable nanobubbles, namely, 100 nm high and a curvature radius of 2 μm.

Interfacial Nanobubbles on Atomically Flat Substrates with Different Hydrophobicities

The dependence of the morphology of interfacial nanobubbles on atomically flat substrates with different wettability ranges was investigated by using PeakForce quantitative nanomechanics. Interfacial nanobubbles were formed and imaged on silicon nitride (Si3N4), mica, and highly ordered pyrolytic graphite (HOPG) substrates that were partly covered by reduced graphene oxide (rGO). The contact angles and sizes of those nanobubbles were measured under the same conditions. Nanobubbles with the same lateral width exhibited different heights on the different substrates, with the order Si3N4≈mica>rGO>HOPG, which is consistent with the trend of the hydrophobicity of the substrates.

Co-expression of G2-EPSPS and glyphosate acetyltransferase GAT genes conferring high tolerance to glyphosate in soybean

Glyphosate is a widely used non-selective herbicide with broad spectrum of weed control around the world. At present, most of the commercial glyphosate tolerant soybeans utilize glyphosate tolerant gene CP4-EPSPS or glyphosate acetyltransferase gene GAT separately. In this study, both glyphosate tolerant gene G2-EPSPS and glyphosate degraded gene GAT were co-transferred into soybean and transgenic plants showed high tolerance to glyphosate. Molecular analysis including PCR, Sothern blot, qRT-PCR, and Western blot revealed that target genes have been integrated into genome and expressed effectively at both mRNA and protein levels. Furthermore, the glyphosate tolerance analysis showed that no typical symptom was observed when compared with a glyphosate tolerant line HJ06-698 derived from GR1 transgenic soybean even at fourfold labeled rate of Roundup. Chlorophyll and shikimic acid content analysis of transgenic plant also revealed that these two indexes were not significantly altered after glyphosate application. These results indicated that co-expression of G2-EPSPS and GAT conferred high tolerance to the herbicide glyphosate in soybean. Therefore, combination of tolerant and degraded genes provides a new strategy for developing glyphosate tolerant transgenic crops.

The Role of Nanobubbles in the Precipitation and Recovery of Organic-Phosphine-Containing Beneficiation Wastewater

Dissolved air flotation (DAF) is broadly applied in wastewater treatment, especially for the recovery of organic pollution with low concentration. However, the mechanism of interaction between nanoscale gas bubbles and nanoparticles in the process of DAF remains unclear. Here, we investigated the role of nanobubbles in the precipitation of styryl phosphoric acid (SPA)-Pb particles and recovering organic phosphine containined in beneficiation wastewater by UV-vis (ultraviolet-visible) spectra, microflotation tests, nanoparticle tracking analysis, dynamic light scattering, and atomic force microscopy measurements. As suggested from the results, nanobubbles can inhibit the crystallization of SPA-Pb precipitation, which makes the sediment flotation recovery below 20%. After the precipitation crystallization is completed, nanobubbles can flocculate precipitated particles, which can promote the flotation recovery of precipitated particles to 90%. On the basis of the results, we proposed a model to explain the different roles of nanobubbles in the process of precipitation and flotation of SPA-Pb particles. This study will be helpful to understand the interaction between nanobubbles and nanoparticles in the application of flotation.