Genome-wide SNP identification and QTL mapping for black rot resistance in cabbage

BACKGROUND: Black rot is a destructive bacterial disease causing large yield and quality losses in Brassica oleracea. To detect quantitative trait loci (QTL) for black rot resistance, we performed whole-genome resequencing of two cabbage parental lines and genome-wide SNP identification using the recently published B. oleracea genome sequences as reference. RESULTS: Approximately 11.5 Gb of sequencing data was produced from each parental line. Reference genome-guided mapping and SNP calling revealed 674,521 SNPs between the two cabbage lines, with an average of one SNP per 662.5 bp. Among 167 dCAPS markers derived from candidate SNPs, 117 (70.1%) were validated as bona fide SNPs showing polymorphism between the parental lines. We then improved the resolution of a previous genetic map by adding 103 markers including 87 SNP-based dCAPS markers. The new map composed of 368 markers and covers 1467.3 cM with an average interval of 3.88 cM between adjacent markers. We evaluated black rot resistance in the mapping population in three independent inoculation tests using F₂:₃ progenies and identified one major QTL and three minor QTLs. CONCLUSION: We report successful utilization of whole-genome resequencing for large-scale SNP identification and development of molecular markers for genetic map construction. In addition, we identified novel QTLs for black rot resistance. The high-density genetic map will promote QTL analysis for other important agricultural traits and marker-assisted breeding of B. oleracea.This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at [email protected]

Coalescence dynamics of platinum group metal nanoparticles revealed by liquid-phase transmission electron microscopy

Summary: Coalescence, one of the major pathways observed in the growth of nanoparticles, affects the structural diversity of the synthesized nanoparticles in terms of sizes, shapes, and grain boundaries. As coalescence events occur transiently during the growth of nanoparticles and are associated with the interaction between nanoparticles, mechanistic understanding is challenging. The ideal platform to study coalescence events may require real-time tracking of nanoparticle growth trajectories with quantitative analysis for coalescence events. Herein, we track nanoparticle growth trajectories using liquid-cell transmission electron microscopy (LTEM) to investigate the role of coalescence in nanoparticle formation and their morphologies. By evaluating multiple coalescence events for different platinum group metals, we reveal that the surface energy and ligand binding energy determines the rate of the reshaping process and the resulting final morphology of coalesced nanoparticles. The coalescence mechanism, based on direct LTEM observation explains the structures of noble metal nanoparticles that emerge in colloidal synthesis

Redox-Sensitive Facet Dependency in Etching of Ceria Nanocrystals Directly Observed by Liquid Cell TEM

Defining the redox activity of different surface facets of ceria nanocrystals is important for designing an efficient catalyst. Especially in liquid-phase reactions, where surface interactions are complicated, direct investigation in a native environment is required to understand the facet-dependent redox properties. Using liquid cell TEM, we herein observed the etching of ceria-based nanocrystals under the control of redox-governing factors. Direct nanoscale observation reveals facet-dependent etching kinetics, thus identifying the specific facet ({100} for reduction and {111} for oxidation) that governs the overall etching under different chemical conditions. Under each redox condition, the contribution of the predominant facet increases as the etching reactivity increases.

Shape Transformation Mechanism of Gold Nanoplates

Shape control is of key importance in utilizing the structure-property relationship of nanocrystals. The high surface-to-volume ratio of nanocrystals induces dynamic surface reactions on exposed facets of nanocrystals, such as adsorption, desorption, and diffusion of surface atoms, all of which are important in overall shape transformation. However, it is difficult to track shape transformation of nanocrystals and understand the underlying mechanism at the level of distinguishing events on individual facets. Herein, we investigate changes of individual surface-exposed facets during diverse shape transformations of Au nanocrystals using liquid phase TEM in various chemical potentials and kinetic Monte Carlo simulations. The results reveal that the diffusion of surface atoms on nanocrystals is the governing factor in determining the final structure in shape transformation, causing the fast transformation of unstable facets to truncated morphology with minimized surface energy. The role of surface diffusion introduced here can be further applied to understanding the formation mechanism of variously shaped nanocrystals.Y

Liquid-Phase Transmission Electron Microscopy for Reliable In Situ Imaging of Nanomaterials

Liquid-phase transmission electron microscopy (LPTEM) is a powerful in situ visualization technique for directly characterizing nanomaterials in the liquid state. Despite its successful application in many fields, several challenges remain in achieving more accurate and reliable observations. We present LPTEM in chemical and biological applications, including studies for the morphological transformation and dynamics of nanoparticles, battery systems, catalysis, biomolecules, and organic systems. We describe the possible interactions and effects of the electron beam on specimens during observation and present sample-specific approaches to mitigate and control these electron-beam effects. We provide recent advances in achieving atomic-level resolution for liquid-phase investigation of structures anddynamics. Moreover, we discuss the development of liquid cell platforms and the introduction of machine-learning data processing for quantitative and objective LPTEM analysis.11Nsciescopu

A Large-Scale Array of Ordered Graphene-Sandwiched Chambers for Quantitative Liquid-Phase Transmission Electron Microscopy

© 2020 Wiley-VCH GmbH. Liquid-phase transmission electron microscopy (TEM) offers a real-time microscopic observation of the nanometer scale for understanding the underlying mechanisms of the growth, etching, and interactions of colloidal nanoparticles. Despite such unique capability and potential application in diverse fields of analytical chemistry, liquid-phase TEM studies rely on information obtained from the limited number of observed events. In this work, a novel liquid cell with a large-scale array of highly ordered nanochambers is constructed by sandwiching an anodic aluminum oxide membrane between graphene sheets. TEM analysis of colloidal gold nanoparticles dispersed in the liquid is conducted, employing the fabricated nanochamber array, to demonstrate the potential of the nanochamber array in quantitative liquid-phase TEM. The independent TEM observations in the multiple nanochambers confirm that the monomer attachment and coalescence processes universally govern the overall growth of nanoparticles, although individual nanoparticles follow different growth trajectories11sciescopu

In Situ Liquid Phase TEM of Nanoparticle Formation and Diffusion in a Phase-Separated Medium

Colloidal nanoparticles are synthesized in a complex reaction mixture that has an inhomogeneous chemical environment induced by local phase separation of the medium. Nanoparticle syntheses based on micelles, emulsions, flow of different fluids, injection of ionic precursors in organic solvents, and mixing the metal organic phase of precursors with an aqueous phase of reducing agents are well established. However, the formation mechanism of nanoparticles in the phase-separated medium is not well understood because of the complexity originating from the presence of phase boundaries as well as nonuniform chemical species, concentrations, and viscosity in different phases. Herein, we investigate the formation mechanism and diffusion of silver nanoparticles in a phase-separated medium by using liquid phase transmission electron microscopy and many-body dissipative particle dynamics simulations. A quantitative analysis of the individual growth trajectories reveals that a large portion of silver nanoparticles nucleate and grow rapidly at the phase boundaries, where metal ion precursors and reducing agents from the two separated phases react to form monomers. The results suggest that the motion of the silver nanoparticles at the interfaces is highly affected by the interaction with polymers and exhibits superdiffusive dynamics because of the polymer relaxation.11Nsciescopu

A Large‐Scale Array of Ordered Graphene‐Sandwiched Chambers for Quantitative Liquid‐Phase Transmission Electron Microscopy

© 2020 Wiley-VCH GmbH. Liquid-phase transmission electron microscopy (TEM) offers a real-time microscopic observation of the nanometer scale for understanding the underlying mechanisms of the growth, etching, and interactions of colloidal nanoparticles. Despite such unique capability and potential application in diverse fields of analytical chemistry, liquid-phase TEM studies rely on information obtained from the limited number of observed events. In this work, a novel liquid cell with a large-scale array of highly ordered nanochambers is constructed by sandwiching an anodic aluminum oxide membrane between graphene sheets. TEM analysis of colloidal gold nanoparticles dispersed in the liquid is conducted, employing the fabricated nanochamber array, to demonstrate the potential of the nanochamber array in quantitative liquid-phase TEM. The independent TEM observations in the multiple nanochambers confirm that the monomer attachment and coalescence processes universally govern the overall growth of nanoparticles, although individual nanoparticles follow different growth trajectories11sciescopu

Ligand-Dependent Coalescence Behaviors of Gold Nanoparticles Studied by Multichamber Graphene Liquid Cell Transmission Electron Microscopy

The formation mechanism of colloidal nanoparticles is complex because significant nonclassical pathways coexist with the conventional nucleation and growth processes. Particularly, the coalescence of the growing clusters determines the final morphology and crystallinity of the synthesized nanoparticles. However, the experimental investigation of the coalescence mechanism is a challenge because the process is highly kinetic and correlates with surface ligands that dynamically modify the surface energy and the interparticle interactions of nanoparticles. Here, we employ quantitative in situ TEM with multichamber graphene liquid cell to observe the coalescence processes occurring in the synthesis of gold nanoparticles in different ligand systems, thus affording us an insight into their ligand-dependent coalescence kinetics. The analyses of numerous liquid-phase TEM trajectories of the coalescence and MD simulations of the ligand shells demonstrate that enhanced ligand mobility, employing a heterogeneous ligand mixture, results in the rapid nanoparticle pairing approach and a fast post-merging structural relaxation.11Nsciescopu

Uniform synthesis of palladium species confined in a small-pore zeolite via full ion-exchange investigated by cryogenic electron microscopy

Finely dispersing noble metal species with high phase homogeneity in zeolites is crucial to develop an efficient catalyst. However, for palladium-impregnated zeolites, fully utilizing active palladium species in small-pore zeolites with high dispersion is challenging despite the establishment of a general synthetic approach of ion-exchange and subsequent thermal treatment to generate encapsulated nanoparticles. Herein, we achieve full dispersion of isolated Pd2+ ions in a small-pore SSZ-13 zeolite via a controlled ion-exchange process, and successfully generate uniformly dispersed nano-sized PdO clusters in SSZ-13 supported by mechanistic understanding of nanoparticle growth. Direct investigation via cryogenic electron microscopy and ultramicrotomy allows the successful artifact-free imaging of electron-beam-sensitive zeolite-based catalysts, and reveals that the formation of nano-sized PdO clusters during thermal treatment is governed by the rapid nucleation and suppressed particle growth in a confined space. Through fully utilizing active Pd species in SSZ-13 by controlled ion-exchange and rationalized thermal treatment, enhanced catalytic performances toward a passive NOx adsorber and CH4 combustion are achieved.11Nsciescopu