Monolithic three-dimensional tier-by-tier integration via van der Waals lamination.

Two-dimensional (2D) semiconductors have shown great potential for monolithic three-dimensional (M3D) integration due to their dangling-bonds-free surface and the ability to integrate to various substrates without the conventional constraint of lattice matching1-10. However, with atomically thin body thickness, 2D semiconductors are not compatible with various high-energy processes in microelectronics11-13, where the M3D integration of multiple 2D circuit tiers is challenging. Here we report an alternative low-temperature M3D integration approach by van der Waals (vdW) lamination of entire prefabricated circuit tiers, where the processing temperature is controlled to 120 °C. By further repeating the vdW lamination process tier by tier, an M3D integrated system is achieved with 10 circuit tiers in the vertical direction, overcoming previous thermal budget limitations. Detailed electrical characterization demonstrates the bottom 2D transistor is not impacted after repetitively laminating vdW circuit tiers on top. Furthermore, by vertically connecting devices within different tiers through vdW inter-tier vias, various logic and heterogeneous structures are realized with desired system functions. Our demonstration provides a low-temperature route towards fabricating M3D circuits with increased numbers of tiers.

Highly Stable HfO2 Memristors through van der Waals Electrode Lamination and Delamination.

Memristors have attracted considerable attention in the past decade, holding great promise for future neuromorphic computing. However, the intrinsic poor stability and large device variability remain key limitations for practical application. Here, we report a simple method to directly visualize the origin of poor stability. By mechanically removing the top electrodes of memristors operated at different states (such as SET or RESET), the memristive layer could be exposed and directly characterized through conductive atomic force microscopy, providing two-dimensional area information within memristors. Based on this technique, we observed the existence of multiple conducting filaments during the formation process and built up a physical model between filament numbers and the cycle-to-cycle variation. Furthermore, by improving the interface quality through the van der Waals top electrode, we could reduce the filament number down to a single filament during all switching cycles, leading to much controlled switching behavior and reliable device operation.

Recombinase Polymerase Amplification Coupled with CRISPR-Cas12a Technology for Rapid and Highly Sensitive Detection of Heterodera avenae and Heterodera filipjevi.

The cereal cyst nematodes Heterodera avenae and Heterodera filipjevi are recognized as cyst nematodes that infect cereal crops and cause severe economic losses worldwide. Rapid, visual detection of cyst nematodes is essential for more effective control of this pest. In this study, recombinase polymerase amplification (RPA) combined with clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a (formerly known as cpf1) was developed for the rapid detection of H. avenae and H. filipjevi from infested field samples. The RPA reaction was performed at a wide range of temperatures from 35 to 42°C within 15 min. There was no cross-reactivity between H. avenae, H. filipjevi, and the common closely related plant-parasitic nematodes, indicating the high specificity of this assay. The detection limit of RPA-Cas12a was as low as 10-4 single second-stage juvenile (J2), 10-5 single cyst, and 0.001 ng of genomic DNA, which is 10 times greater than that of RPA-lateral flow dipstick (LFD) detection. The RPA-Cas12a assay was able to detect 10-1 single J2 of H. avenae and H. filipjevi in 10 g of soil. In addition, the RPA-LFD assay and RPA-Cas12a assays could both quickly detect H. avenae and H. filipjevi from naturally infested soil, and the entire detection process could be completed within 1 h. These results indicated that the RPA-Cas12a assay developed herein is a simple, rapid, specific, sensitive, and visual method that can be easily adapted for the quick detection of H. avenae and H. filipjevi in infested fields.

Realization of Ultra-Scaled MoS2 Vertical Diodes via Double-Side Electrodes Lamination.

Schottky diode is the fundamental building blocks for modern electronics and optoelectronics. Reducing the semiconductor layer thickness could shrink the vertical size of a Schottky diode, improving its speed and integration density. Here, we demonstrate a new approach to fabricate a Schottky diode with ultrashort physical length approaching atomic limit. By mechanically laminating prefabricated metal electrodes on both-sides of two-dimensional MoS2, the intrinsic metal-semiconductor interfaces can be well retained. As a result, we demonstrate the thinnest Schottky diode with a length of 2.6 nm and decent rectification behavior. Furthermore, with a diode length smaller than the semiconductor depletion length, the carrier transport mechanisms are investigated and explained by thickness-dependent and temperature-dependent electrical measurements. Our study not only pushes the scaling limit of a Schottky diode but also provides a general double-sided electrodes integration approach for other ultrathin vertical devices.

Strain-Plasmonic Coupled Broadband Photodetector Based on Monolayer MoS2.

2D Semiconductors are promising in the development of next-generation photodetectors. However, the performances of 2D photodetectors are largely limited by their poor light absorption (due to ultrathin thickness) and small detection range (due to large bandgap). To overcome the limitations, a strain-plasmonic coupled 2D photodetector is designed by mechanically integrating monolayer MoS2 on top of prefabricated Au nanoparticle arrays. Within this structure, the large biaxial tensile strain can greatly reduce the MoS2 bandgap for broadband photodetection, and at the same time, the nanoparticles can significantly enhance the light intensity around MoS2 with much improved light absorption. Together, the strain-plasmonic coupled photodetector can broaden the detection range by 60 nm and increase the signal-to-noise ratio by 650%, representing the ultimate optimization of detection range and detection intensity at the same time. The strain-plasmonic coupling effect is further systematically characterized and confirmed by using Raman and photoluminescence spectrophotometry. Furthermore, the existence of built-in potential and photo-switching behavior is demonstrated between the strained and unstrained region, constructing a self-powered homojunction photodetector. This approach provides a simple strategy to couple strain effect and plasmonic effect, which can provide a new strategy for designing high-performance and broadband 2D optoelectronic devices.

Does energy cost constitute the primary cause of ammonium toxicity in plants?

Nitrate (NO3-) and ammonium (NH4+) are the main nitrogen (N) sources and key determinants for plant growth and development. In recent decades, NH4+, which is a double-sided N compound, has attracted considerable amounts of attention from researchers. Elucidating the mechanisms of NH4+ toxicity and exploring the means to overcome this toxicity are necessary to improve agricultural sustainability. In this review, we discuss the current knowledge concerning the energy consumption and production underlying NH4+ metabolism and toxicity in plants, such as N uptake; assimilation; cellular pH homeostasis; and functions of the plasma membrane (PM), vacuolar H+-ATPase and H+-pyrophosphatase (H+-PPase). We also discuss whether the overconsumption of energy is the primary cause of NH4+ toxicity or constitutes a fundamental strategy for plants to adapt to high-NH4+ stress. In addition, the effects of regulators on energy production and consumption and other physiological processes are listed for evaluating the possibility of high energy costs associated with NH4+ toxicity. This review is helpful for exploring the tolerance mechanisms and for developing NH4+-tolerant varieties as well as agronomic techniques to alleviate the effects of NH4+ stress in the field.

Opposite Beet Cyst Nematode Infection Phenotypes of Transgenic Arabidopsis Between Overexpressing GmSNAP18 and AtSNAP2 and Between Overexpressing GmSHMT08 and AtSHMT4.

The rhg1-a GmSNAP18 (an α-SNAP) and Rhg4 GmSHMT08 are two major cloned genes conferring soybean cyst nematode resistance in Peking-type soybeans, but the application of α-SNAPs and SHMTs in cyst nematode management remains elusive. In this study, GmSNAP18 and GmSHMT08, together with their orthologs in Arabidopsis, AtSNAP2 (an α-SNAP) and AtSHMT4, were individually transformed into Arabidopsis Col-0 to generate the transgenic lines, and the growth of transgenic plants, beet cyst nematode (BCN) infection phenotypes, and AtSNAP2, AtSHMT4, and AtPR1 expression patterns were analyzed using Arabidopsis-BCN compatible interaction system, in addition with protein-protein interaction assay. Pulldown and BiFC assays revealed that GmSNAP18 and GmSHMT08 interacted with AtSHMT4 and AtSNAP2, respectively. Plant root growth was not impacted by overexpression of GmSNAP18 and AtSNAP2. However, overexpression of GmSHMT08 and AtSHMT4 both increased plant height, additionally, overexpression of GmSHMT08 decreased rosette leaf size. Overexpression of GmSNAP18 and GmSHMT08 both suppressed AtPR1 expression and significantly enhanced BCN susceptibility, while overexpression of AtSNAP2 and AtSHMT4 both substantially boosted AtPR1 expression and remarkably enhanced BCN resistance, in transgenic Arabidopsis. Overexpression of GmSNAP18 reduced, while overexpression of AtSNAP2 unaltered AtSHMT4 expression. Overexpression of GmSHMT08 and AtSHMT4 both suppressed AtSNAP2 expression in transgenic Arabidopsis. Thus, different expression patterns of AtPR1 and AtSHMT4 are likely associated with opposite BCN infection phenotypes of Arabidopsis between overexpressing GmSNAP18 and AtSNAP2, and between overexpressing GmSHMT08 and AtSHMT4; and boosted AtPR1 expression are required for enhanced BCN resistance in Arabidopsis. All these results establish a basis for extension of α-SNAPs and SHMTs in cyst nematode management.

Origin and Phylogeography of Chinese Cereal Cyst Nematode Heterodera avenae Revealed by Mitochondrial COI Sequences.

Heterodera avenae, a globally distributed plant-parasitic nematode, is one of the most significant pests on cereal crops. In China, it is widely distributed in cereal-growing areas of 16 provinces and causes serious yield losses. In the present study, a total of 98 populations of H. avenae were collected from major wheat-growing regions in China and six other countries. The mitochondrial COI genes were amplified and analyzed. Forty-one mitochondrial COI haplotypes were identified, suggesting a high genetic diversity and endemism level of H. avenae in China. Phylogenetic analysis showed that H. avenae populations in China were divided into four clades. Significant evolutionary and genetic differences were found between Chinese (except Hubei) and foreign populations. Hap1, the most widely distributed haplotype, was considered to be a separate evolutionary origin in China. The gene flow of H. avenae from the northwestern region to the north China region and Huang-Huai-Hai region was significant, so as the direction between north China and Huang-Huai-Hai region. We speculate that water flowing from the Yellow River and mechanical harvesters promoted gene exchange among these groups. A distance-based redundancy analysis showed that genetic distances observed among H. avenae populations were explained foremost not only by geographic distance but also by temperature and precipitation. This study provides theoretical support for the origin and spread of H. avenae populations in China and elsewhere in the world.

Breeding a Soybean Cultivar Heinong 531 with Peking-Type Cyst Nematode Resistance, Enhanced Yield, and High Seed-Oil Contents.

Soybean cyst nematode (SCN) is a destructive threat to soybean production. It is economically important to develop a new SCN-resistant soybean cultivar with high yield and other good agronomic traits. In this study, a yellow-seed-coated and yellow-hilum-pigmented cultivar Heinong 531 belonging to maturity group I was developed by a pedigree breeding method through a test-cross between a female parental SCN-resistant soybean cultivar Pengdou 158 and a male parental line F1 (high-yield but SCN-susceptible Hefeng 55 × SCN-resistant Kangxian 12). Heinong 531 was evaluated for SCN resistance in both SCN-infested field and autoclaved soil inoculated with hatched second-stage juveniles of SCN HG Type 0. The results indicated that SCN development at all stages in Heinong 531 was suppressed and the female index was only 1.6 to 5.6%. Heinong 531 as well as Pengdou 158 and Kangxian 12 were identified as carrying the Peking-type resistance with both rhg1-a GmSNAP18 and Rhg4 GmSHMT08 genes. In the 2-year regional trials, the average yield of Heinong 531 reached 2805.0 kg/ha, and the 1-year production trial demonstrated an average yield of 2,751.5 kg/ha with yield increase of >12.0% when compared with the local cultivars. The average seed-fat (oil) contents of Heinong 531 reached up to 22.3%. The Peking-type SCN-resistant Heilong 531 with enhanced yield and high seed-oil contents was released in China in June 2021 with the certified number of 'Heishendou 20210004'. These agronomic traits make Heinong 531 a good prospect in a wide attempt to control SCN in the main soybean-producing areas of Northeast China.

Silicon Mediated Plant Immunity against Nematodes: Summarizing the Underline Defence Mechanisms in Plant Nematodes Interaction.

Silicon (Si) is known to stimulate plant resistance against different phytopathogens, i.e., bacteria, fungi, and nematodes. It is an efficient plant growth regulator under various biotic and abiotic stresses. Silicon-containing compounds, including silicon dioxide, SiO2 nanoparticles (NPs), nano-chelated silicon fertilizer (NCSF), sodium siliconate, and sodium metasilicate, are effective in damaging various nematodes that reduce their reproduction, galling, and disease severity. The defence mechanisms in plant-nematodes interaction may involve a physical barrier, plant defence-associated enzyme activity, synthesis of antimicrobial compounds, and transcriptional regulation of defence-related genes. In the current review, we focused on silicon and its compounds in controlling plant nematodes and regulating different defence mechanisms involved in plant-nematodes interaction. Furthermore, the review aims to evaluate the potential role of Si application in improving plant resistance against nematodes and highlight its need for efficient plant-nematodes disease management.

Combining targeted metabolite analyses and transcriptomics to reveal the specific chemical composition and associated genes in the incompatible soybean variety PI437654 infected with soybean cyst nematode HG1.2.3.5.7.

BACKGROUND: Soybean cyst nematode, Heterodera glycines, is one of the most devastating pathogens of soybean and causes severe annual yield losses worldwide. Different soybean varieties exhibit different responses to H. glycines infection at various levels, such as the genomic, transcriptional, proteomic and metabolomic levels. However, there have not yet been any reports of the differential responses of incompatible and compatible soybean varieties infected with H. glycines based on combined metabolomic and transcriptomic analyses. RESULTS: In this study, the incompatible soybean variety PI437654 and three compatible soybean varieties, Williams 82, Zhonghuang 13 and Hefeng 47, were used to clarify the differences in metabolites and transcriptomics before and after the infection with HG1.2.3.5.7. A local metabolite-calibrated database was used to identify potentially differential metabolites, and the differences in metabolites and metabolic pathways were compared between the incompatible and compatible soybean varieties after inoculation with HG1.2.3.5.7. In total, 37 differential metabolites and 20 KEGG metabolic pathways were identified, which were divided into three categories: metabolites/pathways overlapped in the incompatible and compatible soybeans, and metabolites/pathways specific to either the incompatible or compatible soybean varieties. Twelve differential metabolites were found to be involved in predicted KEGG metabolite pathways. Moreover, 14 specific differential metabolites (such as significantly up-regulated nicotine and down-regulated D-aspartic acid) and their associated KEGG pathways (such as the tropane, piperidine and pyridine alkaloid biosynthesis, alanine, aspartate and glutamate metabolism, sphingolipid metabolism and arginine biosynthesis) were significantly altered and abundantly enriched in the incompatible soybean variety PI437654, and likely played pivotal roles in defending against HG1.2.3.5.7 infection. Three key metabolites (N-acetyltranexamic acid, nicotine and D,L-tryptophan) found to be significantly up-regulated in the incompatible soybean variety PI437654 infected by HG1.2.3.5.7 were classified into two types and used for combined analyses with the transcriptomic expression profiling. Associated genes were predicted, along with the likely corresponding biological processes, cellular components, molecular functions and pathways. CONCLUSIONS: Our results not only identified potential novel metabolites and associated genes involved in the incompatible response of PI437654 to soybean cyst nematode HG1.2.3.5.7, but also provided new insights into the interactions between soybeans and soybean cyst nematodes.

High-Resolution Van der Waals Stencil Lithography for 2D Transistors.

2D semiconductors have attracted tremendous attention as an atomically thin channel for transistors with superior immunity to short-channel effects. However, with atomic thin structure, the delicate 2D lattice is not fully compatible with conventional lithography processes that typically involve high-energy photon/electron radiation and unavoidable polymer residues, posing a key limitation for high performance 2D transistors. Here, a novel van der Waals (vdW) stencil lithography technique based on dry mask lamination process is developed. By pre-fabricating polymethyl methacrylate (PMMA) resist with designed patterns, the whole PMMA mask layers could be mechanically released from the sacrifice wafer and physically laminated on top of various 2D semiconductors. The vdW stencil lithography ensures pristine 2D surface without any high-energy electron/photon radiation, polymer residues, or chemical doping effects in conventional lithography process; and the soft nature of PMMA enables intimate contact between the mask and the 2D materials without physical gap, leading to ultra-high resolution down to 60 nm. Together, by applying vdW stencil lithography for 2D semiconductors, high performance transistors are demonstrated. Our method not only demonstrates improved 2D transistor performance without lithography induced damages, but also provides a new vdW stencil lithography technique for 2D materials with high resolution.

Rapid and Visual Detection of Heterodera schachtii Using Recombinase Polymerase Amplification Combined with Cas12a-Mediated Technology.

Heterodera schachtii is a well-known cyst nematode that causes serious economic losses in sugar beet production every year. Rapid and visual detection of H. schachtii is essential for more effective prevention and control. In this study, a species-specific recombinase polymerase amplification (RPA) primer was designed from a specific H. schachtii sequence-characterized amplified region (SCAR) marker. A band was obtained in reactions with DNA from H. schachtii, but absent from nontarget cyst nematodes. The RPA results could be observed by the naked eye, using a lateral flow dipstick (LFD). Moreover, we combined CRISPR technology with RPA to identify positive samples by fluorescence detection. Sensitivity analysis indicated that 10-4 single cysts and single females, 4-3 single second-stage juveniles, and a 0.001 ng genomic DNA template could be detected. The sensitivity of the RPA method for H. schachtii detection is not only higher than that of PCR and qPCR, but can also provide results in <1 h. Consequently, the RPA assay is a practical and useful diagnostic tool for early diagnosis of plant tissues infested by H. schachtii. Sugar beet nematodes were successfully detected in seven of 15 field sugar beet root samples using the RPA assay. These results were consistent with those achieved by conventional PCR, indicating 100% accuracy of the RPA assay in field samples. The RPA assay developed in the present study has the potential for use in the direct detection of H. schachtii infestation in the field.

Source-sink modifications affect leaf senescence and grain mass in wheat as revealed by proteomic analysis.

BACKGROUND: The grain yield of cereals is determined by the synergistic interaction between source activity and sink capacity. However, source-sink interactions are far from being fully understood. Therefore, a field experiment was performed in wheat to investigate the responses of flag leaves and grains to sink/source manipulations. RESULTS: Half-degraining delayed but partial defoliation enhanced leaf senescence. Sink/source manipulations influenced the content of reactive oxygen species in the flag leaf and the concentration of phytohormones, including cytokinins, indoleacetic 3-acid and jasmonic acid, in the flag leaves (LDef) and grains (GDef) in defoliated plants and flag leaves (LDG) and grain (GDG) in de-grained plants. Isobaric tag for relative and absolute quantitation (iTRAQ)-based quantitative proteomic analysis indicated that at 16 days after manipulation, a total of 97 and 59 differentially expressed proteins (DEPs) from various functional categories were observed in the LDG and LDef groups, respectively, compared with the control, and 115 and 121 DEPs were observed in the GDG and GDef groups, respectively. The gene ontology annotation terms of the DEPs mainly included carbon fixation, hydrogen peroxide catabolic process, chloroplast and cytoplasm, oxidoreductase activity and glutamate synthase activity in the flag leaves of manipulated plants and organonitrogen compound metabolic process, cytoplasm, vacuolar membrane, CoA carboxylase activity, starch synthase activity and nutrient reservoir activity in the grains of manipulated plants. KEGG pathway enrichment analysis revealed that photosynthesis, carbon, nitrogen and pyruvate metabolism and glycolysis/gluconeogenesis were the processes most affected by sink/source manipulations. Sink/source manipulations affected the activities of amylase and proteinases and, ultimately, changed the mass per grain. CONCLUSIONS: Manipulations to change the sink/source ratio affect hormone levels; hydrolytic enzyme activities; metabolism of carbon, nitrogen and other main compounds; stress resistance; and leaf senescence and thus influence grain mass.

αß-Dehydrocurvularin isolated from the fungus Aspergillus welwitschiae effectively inhibited the behaviour and development of the root-knot nematode Meloidogyne graminicola in rice roots.

BACKGROUND: The root-knot nematode Meloidogyne graminicola has become a serious threat to rice production as a result of the cultivation changes from transplanting to direct seeding. The nematicidal activity of Aspergillus welwitschiae have been investigated in vitro, and the disease control efficacy of the active compound has been evaluated under greenhouse and field conditions. RESULTS: The active compound αß-dehydrocurvularin (αß-DC), isolated by nematicidal assay-directed fractionation, showed significant nematicidal activity against M. graminicola, with a median lethal concentration (LC50) value of 122.2 µg mL- 1. αß-DC effectively decreased the attraction of rice roots to nematodes and the infection of nematodes and also suppressed the development of nematodes under greenhouse conditions. Moreover, αß-DC efficiently reduced the root gall index under field conditions. CONCLUSIONS: To our knowledge, this is the first report to describe the nematicidal activity of αß-DC against M. graminicola. The results obtained under greenhouse and field conditions provide a basis for developing commercial formulations from αß-DC to control M. graminicola in the future.

Genome-wide characterization of the abscisic acid-, stress- and ripening-induced (ASR) gene family in wheat (Triticum aestivum L.).

BACKGROUND: Abscisic acid-, stress-, and ripening-induced (ASR) genes are a class of plant specific transcription factors (TFs), which play important roles in plant development, growth and abiotic stress responses. The wheat ASRs have not been described in genome-wide yet. METHODS: We predicted the transmembrane regions and subcellular localization using the TMHMM server, and Plant-mPLoc server and CELLO v2.5, respectively. Then the phylogeny tree was built by MEGA7. The exon-intron structures, conserved motifs and TFs binding sites were analyzed by GSDS, MEME program and PlantRegMap, respectively. RESULTS: In wheat, 33ASR genes were identified through a genome-wide survey and classified into six groups. Phylogenetic analyses revealed that the TaASR proteins in the same group tightly clustered together, compared with those from other species. Duplication analysis indicated that the TaASR gene family has expanded mainly through tandem and segmental duplication events. Similar gene structures and conserved protein motifs of TaASRs in wheat were identified in the same groups. ASR genes contained various TF binding cites associated with the stress responses in the promoter region. Gene expression was generally associated with the expected group-specific expression pattern in five tissues, including grain, leaf, root, spike and stem, indicating the broad conservation of ASR genes function during wheat evolution. The qRT-PCR analysis revealed that several ASRs were up-regulated in response to NaCl and PEG stress. CONCLUSION: We identified ASR genes in wheat and found that gene duplication events are the main driving force for ASR gene evolution in wheat. The expression of wheat ASR genes was modulated in responses to multiple abiotic stresses, including drought/osmotic and salt stress. The results provided important information for further identifications of the functions of wheat ASR genes and candidate genes for high abiotic stress tolerant wheat breeding.

Photosynthetic characteristics of non-foliar organs in main C3 cereals.

Photosynthesis in non-foliar organs plays an important role in crop growth and productivity, and it has received considerable research attention in recent years. However, compared with the capability of photosynthetic CO2 fixation in leaves, the distinct attributes of photosynthesis in the non-foliar organs of wheat (a C3 species) are unclear. This review presents a comprehensive examination of the photosynthetic characteristics of non-foliar organs in wheat. Compared with leaves, non-foliar organs had a higher capacity to refix respired CO2 , higher tolerance to environmental stresses and slower terminal senescence after anthesis. Additionally, whether C4 photosynthetic metabolism exists in the non-foliar organs of wheat is discussed, as is the advantage of photosynthesis in non-foliar organs during times of abiotic stress. Introducing the photosynthesis-related genes of C4 plants into wheat, which are specifically expressed in non-foliar organs, can be a promising approach for improving wheat productivity.

Priming effect of root-applied silicon on the enhancement of induced resistance to the root-knot nematode Meloidogyne graminicola in rice.

BACKGROUND: Silicon (Si) can confer plant resistance to both abiotic and biotic stress. In the present study, the priming effect of Si on rice (Oryza sativa cv Nipponbare) against the root-knot nematode Meloidogyne graminicola and its histochemical and molecular impact on plant defense mechanisms were evaluated. RESULTS: Si amendment significantly reduced nematodes in rice roots and delayed their development, while no obvious negative effect on giant cells was observed. Increased resistance in rice was correlated with higher transcript levels of defense-related genes (OsERF1, OsEIN2 and OsACS1) in the ethylene (ET) pathway. Si amendment significantly reduced nematode numbers in rice plants with enhanced ET signaling but had no effect in plants deficient in ET signaling, indicating that the priming effects of Si were dependent on the ET pathway. A higher deposition of callose and accumulation of phenolic compounds were observed in rice roots after nematode attack in Si-amended plants than in the controls. CONCLUSION: These findings indicate that the priming effect may partially depend on the production of phenolic compounds and hydrogen peroxide. Further research is required to model the ethylene signal transduction pathway that occurs in the Si-plant-nematode interaction system and gain a better understanding of Si-induced defense in rice.

Global dissection of alternative splicing in paleopolyploid soybean.

Alternative splicing (AS) is common in higher eukaryotes and plays an important role in gene posttranscriptional regulation. It has been suggested that AS varies dramatically among species, tissues, and duplicated gene families of different sizes. However, the genomic forces that govern AS variation remain poorly understood. Here, through genome-wide identification of AS events in the soybean (Glycine max) genome using high-throughput RNA sequencing of 28 samples from different developmental stages, we found that more than 63% of multiexonic genes underwent AS. More AS events occurred in the younger developmental stages than in the older developmental stages for the same type of tissue, and the four main AS types, exon skipping, intron retention, alternative donor sites, and alternative acceptor sites, exhibited different characteristics. Global computational analysis demonstrated that the variations of AS frequency and AS types were significantly correlated with the changes of gene features and gene transcriptional level. Further investigation suggested that the decrease of AS within the genome-wide duplicated genes were due to the diminution of intron length, exon number, and transcriptional level. Altogether, our study revealed that a large number of genes were alternatively spliced in the soybean genome and that variations in gene structure and transcriptional level may play important roles in regulating AS.