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

Unraveling the mystery of ultrafine bubbles: Establishment of thermodynamic equilibrium for sub-micron bubbles and its implications

Hypothesis: We test the validity of the Young-Laplace equation and Henry's law for sub-micron bubble suspensions, which has long been a questionable issue. Application of the two theories allows characterization of bubble diameter and gas molecule partitioning between gaseous and dissolved phases using two easily measurable variables: total gas content (C-T) and bubble volume concentration (BVC). Experiments: We measure C-T and BVC for sub-micron bubble suspensions generated from three pure gases, which allows calculation of bubble diameter for each suspension using the Young-Laplace equation and Henry's law. Uncertainties involved in the experimental measurements are assessed. Bubble size for each suspension is also directly measured using a dynamic light scattering (DLS) technique for comparison. Findings: Applying the two theories we calculate that the bubble diameters are in the range of 304518 nm, which correspond very well with the DLS-measured diameters. Sensitivity analyses demonstrate that the correspondence of the calculated and DLS-measured bubble diameters should take place only if the two theories are valid. The gas molecule partitioning analysis shows that >96% of gas molecules in the suspension exist as dissolved phase, which suggests the significance of the dissolved phase for applications of the bubble suspensions. (C) 2020 Elsevier Inc. All rights reserved.N

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

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