Henan Agricultural University

This paper reports the genome sequence of domesticated tomato, a major crop plant, and a draft sequence for its closest wild relative; comparative genomics reveal very little divergence between the two genomes but some important differences with the potato genome, another important food crop in the genus Solanum. Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium2, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.

Plant microbiomes are essential to host health and productivity but the ecological processes that govern crop microbiome assembly are not fully known. Here we examined bacterial communities across 684 samples from soils (rhizosphere and bulk soil) and multiple compartment niches (rhizoplane, root endosphere, phylloplane, and leaf endosphere) in maize (Zea mays)-wheat (Triticum aestivum)/barley (Hordeum vulgare) rotation system under different fertilization practices at two contrasting sites. Our results demonstrate that microbiome assembly along the soil-plant continuum is shaped predominantly by compartment niche and host species rather than by site or fertilization practice. From soils to epiphytes to endophytes, host selection pressure sequentially increased and bacterial diversity and network complexity consequently reduced, with the strongest host effect in leaf endosphere. Source tracking indicates that crop microbiome is mainly derived from soils and gradually enriched and filtered at different plant compartment niches. Moreover, crop microbiomes were dominated by a few dominant taxa (c. 0.5% of bacterial phylotypes), with bacilli identified as the important biomarker taxa for wheat and barley and Methylobacteriaceae for maize. Our work provides comprehensive empirical evidence on host selection, potential sources and enrichment processes for crop microbiome assembly, and has important implications for future crop management and manipulation of crop microbiome for sustainable agriculture.

Transboundary and Emerging DiseasesVolume 65, Issue 6 p. 1482-1484 OUTBREAK ALERTS Emergence of African Swine Fever in China, 2018 Xintao Zhou, Xintao Zhou Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, ChinaThese authors contributed equally to this studySearch for more papers by this authorNan Li, Nan Li Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, ChinaThese authors contributed equally to this studySearch for more papers by this authorYuzi Luo, Yuzi Luo State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, ChinaThese authors contributed equally to this studySearch for more papers by this authorYe Liu, Ye Liu Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, ChinaSearch for more papers by this authorFaming Miao, Faming Miao Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, ChinaSearch for more papers by this authorTeng Chen, Teng Chen Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, ChinaSearch for more papers by this authorShoufeng Zhang, Shoufeng Zhang Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, ChinaSearch for more papers by this authorPeili Cao, Peili Cao State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, ChinaSearch for more papers by this authorXiangdong Li, Xiangdong Li National Research Center for Veterinary Medicine, Luoyang, ChinaSearch for more papers by this authorKegong Tian, Corresponding Author Kegong Tian tiankg@263.net orcid.org/0000-0001-5362-1415 National Research Center for Veterinary Medicine, Luoyang, China College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China Correspondence Rongliang Hu, Laboratory of Epidemiology and Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, 666 Liuying West Road, Jingyue Economic Development Zone, Changchun, Jilin 130122, China. Email: ronglianghu@hotmail.com and Hua-Ji Qiu, Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Road, Harbin 150069, Heilongjiang, China. Email: qiuhuaji@caas.cn and Kegong Tian, National Research Center for Veterinary Medicine, High-Tech District, Luoyang, China. Email: tiankg@263.netSearch for more papers by this authorHua-Ji Qiu, Corresponding Author Hua-Ji Qiu qiuhuaji@caas.cn State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China Correspondence Rongliang Hu, Laboratory of Epidemiology and Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, 666 Liuying West Road, Jingyue Economic Development Zone, Changchun, Jilin 130122, China. Email: ronglianghu@hotmail.com and Hua-Ji Qiu, Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Road, Harbin 150069, Heilongjiang, China. Email: qiuhuaji@caas.cn and Kegong Tian, National Research Center for Veterinary Medicine, High-Tech District, Luoyang, China. Email: tiankg@263.netSearch for more papers by this authorRongliang Hu, Corresponding Author Rongliang Hu ronglianghu@hotmail.com Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China Correspondence Rongliang Hu, Laboratory of Epidemiology and Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, 666 Liuying West Road, Jingyue Economic Development Zone, Changchun, Jilin 130122, China. Email: ronglianghu@hotmail.com and Hua-Ji Qiu, Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Road, Harbin 150069, Heilongjiang, China. Email: qiuhuaji@caas.cn and Kegong Tian, National Research Center for Veterinary Medicine, High-Tech District, Luoyang, China. Email: tiankg@263.netSearch for more papers by this author Xintao Zhou, Xintao Zhou Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, ChinaThese authors contributed equally to this studySearch for more papers by this authorNan Li, Nan Li Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, ChinaThese authors contributed equally to this studySearch for more papers by this authorYuzi Luo, Yuzi Luo State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, ChinaThese authors contributed equally to this studySearch for more papers by this authorYe Liu, Ye Liu Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, ChinaSearch for more papers by this authorFaming Miao, Faming Miao Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, ChinaSearch for more papers by this authorTeng Chen, Teng Chen Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, ChinaSearch for more papers by this authorShoufeng Zhang, Shoufeng Zhang Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, ChinaSearch for more papers by this authorPeili Cao, Peili Cao State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, ChinaSearch for more papers by this authorXiangdong Li, Xiangdong Li National Research Center for Veterinary Medicine, Luoyang, ChinaSearch for more papers by this authorKegong Tian, Corresponding Author Kegong Tian tiankg@263.net orcid.org/0000-0001-5362-1415 National Research Center for Veterinary Medicine, Luoyang, China College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China Correspondence Rongliang Hu, Laboratory of Epidemiology and Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, 666 Liuying West Road, Jingyue Economic Development Zone, Changchun, Jilin 130122, China. Email: ronglianghu@hotmail.com and Hua-Ji Qiu, Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Road, Harbin 150069, Heilongjiang, China. Email: qiuhuaji@caas.cn and Kegong Tian, National Research Center for Veterinary Medicine, High-Tech District, Luoyang, China. Email: tiankg@263.netSearch for more papers by this authorHua-Ji Qiu, Corresponding Author Hua-Ji Qiu qiuhuaji@caas.cn State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China Correspondence Rongliang Hu, Laboratory of Epidemiology and Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, 666 Liuying West Road, Jingyue Economic Development Zone, Changchun, Jilin 130122, China. Email: ronglianghu@hotmail.com and Hua-Ji Qiu, Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Road, Harbin 150069, Heilongjiang, China. Email: qiuhuaji@caas.cn and Kegong Tian, National Research Center for Veterinary Medicine, High-Tech District, Luoyang, China. Email: tiankg@263.netSearch for more papers by this authorRongliang Hu, Corresponding Author Rongliang Hu ronglianghu@hotmail.com Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China Correspondence Rongliang Hu, Laboratory of Epidemiology and Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, 666 Liuying West Road, Jingyue Economic Development Zone, Changchun, Jilin 130122, China. Email: ronglianghu@hotmail.com and Hua-Ji Qiu, Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Road, Harbin 150069, Heilongjiang, China. Email: qiuhuaji@caas.cn and Kegong Tian, National Research Center for Veterinary Medicine, High-Tech District, Luoyang, China. Email: tiankg@263.netSearch for more papers by this author First published: 13 August 2018 https://doi.org/10.1111/tbed.12989Citations: 287 Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. 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In this study, several simple equations are suggested to investigate the effects of size and density on the number, surface area, stiffening efficiency, and specific surface area of nanoparticles in polymer nanocomposites. In addition, the roles of nanoparticle size and interphase thickness in the interfacial/interphase properties and tensile strength of nanocomposites are explained by various equations. The aggregates/agglomerates of nanoparticles are also assumed as large particles in nanocomposites, and their influences on the nanoparticle characteristics, interface/interphase properties, and tensile strength are discussed. The small size advantageously affects the number, surface area, stiffening efficiency, and specific surface area of nanoparticles. Only 2 g of isolated and well-dispersed nanoparticles with radius of 10 nm (R = 10 nm) and density of 2 g/cm3 produce the significant interfacial area of 250 m2 with polymer matrix. Moreover, only a thick interphase cannot produce high interfacial/interphase parameters and significant mechanical properties in nanocomposites because the filler size and aggregates/agglomerates also control these terms. It is found that a thick interphase (t = 25 nm) surrounding the big nanoparticles (R = 50 nm) only improves the B interphase parameter to about 4, while B = 13 is obtained by the smallest nanoparticles and the thickest interphase.

Exosomes are well-known key mediators of intercellular communication and contribute to various physiological and pathological processes. Their biogenesis involves four key steps, including cargo sorting, MVB formation and maturation, transport of MVBs, and MVB fusion with the plasma membrane. Each process is modulated through the competition or coordination of multiple mechanisms, whereby diverse repertoires of molecular cargos are sorted into distinct subpopulations of exosomes, resulting in the high heterogeneity of exosomes. Intriguingly, cancer cells exploit various strategies, such as aberrant gene expression, posttranslational modifications, and altered signaling pathways, to regulate the biogenesis, composition, and eventually functions of exosomes to promote cancer progression. Therefore, exosome biogenesis-targeted therapy is being actively explored. In this review, we systematically summarize recent progress in understanding the machinery of exosome biogenesis and how it is regulated in the context of cancer. In particular, we highlight pharmacological targeting of exosome biogenesis as a promising cancer therapeutic strategy.

The sweetpotato whitefly Bemisia tabaci is a highly destructive agricultural and ornamental crop pest. It damages host plants through both phloem feeding and vectoring plant pathogens. Introductions of B. tabaci are difficult to quarantine and eradicate because of its high reproductive rates, broad host plant range, and insecticide resistance. A total of 791 Gb of raw DNA sequence from whole genome shotgun sequencing, and 13 BAC pooling libraries were generated by Illumina sequencing using different combinations of mate-pair and pair-end libraries. Assembly gave a final genome with a scaffold N50 of 437 kb, and a total length of 658 Mb. Annotation of repetitive elements and coding regions resulted in 265.0 Mb TEs (40.3%) and 20 786 protein-coding genes with putative gene family expansions, respectively. Phylogenetic analysis based on orthologs across 14 arthropod taxa suggested that MED/Q is clustered into a hemipteran clade containing A. pisum and is a sister lineage to a clade containing both R. prolixus and N. lugens. Genome completeness, as estimated using the CEGMA and Benchmarking Universal Single-Copy Orthologs pipelines, reached 96% and 79%. These MED/Q genomic resources lay a foundation for future 'pan-genomic' comparisons of invasive vs. noninvasive, invasive vs. invasive, and native vs. exotic Bemisia, which, in return, will open up new avenues of investigation into whitefly biology, evolution, and management.

BACKGROUND: Agricultural food production is at the base of food and fodder, with fertilization having fundamentally and continuously increased crop yield over the last decades. The performance of crops is intimately tied to their microbiome as they together form holobionts. The importance of the microbiome for plant performance is, however, notoriously ignored in agricultural systems as fertilization disconnects the dependency of plants for often plant-beneficial microbial processes. Moreover, we lack a holistic understanding of how fertilization regimes affect the soil microbiome. Here, we examined the effect of a 2-year fertilization regime (no nitrogen fertilization control, nitrogen fertilization, and nitrogen fertilization plus straw amendment) on entire soil microbiomes (bacteria, fungi, and protist) in three common agricultural soil types cropped with maize in two seasons. RESULTS: We found that the application of nitrogen fertilizers more strongly affected protist than bacterial and fungal communities. Nitrogen fertilization indirectly reduced protist diversity through changing abiotic properties and bacterial and fungal communities which differed between soil types and sampling seasons. Nitrogen fertilizer plus straw amendment had greater effects on soil physicochemical properties and microbiome diversity than nitrogen addition alone. Moreover, nitrogen fertilization, even more together with straw, increased soil microbiome network complexity, suggesting that the application of nitrogen fertilizers tightened soil microbiomes interactions. CONCLUSIONS: Together, our results suggest that protists are the most susceptible microbiome component to the application of nitrogen fertilizers. As protist communities also exhibit the strongest seasonal dynamics, they serve as the most sensitive bioindicators of soil changes. Changes in protist communities might have long-term effects if some of the key protist hubs that govern microbiome complexities as top microbiome predators are altered. This study serves as the stepping stone to promote protists as promising agents in targeted microbiome engineering to help in reducing the dependency on exogenous unsustainably high fertilization and pesticide applications.

BACKGROUND: Plants live with diverse microbial communities which profoundly affect multiple facets of host performance, but if and how host development impacts the assembly, functions and microbial interactions of crop microbiomes are poorly understood. Here we examined both bacterial and fungal communities across soils, epiphytic and endophytic niches of leaf and root, and plastic leaf of fake plant (representing environment-originating microbes) at three developmental stages of maize at two contrasting sites, and further explored the potential function of phylloplane microbiomes based on metagenomics. RESULTS: Our results suggested that plant developmental stage had a much stronger influence on the microbial diversity, composition and interkingdom networks in plant compartments than in soils, with the strongest effect in the phylloplane. Phylloplane microbiomes were co-shaped by both plant growth and seasonal environmental factors, with the air (represented by fake plants) as its important source. Further, we found that bacterial communities in plant compartments were more strongly driven by deterministic processes at the early stage but a similar pattern was for fungal communities at the late stage. Moreover, bacterial taxa played a more important role in microbial interkingdom network and crop yield prediction at the early stage, while fungal taxa did so at the late stage. Metagenomic analyses further indicated that phylloplane microbiomes possessed higher functional diversity at the early stage than the late stage, with functional genes related to nutrient provision enriched at the early stage and N assimilation and C degradation enriched at the late stage. Coincidently, more abundant beneficial bacterial taxa like Actinobacteria, Burkholderiaceae and Rhizobiaceae in plant microbiomes were observed at the early stage, but more saprophytic fungi at the late stage. CONCLUSIONS: Our results suggest that host developmental stage profoundly influences plant microbiome assembly and functions, and the bacterial and fungal microbiomes take a differentiated ecological role at different stages of plant development. This study provides empirical evidence for host exerting strong effect on plant microbiomes by deterministic selection during plant growth and development. These findings have implications for the development of future tools to manipulate microbiome for sustainable increase in primary productivity. Video Abstract.

There is a global need to use plants to restore the ecological environment. There is no systematic review of phytoremediation mechanisms and the parameters for environmental pollution. Here, we review this situation and describe the purification rate of different plants for different pollutants, as well as methods to improve the purification rate of plants. This is needed to promote the use of plants to restore the ecosystems and the environment. We found that plants mainly use their own metabolism including the interaction with microorganisms to repair their ecological environment. In the process of remediation, the purification factors of plants are affected by many conditions such as light intensity, stomatal conductance, temperature and microbial species. In addition the efficiency of phytoremediation is depending on the plants species-specific metabolism including air absorption and photosynthesis, diversity of soil microorganisms and heavy metal uptake. Although the use of nanomaterials and compost promote the restoration of plants to the environment, a high dose may have negative impacts on the plants. In order to improve the practicability of the phytoremediation on environmental restoration, further research is needed to study the effects of different kinds of catalysts on the efficiency of phytoremediation. Thus, the present review provides a recent update for development and applications of phytoremediation in different environments including air, water, and soil.

Fertilization has a large impact on the soil microbial communities, which play pivotal roles in soil biogeochemical cycling and ecological processes. While the effects of changes in nutrient availability due to fertilization on the soil microbial communities have received considerable attention, specific microbial taxa strongly influenced by long-term organic and inorganic fertilization, their potential effects and associations with soil nutrients remain unclear. Here we use deep 16S amplicon sequencing to investigate bacterial community characteristics in a fluvo-aquic soil treated for 24 years with inorganic fertilizers and organics (manure and straw)-inorganic fertilizers, and uncover potential links between soil nutrient parameters and specific bacterial taxa. Our results showed that combined organic-inorganic fertilization increased soil organic carbon (SOC) and total nitrogen (TN) contents and altered bacterial community composition, while inorganic fertilization had little impact on soil nutrients and bacterial community composition. SOC and TN emerged as the major determinants of community composition. The abundances of specific taxa, especially Arenimonas, Gemmatimonas and an unclassified member of Xanthomonadaceae, were substantially increased by organic-inorganic amendments rather than inorganic amendments only. A co-occurrence based network analysis demonstrated that SOC and TN had strong positive associations with some taxa (Gemmatimonas and the members of Acidobacteria subgroup 6, Myxococcales, Betaproteobacteria and Bacteroidetes), and Gemmatimonas, Flavobacterium and an unclassified member of Verrucomicrobia were identified as the keystone taxa. These specific taxa identified above are implicated in the decomposition of complex organic matters and soil carbon, nitrogen and phosphorus transformations. The present work strengthens our current understanding of the soil microbial community structure and functions under long-term fertilization management and provides certain theoretical support for selection of rational fertilization strategies.

The postdomestication adaptation of maize to longer days required reduced photoperiod sensitivity to optimize flowering time. We performed a genome-wide association study and confirmed that ZmCCT, encoding a CCT domain-containing protein, is associated with the photoperiod response. In early-flowering maize we detected a CACTA-like transposable element (TE) within the ZmCCT promoter that dramatically reduced flowering time. TE insertion likely occurred after domestication and was selected as maize adapted to temperate zones. This process resulted in a strong selective sweep within the TE-related block of linkage disequilibrium. Functional validations indicated that the TE represses ZmCCT expression to reduce photoperiod sensitivity, thus accelerating maize spread to long-day environments.

Phosphorus (P) adsorption–desorption in soil is an important internal cycle related to soil fertility problems, as well as for determining the environmental fate of P. Soil organic matter (SOM) has been identified as an important factor affecting the adsorption–desorption of soil P through different mechanisms. In this study, humic acids were added to change the SOM content in black soil. Following an incubation period of 30 days, the changes in soil P adsorption–desorption capacity were studied. The results indicated that increased SOM led to increases in the soil available P and the P activation coefficient. All soil treatments fitted well with both Langmuir and Freundlich equations. The P adsorption and desorption characteristics were analyzed using the Langmuir equation as a local isotherm. The maximum adsorption capacity of P increased with the increase in SOM, but the P bonding energy and maximum buffering capacity first decreased, and then increased, with the lowest values obtained with a SOM content of 75.3 mg kg−1. Both the maximum desorption capacity of P and the ratio of soil P desorption showed a fluctuating trend, which were the greatest when the SOM content reached 75.3 g kg−1 in black soil, showing an improved ability to release P. Thus, the addition of organic matter could efficiently enhance P availability by reducing the strength of P adsorption and the maximum phosphate buffering capacity and increasing the desorption of P to some extent, with the greatest P availability obtained at a SOM content of 75.3 g kg−1.

It is a long-standing goal of scientists and breeders to precisely control a gene for studying its function as well as improving crop yield, quality, and tolerance to various environmental stresses. The discovery and modification of CRISPR/Cas system, a nature-occurred gene editing tool, opens an era for studying gene function and precision crop breeding. In this review, we first introduce the brief history of CRISPR/Cas discovery followed the mechanism and application of CRISPR/Cas system on gene function study and crop improvement. Currently, CRISPR/Cas genome editing has been becoming a mature cutting-edge biotechnological tool for crop improvement that already used in many different traits in crops, including pathogen resistance, abiotic tolerance, plant development and morphology and even secondary metabolism and fiber development. Finally, we point out the major issues associating with CRISPR/Cas system and the future research directions. Key Scientific Concepts of Review: CRISPR/Cas9 system is a robust and powerful biotechnological tool for targeting an individual DNA and RNA sequence in the genome. It can be used to target a sequence for gene knockin, knockout and replacement as well as monitoring and regulating gene expression at the genome and epigenome levels by binding a specific sequence. Agrobacterium-mediated method is still the major and efficient method for delivering CRISPR/Cas regents into targeted plant cells. However, other delivery methods, such as virus-mediated method, have been developed and enhanced the application potentials of CRISPR/Cas9-based crop improvement. PAM requirement offers the CRISPR/Cas9-targted genetic loci and also limits the application of CRISPR/Cas9. Discovering new Cas proteins and modifying current Cas enzymes play an important role in CRISPR/Cas9-based genome editing. Developing a better CRISPR/Cas9 system, including the delivery system and the methods eliminating off-target effects, and finding key/master genes for controlling crop growth and development is two major directions for CRISPR/Cas9-based crop improvement.

Summary: Creation of Circos plot is one of the most efficient approaches to visualize genomic data. However, the installation and use of existing tools to make Circos plot are challenging for users lacking of coding experiences. To address this issue, we developed an R/Shiny application shinyCircos, a graphical user interface for interactive creation of Circos plot. shinyCircos can be easily installed either on computers for personal use or on local or public servers to provide online use to the community. Furthermore, various types of Circos plots could be easily generated and decorated with simple mouse-click. Availability and implementation: shinyCircos and its manual are freely available at https://github.com/venyao/shinyCircos. shinyCircos is deployed at https://yimingyu.shinyapps.io/shinycircos/ and http://shinycircos.ncpgr.cn/ for online use. Contact: diana1983941@mail.hzau.edu.cn or yaowen@henau.edu.cn.

Mycorrhizal inoculation stimulates growth, photosynthesis and nutrient uptake in a wide range of host plants. However, the ultimate effects of arbuscular mycorrhyzal (AM) symbiosis vary with the plants and fungal species involved in the association. Therefore, identification of the appropriate combinations of AM fungi (AMF) that interact synergistically to improve their benefits is of high significance. Here, three AM fungal compositions namely VT (Claroideoglomus sp., Funneliformis sp., Diversispora sp., Glomus sp. and Rhizophagus sp.) and BF (G. intradices, G. microageregatum BEG and G. Claroideum BEG 210), and Funneliformis mosseae (Fm) were investigated with respect to the growth, gas exchange parameters, enzymes activities in Calvin cycles and related gene expression in cucumber seedlings. The results showed that VT, BF and Fm could successfully colonize cucumber root to a different degree with the colonization rates 82.38%, 74.65% and 70.32% at 46 d post inoculation, respectively. The plant height, stem diameter, dry weight, root to shoot ratio of cucumber seedlings inoculated with AMF increased significantly compared with the non-inoculated control. Moreover, AMF colonization greatly increased the root activity, chlorophyll content, net photosynthetic rate, light saturated rate of the CO2 assimilation (Asat), maximum carboxylation rates (Vcmax) and maximum ribulose-1,5-bis-phosphate (RuBP) regeneration rate (Jmax), which were increased by 52.81%, 30.75%, 58.76%, 47.00%, 69.15% and 65.53% when inoculated with VT, respectively. The activities of some key enzymes such RuBP carboxylase/oxygenase (RuBisCO), D-fructose-1,6-bisphosphatase (FBPase), D-fructose-6-phosphatase (F6P) and ribulose-5-phosphate kinase (Ru5PK), and related gene expression involved in the Calvin cycle including RCA, FBPase, FBPA, SBPase, rbcS and rbcL were upregulated by AMF colonization. AMF inoculation also improved macro- and micro nutrient contents such as N, P, K, S, Ca, Cu, Fe, Mn, Mg and Zn in roots. Further analysis revealed that inoculation with VT had relatively better effect on growth of cucumber seedling followed by BF and Fm, indicating that AMF composition consisting of distant AMF species may have a better effect than a single or closely related AMF spp. This study advances the understanding of plant responses to different AM fungi towards development of strategies on AMF-promoted vegetable production.

Deposition of liquid droplets on solid surfaces is of great importance to many fundamental scientific principles and technological applications, such as spraying, coating, and printing. For example, during the process of pesticide spraying, more than 50% of agrochemicals are lost because of the undesired bouncing and splashing behaviors on hydrophobic or superhydrophobic leaves. We show that this kind of splashing on superhydrophobic surfaces can be greatly inhibited by adding a small amount of a vesicular surfactant, Aerosol OT. Rather than reducing splashing by increasing the viscosity via polymer additives, the vesicular surfactant confines the motion of liquid with the help of wettability transition and thus inhibits the splash. Significantly, the vesicular surfactant exhibits a distinguished ability to alter the surface wettability during the first inertial spreading stage of ~2 ms because of its dense aggregates at the air/water interface. A comprehensive model proposed by this idea could help in understanding the complex interfacial interactions at the solid/liquid/air interface.

The rapid development and application of molecular marker assays have facilitated genomic selection and genome-wide linkage and association studies in wheat breeding. Although PCR-based markers (e.g. simple sequence repeats and functional markers) and genotyping by sequencing have contributed greatly to gene discovery and marker-assisted selection, the release of a more accurate and complete bread wheat reference genome has resulted in the design of single-nucleotide polymorphism (SNP) arrays based on different densities or application targets. Here, we evaluated seven types of wheat SNP arrays in terms of their SNP number, distribution, density, associated genes, heterozygosity and application. The results suggested that the Wheat 660K SNP array contained the highest percentage (99.05%) of genome-specific SNPs with reliable physical positions. SNP density analysis indicated that the SNPs were almost evenly distributed across the whole genome. In addition, 229 266 SNPs in the Wheat 660K SNP array were located in 66 834 annotated gene or promoter intervals. The annotated genes revealed by the Wheat 660K SNP array almost covered all genes revealed by the Wheat 35K (97.44%), 55K (99.73%), 90K (86.9%) and 820K (85.3%) SNP arrays. Therefore, the Wheat 660K SNP array could act as a substitute for other 6 arrays and shows promise for a wide range of possible applications. In summary, the Wheat 660K SNP array is reliable and cost-effective and may be the best choice for targeted genotyping and marker-assisted selection in wheat genetic improvement.

Omega-3 polyunsaturated fatty acids (omega-3 PUFAs), which are essential fatty acids that humans should obtain from diet, have potential benefits for human health. In addition to altering the structure and function of cell membranes, omega-3 PUFAs (docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), alpha-linolenic acid (ALA), and docosapentaenoic acid (DPA)) exert different effects on intestinal immune tolerance and gut microbiota maintenance. Firstly, we review the effect of omega-3 PUFAs on gut microbiota. And the effects of omega-3 PUFAs on intestinal immunity and inflammation were described. Furthermore, the important roles of omega-3 PUFAs in maintaining the balance between gut immunity and the gut microbiota were discussed. Additional factors, such as obesity and diseases (NAFLD, gastrointestinal malignancies or cancer, bacterial and viral infections), which are associated with variability in omega-3 PUFA metabolism, can influence omega-3 PUFAs-microbiome-immune system interactions in the intestinal tract and also play roles in regulating gut immunity. This review identifies several pathways by which the microbiota modulates the gut immune system through omega-3 PUFAs. Omega-3 supplementation can be targeted to specific pathways to prevent and alleviate intestinal diseases, which may help researchers identify innovative diagnostic methods.

Nanoscale metal–organic frameworks (nMOF) materials represent an attractive tool for various biomedical applications. Due to the chemical versatility, enormous porosity, and tunable degradability of nMOFs, they have been adopted as carriers for delivery of imaging and/or therapeutic cargos. However, the relatively low stability of most nMOFs has limited practical in vivo applications. Here we report the production and characterization of an intrinsically radioactive UiO-66 nMOF (89Zr-UiO-66) with incorporation of positron-emitting isotope zirconium-89 (89Zr). 89Zr-UiO-66 was further functionalized with pyrene-derived polyethylene glycol (Py–PGA-PEG) and conjugated with a peptide ligand (F3) to nucleolin for targeting of triple-negative breast tumors. Doxorubicin (DOX) was loaded onto UiO-66 with a relatively high loading capacity (1 mg DOX/mg UiO-66) and served as both a therapeutic cargo and a fluorescence visualizer in this study. Functionalized 89Zr-UiO-66 demonstrated strong radiochemical and material stability in different biological media. Based on the findings from cellular targeting and in vivo positron emission tomography (PET) imaging, we can conclude that 89Zr-UiO-66/Py–PGA-PEG-F3 can serve as an image-guidable, tumor-selective cargo delivery nanoplatform. In addition, toxicity evaluation confirmed that properly PEGylated UiO-66 did not impose acute or chronic toxicity to the test subjects. With selective targeting of nucleolin on both tumor vasculature and tumor cells, this intrinsically radioactive nMOF can find broad application in cancer theranostics.

Porcine reproductive and respiratory syndrome virus (PRRSV) has been epidemic more than 30 years in America and 20 years in China. It is still one of the most important causative agents to the worldwide swine industry. Here, we systematically analyzed the prevalence status of PRRSV in China by a molecular epidemiological perspective. Now both PRRSV-1 and PRRSV-2 are circulating and approximately more than 80% of pig farms are seropositive for PRRSV. For PRRSV-2, there are four lineages (lineage 1, lineage 3, lineage 5, lineage 8) circulating in the fields. Lineage 8 (CH-1a-like) and lineage 5 (BJ-4-like) appeared almost at the same time during 1995-1996. Notably, BJ-4 shares 99.6% and 99.8% identity with VR2332 and RespPRRS MLV, respectively. It means that lineage 5 is likely to be imported from America. Now highly pathogenic PRRSV (HP-PRRSV) which was considered to be evolved from local diversity of lineage 8 strains is predominant with different variants. Lineage 3 appeared in 2010 which is mainly sporadic in south of China. Lineage 1, also known as NADC30-like strains in China, has been prevalent since 2013 and leads to PRRS pandemic again. For PRRSV-1, although sporadic at present, more than 9 provinces/regions have been reported. All the circulating strains belong to subtype I. It should be paid more attention since there are no vaccines available. Our analysis would help to deeply understand the prevalent status of PRRSV in China and provide useful information for prevention and control of porcine reproductive and respiratory syndrome (PRRS).