Whole-genome re-sequencing, diversity analysis, and stress-resistance analysis of 77 grape rootstock genotypes.

Introduction: Grape rootstocks play critical role in the development of the grape industry over the globe for their higher adaptability to various environments, and the evaluation of their genetic diversity among grape genotypes is necessary to the conservation and utility of genotypes. Methods: To analyze the genetic diversity of grape rootstocks for a better understanding multiple resistance traits, whole-genome re-sequencing of 77 common grape rootstock germplasms was conducted in the present study. Results: About 645 billion genome sequencing data were generated from the 77 grape rootstocks at an average depth of ~15.5×, based on which the phylogenic clusters were generated and the domestication of grapevine rootstocks was explored. The results indicated that the 77 rootstocks originated from five ancestral components. Through phylogenetic, principal components, and identity-by-descent (IBD) analyses, these 77 grape rootstocks were assembled into ten groups. It is noticed that the wild resources of V. amurensis and V. davidii, originating from China and being generally considered to have stronger resistance against biotic and abiotic stresses, were sub-divided from the other populations. Further analysis indicated that a high level of linkage disequilibrium was found among the 77 rootstock genotypes, and a total of 2,805,889 single nucleotide polymorphisms (SNPs) were excavated, GWAS analysis among the grape rootstocks located 631, 13, 9, 2, 810, and 44 SNP loci that were responsible to resistances to phylloxera, root-knot nematodes, salt, drought, cold and waterlogging traits. Discussion: This study generated a significant amount of genomic data from grape rootstocks, thus providing a theoretical basis for further research on the resistance mechanism of grape rootstocks and the breeding of resistant varieties. These findings also reveal that China originated V. amurensis and V. davidii could broaden the genetic background of grapevine rootstocks and be important germplasm used in breeding high stress-resistant grapevine rootstocks.

Transcriptome and metabolite integrated analysis reveals that exogenous ethylene controls berry ripening processes in grapevine.

Although grapevine (Vitis vinifera L.) is generally classified as a non-climacteric fruit, the regulatory mechanisms of ethylene in the ripening of non-climacteric fruit are still poorly understood. In this study, exogenous ethephon (ETH) strongly stimulated fruit color and anthocyanin accumulation, which was consistent with the increased expression of anthocyanin structural, regulatory, and transport genes. ETH application increased ABA content and decreased IAA content by coordinating ABA and auxin biosynthesis regulatory network. ETH treatment also accelerated sugar (glucose and fructose) accumulation by enhancing the gene expression involved in sugar transport and sucrose cleavage. ETH treatment blocked the synthesis of cellulose and accelerated the degradation of pectin, which was strongly associated with berry softening. To further confirm the function of ethylene biosynthesis and signaling genes, transient overexpression of VvACO4 and VvEIL3 were performed in both in tomato and strawberry fruits. These findings of the ethylene cascade add to our understanding of ethylene in non-climacteric berry ripening regulation and revealed a complex involvement of ethylene and its interplay with phytohormones during grapevine berry ripening.

The BTB protein MdBT2 recruits auxin signaling components to regulate adventitious root formation in apple.

Ubiquitination is an important post-translational protein modification. Although BROAD-COMPLEX, TRAMTRACK AND BRIC A BRAC and TRANSCRIPTION ADAPTOR PUTATIVE ZINC FINGER domain protein 2 (BT2) is involved in many biological processes, its role in apple (Malus domestic) root formation remains unclear. Here, we revealed that MdBT2 inhibits adventitious root (AR) formation through interacting with AUXIN RESPONSE FACTOR8 (MdARF8) and INDOLE-3-ACETIC ACID INDUCIBLE3 (MdIAA3). MdBT2 facilitated MdARF8 ubiquitination and degradation through the 26S proteasome pathway and negatively regulated GRETCHEN HAGEN 3.1 (MdGH3.1) and MdGH3.6 expression. MdARF8 regulates AR formation through inducing transcription of MdGH3s (MdGH3.1, MdGH3.2, MdGH3.5, and MdGH3.6). In addition, MdBT2 facilitated MdIAA3 stability and slightly promoted its interaction with MdARF8. MdIAA3 inhibited AR formation by forming heterodimers with MdARF8 as well as other MdARFs (MdARF5, MdARF6, MdARF7, and MdARF19). Our findings reveal that MdBT2 acts as a negative regulator of AR formation in apple.

Activating Silent Synapses in Sulfurized Indium Selenide for Neuromorphic Computing.

The transformation from silent to functional synapses is accompanied by the evolutionary process of human brain development and is essential to hardware implementation of the evolutionary artificial neural network but remains a challenge for mimicking silent to functional synapse activation. Here, we developed a simple approach to successfully realize activation of silent to functional synapses by controlled sulfurization of chemical vapor deposition-grown indium selenide crystals. The underlying mechanism is attributed to the migration of sulfur anions introduced by sulfurization. One of our most important findings is that the functional synaptic behaviors can be modulated by the degree of sulfurization and temperature. In addition, the essential synaptic behaviors including potentiation/depression, paired-pulse facilitation, and spike-rate-dependent plasticity are successfully implemented in the partially sulfurized functional synaptic device. The developed simple approach of introducing sulfur anions in layered selenide opens an effective new avenue to realize activation of silent synapses for application in evolutionary artificial neural networks.

ROA: A Rapid Learning Scheme for In-Situ Memristor Networks.

Memristors show great promise in neuromorphic computing owing to their high-density integration, fast computing and low-energy consumption. However, the non-ideal update of synaptic weight in memristor devices, including nonlinearity, asymmetry and device variation, still poses challenges to the in-situ learning of memristors, thereby limiting their broad applications. Although the existing offline learning schemes can avoid this problem by transferring the weight optimization process into cloud, it is difficult to adapt to unseen tasks and uncertain environments. Here, we propose a bi-level meta-learning scheme that can alleviate the non-ideal update problem, and achieve fast adaptation and high accuracy, named Rapid One-step Adaption (ROA). By introducing a special regularization constraint and a dynamic learning rate strategy for in-situ learning, the ROA method effectively combines offline pre-training and online rapid one-step adaption. Furthermore, we implemented it on memristor-based neural networks to solve few-shot learning tasks, proving its superiority over the pure offline and online schemes under noisy conditions. This method can solve in-situ learning in non-ideal memristor networks, providing potential applications of on-chip neuromorphic learning and edge computing.

The apple C2H2-type zinc finger transcription factor MdZAT10 positively regulates JA-induced leaf senescence by interacting with MdBT2.

Jasmonic acid (JA) plays an important role in regulating leaf senescence. However, the molecular mechanisms of leaf senescence in apple (Malus domestica) remain elusive. In this study, we found that MdZAT10, a C2H2-type zinc finger transcription factor (TF) in apple, markedly accelerates leaf senescence and increases the expression of senescence-related genes. To explore how MdZAT10 promotes leaf senescence, we carried out liquid chromatography/mass spectrometry screening. We found that MdABI5 physically interacts with MdZAT10. MdABI5, an important positive regulator of leaf senescence, significantly accelerated leaf senescence in apple. MdZAT10 was found to enhance the transcriptional activity of MdABI5 for MdNYC1 and MdNYE1, thus accelerating leaf senescence. In addition, we found that MdZAT10 expression was induced by methyl jasmonate (MeJA), which accelerated JA-induced leaf senescence. We also found that the JA-responsive protein MdBT2 directly interacts with MdZAT10 and reduces its protein stability through ubiquitination and degradation, thereby delaying MdZAT10-mediated leaf senescence. Taken together, our results provide new insight into the mechanisms by which MdZAT10 positively regulates JA-induced leaf senescence in apple.

Floating solid-state thin films with dynamic structural colour.

Thin-film architectures are a staple in a wide range of technologies, such as semiconductor devices, optical coatings, magnetic recording, solar cells and batteries. Despite the industrial success of thin-film technology, mostly due to the easy fabrication and low cost, a fundamental drawback remains: it is challenging to alter the features of the film once fabricated. Here we report a methodology to modify the thickness and sequence of the innermost solid-state thin-film layers. We start with a thin-film stack of amorphous iron oxide and silver. By applying a suitable voltage bias and then reversing it, we can float the silver layer above or below the oxide layer by virtue of the migration of silver atoms. Scanning transmission electron microscopy reveals various sequences and thicknesses of the silver and oxide layers achieved with different experimental conditions. As a proof-of-principle, we show a dynamic change of structural colours of the stack derived from this process. Our results may offer opportunities to dynamically reconfigure thin-film-based functional nanodevices in situ.

Low nitrate alleviates iron deficiency by regulating iron homeostasis in apple.

Iron (Fe) is an essential element for plant growth, development and metabolism. Due to its lack of solubility and low bioavailability in soil, Fe levels are usually far below the optimum amount for most plants' growth and development. In apple production, excessive use of nitrogen fertilizer may cause iron chlorosis symptoms in the newly growing leaves, but the regulatory mechanisms underlying this phenomenon are unclear. In this study, low nitrate (NO3- , LN) application alleviated the symptoms of Fe deficiency and promoted lower rhizosphere pH, which was beneficial for root Fe acquisition. At the same time, LN treatment increased citrate and abscisic acid accumulation in roots, which promoted Fe transport from root to shoot and maintained Fe homeostasis. Moreover, qRT-PCR analysis showed that nitrate application caused differential expression of genes related to Fe uptake and transport, as well as transcriptional regulators. In summary, our data reveal that low nitrate alleviated Fe deficiency through multiple pathways, demonstrating a new option for minimizing Fe deficiency by regulating the balance between nutrients.

The BTB-TAZ protein MdBT2 negatively regulates the drought stress response by interacting with the transcription factor MdNAC143 in apple.

Drought stress is a severe source of abiotic stress that can affect apple yield and quality, yet the underlying molecular mechanism of the drought stress response and the role of MdBT2 in the process remain unclear. Here, we find that MdBT2 negatively regulates the drought stress response. Both in vivo and in vitro assays indicated that MdBT2 interacted physically with and ubiquitinated MdNAC143, a member of the NAC TF family that is a positive regulator under drought stress. In addition, MdBT2 promotes the degradation of MdNAC143 via the 26S proteasome system. A series of transgenic assays in apple calli and Arabidopsis verify that MdBT2 confers susceptibility to drought stress at least in part by the regulation of MdNAC143. Overall, our findings provide new insight into the mechanism of MdBT2, which functions antagonistically to MdNAC143 in regulating drought stress by regulating the potential downstream target protein MdNAC143 for proteasomal degradation in apple.

Auxin regulates anthocyanin biosynthesis through the auxin repressor protein MdIAA26.

Auxin plays an important role in plant growth and development; for example, it regulates the elongation and division of plant cells, the formation of plantlet's geotropism and phototropism, and the growth of main lateral roots and hypocotyl. IAA gene is associated with auxin and can response to biotic and abiotic stress in plants. However, the regulatory effect of auxin on anthocyanin accumulation has been rarely reported. In this study, we show that auxin inhibites the accumulation of anthocyanin and decreases the expression of genes related to anthocyanin synthesis in calli, leaves, and seedlings of apple. The expression levels of MdIAA family genes were determined, and we found that MdIAA26 significantly responded to auxin, which also induced MdIAA26 degradation. Functional analysis of MdIAA26 showed that overexpressing MdIAA26 in apple calli and Arabidopsis could promote the accumulation of anthocyanin and up-regulate the genes related to anthocyanin synthesis. Furthermore, the MdIAA26-overexpressing Arabidopsis could counteract auxin-induced inhibition on anthocyanin accumulation, which indicates that auxin inhibits the accumulation of anthocyanin in apple by degrading MdIAA26 protein.

Genome-Wide Identification of Apple Ubiquitin SINA E3 Ligase and Functional Characterization of MdSINA2.

SINA (Seven in absentia) proteins are a small family of ubiquitin ligases that play important roles in regulating plant growth and developmental processes as well as in responses to diverse types of biotic and abiotic stress. However, the characteristics of the apple SINA family have not been previously studied. Here, we identified 11 MdSINAs members in the apple genome based on their conserved, N-terminal RING and C-terminal SINA domains. We also reconstructed a phylogeny of these genes; characterized their chromosomal location, structure, and motifs; and identified two major groups of MdSINA genes. Subsequent qRT-PCR analyses were used to characterize the expression of MdSINA genes in various tissues and organs, and levels of expression were highest in leaves. MdSINAs were significantly induced under ABA and carbon- and nitrate-starvation treatment. Except for MdSINA1 and MdSINA7, the other MdSINA proteins could interact with each other. Moreover, MdSINA2 was found to be localized in the nucleus using Agrobacterium-mediated transient expression. Western-blot analysis showed that MdSINA2 accumulated extensively under light, decreased under darkness, and became insensitive to light when the RING domain was disrupted. Finally, ABA-hypersensitive phenotypes were confirmed by transgenic calli and the ectopic expression of MdSINA2 in Arabidopsis. In conclusion, our results suggest that MdSINA genes participate in the responses to different types of stress, and that MdSINA2 might act as a negative regulator in the ABA stress response.

Phosphate regulates malate/citrate-mediated iron uptake and transport in apple.

The accumulation of iron (Fe) in the apical meristem is considered as a critical factor involved in limiting the elongation of roots under low phosphate (Pi) conditions. Furthermore, the antagonism between Fe and Pi largely affects the effective utilization of Fe. Although the lack of Pi serves to increase the effectiveness of Fe in rice under both Fe-sufficient and Fe-deficient conditions, the underlying physiological mechanism governing this phenomenon is still unclear. In this study, we found that low Pi alleviated the Fe-deficiency phenotype in apples. Additionally, low Pi treatments increased ferric-chelated reductase (FCR) activity in the rhizosphere, promoted proton exocytosis, and enhanced the Fe concentration in both the roots and shoots. In contrast, high Pi treatments inhibited this process. Under conditions of low Pi, malate and citrate exudation from apple roots occurred under both Fe-sufficient and Fe-deficient conditions. In addition, treatment with 0.5 mM malate and citrate effectively alleviated the Fe and Pi deficiencies. Taken together, these data support the conclusion that a low Pi supply promotes organic acids exudation and enhances Fe absorption during Fe deficiency in apples.

Decoding the metallic bridging dynamics in nanogap atomic switches.

Atomic switches are promising candidates as the basic building blocks for large-scale neuromorphic networks due to their tunable switching behaviors. Several neuromorphic components based on atomic switches have been demonstrated, including artificial synapses, artificial neurons and short-term to long-term memory, making it possible to construct neuromorphic systems using a unified device. Although the mechanism of atomic switches has been actively studied, most of the discussions in previous studies are qualitative and failed to provide a comprehensive view of the dynamics that can precisely describe the metallic bridging under an electric field. In this paper, we designed a gap-type atomic switch and realized various switching behaviors, including both volatile and non-volatile resistive switching. Employing advanced microanalysis technology, we experimentally studied the switching mechanism and captured the nanoscale metallic filament in gap-type atomic switches. Furthermore, based on the experimental findings as well as on the electrochemistry fundamental and electron tunneling effect, we proposed a physical model that precisely reproduced the sophisticated switching behaviors. Our model mathematically described the growth/shrinkage dynamics of nanoscale metallic filaments, providing a direction for studying the switching behaviors from a quantitative view. The simulation results are in good agreement with the experimental findings in both DC sweep and pulse operation modes. In addition, we have demonstrated neuronal tonic spiking and short-term to long-term memory in experiment and simulation, indicating that our model can be applied to the circuit level simulation of large-scale atomic switch arrays for neuromorphic applications.

Tunable Resistive Switching Enabled by Malleable Redox Reaction in the Nano-Vacuum Gap.

Neuromorphic computing has emerged as a highly promising alternative to conventional computing. The key to constructing a large-scale neural network in hardware for neuromorphic computing is to develop artificial neurons with leaky integrate-and-fire behavior and artificial synapses with synaptic plasticity using nanodevices. So far, these two basic computing elements have been built in separate devices using different materials and technologies, which poses a significant challenge to system design and manufacturing. In this work, we designed a resistive device embedded with an innovative nano-vacuum gap between a bottom electrode and a mixed-ionic-electronic-conductor (MIEC) layer. Through redox reaction on the MIEC surface, metallic filaments dynamically grew within the nano-vacuum gap. The nano-vacuum gap provided an additional control factor for controlling the evolution dynamics of metallic filaments by tuning the electron tunneling efficiency, in analogy to a pseudo-three-terminal device, resulting in tunable switching behavior in various forms from volatile to nonvolatile switching in a single device. Our device demonstrated cross-functions, in particular, tunable neuronal firing and synaptic plasticity on demand, providing seamless integration for building large-scale artificial neural networks for neuromorphic computing.

Highly Compact Artificial Memristive Neuron with Low Energy Consumption.

Neuromorphic systems aim to implement large-scale artificial neural network on hardware to ultimately realize human-level intelligence. The recent development of nonsilicon nanodevices has opened the huge potential of full memristive neural networks (FMNN), consisting of memristive neurons and synapses, for neuromorphic applications. Unlike the widely reported memristive synapses, the development of artificial neurons on memristive devices has less progress. Sophisticated neural dynamics is the major obstacle behind the lagging. Here a rich dynamics-driven artificial neuron is demonstrated, which successfully emulates partial essential neural features of neural processing, including leaky integration, automatic threshold-driven fire, and self-recovery, in a unified manner. The realization of bioplausible artificial neurons on a single device with ultralow power consumption paves the way for constructing energy-efficient large-scale FMNN and may boost the development of neuromorphic systems with high density, low power, and fast speed.

Enabling Transient Electronics with Degradation on Demand via Light-Responsive Encapsulation of a Hydrogel-Oxide Bilayer.

Physically transient electronics, which can disappear under certain conditions in aqueous solutions or biofluids, has attracted increasing attention because of its potential applications as "green" electronics and biomedical devices. Till now, the excitation of the transient process is achieved by passive dissolution of the encapsulation layer, which has a very limited control over the process. Here, we report a novel light-triggered encapsulation strategy via a bilayer of a light-responsive hydrogel and oxide to control the degradation on demand in aqueous environment. The hydrogel serving as a barrier between the environment and oxide limited the water's movement and penetration, leading to improved stable operation time. More importantly, the light-responsive hydrogel underwent a gel-to-solution transition upon applying ultraviolet (UV) light. The drastic change of the water movement enabled a transient process triggered on demand. Via this encapsulation scheme, we demonstrated fully soluble resistors and resistive random access memory devices with the UV light-triggered transient process. This work provides a new pathway to design transient devices with controllable degradation to meet various requirements of green electronics and biomedical devices.

Super Nonlinear Electrodeposition-Diffusion-Controlled Thin-Film Selector.

Selector elements with high nonlinearity are an indispensable part in constructing high density, large-scale, 3D stackable emerging nonvolatile memory and neuromorphic network. Although significant efforts have been devoted to developing novel thin-film selectors, it remains a great challenge in achieving good switching performance in the selectors to satisfy the stringent electrical criteria of diverse memory elements. In this work, we utilized high-defect-density chalcogenide glass (Ge2Sb2Te5) in conjunction with high mobility Ag element (Ag-GST) to achieve a super nonlinear selective switching. A novel electrodeposition-diffusion dynamic selector based on Ag-GST exhibits superior selecting performance including excellent nonlinearity (<5 mV/dev), ultra-low leakage (<10 fA), and bidirectional operation. With the solid microstructure evidence and dynamic analyses, we attributed the selective switching to the competition between the electrodeposition and diffusion of Ag atoms in the glassy GST matrix under electric field. A switching model is proposed, and the in-depth understanding of the selective switching mechanism offers an insight of switching dynamics for the electrodeposition-diffusion-controlled thin-film selector. This work opens a new direction of selector designs by combining high mobility elements and high-defect-density chalcogenide glasses, which can be extended to other materials with similar properties.

Identification of a Novel Alternative Splicing Variant of VvPMA1 in Grape Root under Salinity.

It has been well-demonstrated that the control of plasma membrane H+-ATPase (PM H+-ATPase) activity is important to plant salt tolerance. This study found a significant increase in PM H+-ATPase (PMA) activity in grape root exposed to NaCl. Furthermore, 7 Vitis vinifera PM H+-ATPase genes (VvPMAs) were identified within the grape genome and the expression response of these VvPMAs in grape root under salinity was analyzed. Two VvPMAs (VvPMA1 and VvPMA3) were expressed more strongly in roots than the other five VvPMAs. Moreover, roots exhibited diverse patterns of gene expression of VvPMA1 and VvPMA3 responses to salt stress. Interestingly, two transcripts of VvPMA1, which were created through alternative splicing (AS), were discovered and isolated from salt stressed root. Comparing the two VvPMA1 cDNA sequences (designated VvPMA1α and VvPMA1ß) with the genomic sequence revealed that the second intron was retained in the VvPMA1ß cDNA. This intron retention was predicted to generate a novel VvPMA1 through N-terminal truncation because of a 5'- terminal frame shift. Yeast complementation assays of the two splice variants showed that VvPMA1ß could enhance the ability to complement Saccharomyces cerevisiae deficient in PM H+-ATPase activity. In addition, the expression profiles of VvPMA1α and VvPMA1ß differed under salinity. Our data suggests that through AS, the N-terminal length of VvPMA1 may be regulated to accurately modulate PM H+-ATPase activity of grape root in salt stress.

Phase-Change Memory Materials by Design: A Strain Engineering Approach.

Van der Waals heterostructure superlattices of Sb2 Te1 and GeTe are strain-engineered to promote switchable atomic disordering, which is confined to the GeTe layer. Careful control of the strain in the structures presents a new degree of freedom to design the properties of functional superlattice structures for data storage and photonics applications.