Jiangsu Academy of Agricultural Sciences

Polyploidization has provided much genetic variation for plant adaptive evolution, but the mechanisms by which the molecular evolution of polyploid genomes establishes genetic architecture underlying species differentiation are unclear. Brassica is an ideal model to increase knowledge of polyploid evolution. Here we describe a draft genome sequence of Brassica oleracea, comparing it with that of its sister species B. rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks, asymmetrical amplification of transposable elements, differential gene co-retention for specific pathways and variation in gene expression, including alternative splicing, among a large number of paralogous and orthologous genes. Genes related to the production of anticancer phytochemicals and morphological variations illustrate consequences of genome duplication and gene divergence, imparting biochemical and morphological variation to B. oleracea. This study provides insights into Brassica genome evolution and will underpin research into the many important crops in this genus. Brassica oleracea is plant species comprising economically important vegetable crops. Here, the authors report the draft genome sequence of B. oleracea and, through a comparative analysis with the closely related B. rapa, reveal insights into Brassicaevolution and divergence of interspecific genomes and intraspecific subgenomes.

An increasing need of nanotechnology in various industries may cause a huge environment dispersion of nanoparticles in coming years. A concern about nanoparticles interaction with flora and fauna is raised due to a growing load of it in the environment. In recent years, several investigators have shown impact of nanoparticles on plant growth and their accumulation in food source. This review examines the research performed in the last decade to show how metal and metal oxide nanoparticles are influencing the plant metabolism. We addressed here, the impact of nanoparticle on plant in relation to its size, concentration, and exposure methodology. Based on the available reports, we proposed oxidative burst as a general mechanism through which the toxic effects of nanoparticles are spread in plants. This review summarizes the current understanding and the future possibilities of plant-nanoparticle research.

Abstract Cropland is a main source of global nitrogen pollution 1,2 . Mitigating nitrogen pollution from global croplands is a grand challenge because of the nature of non-point-source pollution from millions of farms and the constraints to implementing pollution-reduction measures, such as lack of financial resources and limited nitrogen-management knowledge of farmers 3 . Here we synthesize 1,521 field observations worldwide and identify 11 key measures that can reduce nitrogen losses from croplands to air and water by 30–70%, while increasing crop yield and nitrogen use efficiency (NUE) by 10–30% and 10–80%, respectively. Overall, adoption of this package of measures on global croplands would allow the production of 17 ± 3 Tg (10 12 g) more crop nitrogen (20% increase) with 22 ± 4 Tg less nitrogen fertilizer used (21% reduction) and 26 ± 5 Tg less nitrogen pollution (32% reduction) to the environment for the considered base year of 2015. These changes could gain a global societal benefit of 476 ± 123 billion US dollars (USD) for food supply, human health, ecosystems and climate, with net mitigation costs of only 19 ± 5 billion USD, of which 15 ± 4 billion USD fertilizer saving offsets 44% of the gross mitigation cost. To mitigate nitrogen pollution from croplands in the future, innovative policies such as a nitrogen credit system (NCS) could be implemented to select, incentivize and, where necessary, subsidize the adoption of these measures.

Agricultural production and quality are adversely affected by various abiotic stresses worldwide and this will be exacerbated by the deterioration of global climate. To feed a growing world population, it is very urgent to breed stress-tolerant crops with higher yields and improved qualities against multiple environmental stresses. Since conventional breeding approaches had marginal success due to the complexity of stress tolerance traits, the transgenic approach is now being popularly used to breed stress-tolerant crops. So identifying and characterizing the critical genes involved in plant stress responses is an essential prerequisite for engineering stress-tolerant crops. Far beyond the manipulation of single functional gene, engineering certain regulatory genes has emerged as an effective strategy now for controlling the expression of many stress-responsive genes. Transcription factors (TFs) are good candidates for genetic engineering to breed stress-tolerant crop because of their role as master regulators of many stress-responsive genes. Many TFs belonging to families AP2/EREBP, MYB, WRKY, NAC, bZIP have been found to be involved in various abiotic stresses and some TF genes have also been engineered to improve stress tolerance in model and crop plants. In this review, we take five large families of TFs as examples and review the recent progress of TFs involved in plant abiotic stress responses and their potential utilization to improve multiple stress tolerance of crops in the field conditions.

Abiotic stresses adversely affect plant growth and agricultural productivity. According to the current climate prediction models, crop plants will face a greater number of environmental stresses, which are likely to occur simultaneously in the future. So it is very urgent to breed broad-spectrum tolerant crops in order to meet an increasing demand for food productivity due to global population increase. As one of the largest families of transcription factors (TFs) in plants, NAC TFs play vital roles in regulating plant growth and development processes including abiotic stress responses. Lots of studies indicated that many stress-responsive NAC TFs had been used to improve stress tolerance in crop plants by genetic engineering. In this review, the recent progress in NAC TFs was summarized, and the potential utilization of NAC TFs in breeding abiotic stress tolerant transgenic crops was also be discussed. In view of the complexity of field conditions and the specificity in multiple stress responses, we suggest that the NAC TFs commonly induced by multiple stresses should be promising candidates to produce plants with enhanced multiple stress tolerance. Furthermore, the field evaluation of transgenic crops harboring NAC genes, as well as the suitable promoters for minimizing the negative effects caused by over-expressing some NAC genes, should be considered.

Grain size and shape are important components determining rice grain yield, and they are controlled by quantitative trait loci (QTLs). Here, we report the cloning and functional characterization of a major grain length QTL, qGL3, which encodes a putative protein phosphatase with Kelch-like repeat domain (OsPPKL1). We found a rare allele qgl3 that leads to a long grain phenotype by an aspartate-to-glutamate transition in a conserved AVLDT motif of the second Kelch domain in OsPPKL1. The rice genome has other two OsPPKL1 homologs, OsPPKL2 and OsPPKL3. Transgenic studies showed that OsPPKL1 and OsPPKL3 function as negative regulators of grain length, whereas OsPPKL2 as a positive regulator. The Kelch domains are essential for the OsPPKL1 biological function. Field trials showed that the application of the qgl3 allele could significantly increase grain yield in both inbred and hybrid rice varieties, due to its favorable effect on grain length, filling, and weight.

The extensive use of chemical fertilizers poses serious collateral problems such as environmental pollution, pest resistance development and food safety decline. Researches focused on applying plant-beneficial microorganisms to partially replace chemical fertilizer use is increasing due to the requirement of sustainable agriculture development. Thus to investigate the possibility of a plant-beneficial Trichoderma strain and its bio-organic fertilizer product in saving chemical fertilizer application and in improving crop quality, a field trial and continuous pot experiments were carried out with tomato. Four treatments were set up: a reduced application of chemical fertilizer (75% of the conventional application) plus Trichoderma-enriched bio-organic fertilizer (BF), organic fertilizer (OF) or Trichoderma spore suspension (SS), with using the 100% rate of the conventional chemical fertilizer as the control (CF). The results showed that the total soluble sugar, Vitamin C and nitrate accumulations were, respectively, +up to 24%, +up to 57% and -up to 62% in the tomatoes of the BF treatment compared to those of the control (CF). And both of the pot and field trials revealed that reduced rates of chemical fertilizer plus bio-organic fertilizer produced tomato yields equivalent to those obtained using the 100% of the chemical fertilizer. However, application with the inoculant alone (SS) or combined with the organic fertilizer alone (OF) would lead to a yield decreases of 6-38% and 9-35% over the control. Since the increased abundance of soil microflora and the enhanced soil fertility frequently showed positive linear correlations especially in the BF-treated soils, we conclude that the efficacy of this bio-organic fertilizer for maintaining a stable tomato yield and improving tomato quality may be due to the improved soil microbial activity. Thus, the results suggest that the Trichoderma bio-organic fertilizer could be employed in combination with the appropriate rates of chemical fertilizers to get maximum benefits regarding yield, quality and fertilizer savings.

Abiotic stresses due to environmental factors could adversely affect the growth and development of crops. Among the abiotic stresses, drought and heat stress are two critical threats to crop growth and sustainable agriculture worldwide. Considering global climate change, incidence of combined drought and heat stress is likely to increase. The aim of this study was to shed light on plant growth performance and leaf physiology of three tomatoes cultivars (‘Arvento’, ‘LA1994’ and ‘LA2093’) under control, drought, heat and combined stress. Shoot fresh and dry weight, leaf area and relative water content of all cultivars significantly decreased under drought and combined stress as compared to control. The net photosynthesis and starch content were significantly lower under drought and combined stress than control in the three cultivars. Stomata and pore length of the three cultivars significantly decreased under drought and combined stress as compared to control. The tomato ‘Arvento’ was more affected by heat stress than ‘LA1994’ and ‘LA2093’ due to significant decreases in shoot dry weight, chlorophyll a and carotenoid content, starch content and NPQ (non-photochemical quenching) only in ‘Arvento’ under heat treatment. By comparison, the two heat-tolerant tomatoes were more affected by drought stress compared to ‘Arvento’ as shown by small stomatal and pore area, decreased sucrose content, ΦPSII (quantum yield of photosystem II), ETR (electron transport rate) and qL (fraction of open PSII centers) in ‘LA1994’ and ‘LA2093’. The three cultivars showed similar response when subjected to the combination of drought and heat stress as shown by most physiological parameters, even though only ‘LA1994’ and ‘LA2093’ showed decreased Fv/Fm (maximum potential quantum efficiency of photosystem II), ΦPSII, ETR and qL under combined stress. The cultivars differing in heat sensitivity did not show difference in the combined stress sensitivity, indicating that selection for tomatoes with combined stress tolerance might not be correlated with the single stress tolerance. In this study, drought stress had a predominant effect on tomato over heat stress, which explained why simultaneous application of heat and drought revealed similar physiological responses to the drought stress. These results will uncover the difference and linkage between the physiological response of tomatoes to drought, heat and combined stress and be important for the selection and breeding of tolerant tomato cultivars under single and combine stress.

Plant diseases caused by fungi and oomycetes pose an increasing threat to food security and ecosystem health worldwide. These filamentous pathogens, while taxonomically distinct, modulate host defense responses by secreting effectors, which are typically identified based on the presence of signal peptides. Here we show that Phytophthora sojae and Verticillium dahliae secrete isochorismatases (PsIsc1 and VdIsc1, respectively) that are required for full pathogenesis. PsIsc1 and VdIsc1 can suppress salicylate-mediated innate immunity in planta and hydrolyse isochorismate in vitro. A conserved triad of catalytic residues is essential for both functions. Thus, the two proteins are isochorismatase effectors that disrupt the plant salicylate metabolism pathway by suppressing its precursor. Furthermore, these proteins lack signal peptides, but exhibit characteristics that lead to unconventional secretion. Therefore, this secretion pathway is a novel mechanism for delivering effectors and might play an important role in host-pathogen interactions.

Berries are a good source of natural antioxidants. In the present study, the total antioxidant capacity and phenolic composition of three berry fruits (blueberry, blackberry, and strawberry) cultivated in Nanjing were investigated. Blueberry, with a Trolox equivalent antioxidant capacity (TEAC) value of 14.98 mmol Trolox/100 g dry weight (DW), exhibited the strongest total antioxidant capacity using both the 2,2-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS) and the 2,2-diphenyl-1-picrylhydrazyl (DPPH) methods. Blueberry also had the highest total phenolic content (TPC, 9.44 mg gallic acid/g DW), total flavonoid content (TFC, 36.08 mg rutin/g DW), and total anthocyanidin content (TAC, 24.38 mg catechin/g DW). A preliminary analysis using high performance liquid chromatography (HPLC) showed that the blueberry, blackberry, and strawberry samples tested contained a range of phenolic acids (including gallic acid, protocatechuic acid, p-hydroxybenzoic acid, vanillic acid, caffeic acid, p-coumaric acid, ferulic acid, ellagic acid, and cinnamic acid) and various types of flavonoids (flavone: luteolin; flavonols: rutin, myricetin, quercetrin, and quercetin; flavanols: gallocatechin, epigallocatechin, catechin, and catechin gallate; anthocyanidins: malvidin-3-galactoside, malvidin-3-glucoside, and cyanidin). In particular, the blueberries had high levels of proanthocyanidins and anthocyanidins, which might be responsible for their strong antioxidant activities. These results indicate a potential market role for berries (especially blueberries) as a functional food ingredient or nutraceutical.

The gut microbiota plays an important role in nutrient digestibility in animals. To examine changes in the pig gut microbiota across growth stages and its effects on nutrient digestion, the gut microbiota population in pigs at 28 days (before weaning), and 60, 90, and 150 days of age was assessed by 16S rDNA gene sequencing. The apparent digestibility of crude fiber (CF), neutral detergent fiber (NDF), acid detergent fiber (ADF), crude protein (CP) and ether extract (EE) was also assessed in these pigs. A total of 19,875 operational taxonomic units (OTUs) were identified from all samples. Both bacterial abundance and diversity increased with age. A total of 22 phyla and 249 genera were identified from all fecal samples; Firmicutes and Bacteroidetes were the most dominant phyla in all samples. With increasing age, the proportion of TM7 and Tenericutes increased, whereas the proportion of Lentisphaerae and Synergistetes decreased. The abundance of 36 genera varied with age, and the apparent digestibility of CF increased with age. Three phyla, Proteobacteria, Tenericutes and TM7, and 11 genera, including Anaeroplasma, Campylobacter, and Clostridium, were correlated with apparent CF digestibility.

Pan-genomes from large natural populations can capture genetic diversity and reveal genomic complexity. Using de novo long-read assembly, we generated a graph-based super pan-genome of rice consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice. Our pan-genome reveals extensive structural variations (SVs) and gene presence/absence variations. Additionally, our pan-genome enables the accurate identification of nucleotide-binding leucine-rich repeat genes and characterization of their inter- and intraspecific diversity. Moreover, we uncovered grain weight-associated SVs which specify traits by affecting the expression of their nearby genes. We characterized genetic variants associated with submergence tolerance, seed shattering and plant architecture and found independent selection for a common set of genes that drove adaptation and domestication in Asian and African rice. This super pan-genome facilitates pinpointing of lineage-specific haplotypes for trait-associated genes and provides insights into the evolutionary events that have shaped the genomic architecture of various rice species.

The importance of microbial facultative endosymbionts to insects is increasingly being recognized, but our understanding of how the fitness effects of infection are distributed across symbiont taxa is limited. In the pea aphid, some of the seven known species of facultative symbionts influence their host's resistance to natural enemies, including parasitoid wasps and a pathogenic fungus. Here we show that protection against this entomopathogen, Pandora neoaphidis, can be conferred by strains of four distantly related symbionts (in the genera Regiella, Rickettsia, Rickettsiella and Spiroplasma). They reduce mortality and also decrease fungal sporulation on dead aphids which may help protect nearby genetically identical insects. Pea aphids thus obtain protection from natural enemies through association with a wider range of microbial associates than has previously been thought. Providing resistance against natural enemies appears to be a particularly common way for facultative endosymbionts to increase in frequency within host populations.

Summary Allotetraploid oilseed rape ( Brassica napus L.) is an agriculturally important crop. Cultivation and breeding of B . napus by humans has resulted in numerous genetically diverse morphotypes with optimized agronomic traits and ecophysiological adaptation. To further understand the genetic basis of diversification and adaptation, we report a draft genome of an Asian semi‐winter oilseed rape cultivar ‘ ZS 11’ and its comprehensive genomic comparison with the genomes of the winter‐type cultivar ‘Darmor‐ bzh ’ as well as two progenitors. The integrated BAC ‐to‐ BAC and whole‐genome shotgun sequencing strategies were effective in the assembly of repetitive regions (especially young long terminal repeats) and resulted in a high‐quality genome assembly of B . napus ‘ ZS 11’. Within a short evolutionary period (~6700 years ago), semi‐winter‐type ‘ ZS 11’ and the winter‐type ‘Darmor‐ bzh ’ maintained highly genomic collinearity. Even so, certain genetic differences were also detected in two morphotypes. Relative to ‘Darmor‐ bzh ’, both two subgenomes of ‘ ZS 11’ are closely related to its progenitors, and the ‘ ZS 11’ genome harbored several specific segmental homoeologous exchanges ( HE s). Furthermore, the semi‐winter‐type ‘ ZS 11’ underwent potential genomic introgressions with B . rapa (A r ). Some of these genetic differences were associated with key agronomic traits. A key gene of A03. FLC 3 regulating vernalization‐responsive flowering time in ‘ ZS 11’ was first experienced HE , and then underwent genomic introgression event with A r , which potentially has led to genetic differences in controlling vernalization in the semi‐winter types. Our observations improved our understanding of the genetic diversity of different B . napus morphotypes and the cultivation history of semi‐winter oilseed rape in Asia.

A knowledge gap still remains concerning the in situ influences of nanoparticles on plant systems, partly due to the absence of soil microorganisms. Arbuscular mycorrhizal fungi (AMF) can form a mutualistic symbiosis with the roots of over 90% of land plants. This investigation sought to reveal the responses of mycorrhizal clover (Trifolium repens) to silver nanoparticles (AgNPs) and iron oxide nanoparticles (FeONPs) along a concentration gradient of each. FeONPs at 3.2 mg/kg significantly reduced mycorrhizal clover biomass by 34% by significantly reducing the glomalin content and root nutrient acquisition of AMF. In contrast, no negative effects of AgNPs at concentrations over 0.1 mg/kg were observed; however, AgNPs at 0.01 mg/kg inhibited mycorrhizal clover growth. In response to the elevated AgNPs content, the ability of AMF to alleviate AgNPs stress (via increased growth and ecological behaviors) was enhanced, which decreased Ag content and the activities of antioxidant enzymes in plants. These results were further supported by X-ray microcomputed tomography. Our findings suggest that in soil ecosystem, the influence of nanometals on plant systems would be more complicated than expected, and more attention should be focused on plant responses in combination with those of soil microorganisms.

Rice disease recognition is crucial in automated rice disease diagnosis systems. At present, deep convolutional neural network (CNN) is generally considered the state-of-the-art solution in image recognition. In this paper, we propose a novel rice blast recognition method based on CNN. A dataset of 2906 positive samples and 2902 negative samples is established for training and testing the CNN model. In addition, we conduct comparative experiments for qualitative and quantitatively analysis in our evaluation of the effectiveness of the proposed method. The evaluation results show that the high-level features extracted by CNN are more discriminative and effective than traditional hand-crafted features including local binary patterns histograms (LBPH) and Haar-WT (Wavelet Transform). Moreover, quantitative evaluation results indicate that CNN with Softmax and CNN with support vector machine (SVM) have similar performances, with higher accuracy, larger area under curve (AUC), and better receiver operating characteristic (ROC) curves than both LBPH plus an SVM as the classifier and Haar-WT plus an SVM as the classifier. Therefore, our CNN model is a top performing method for rice blast disease recognition and can be potentially employed in practical applications.

Identification of the mycotoxins produced by different species of Fusarium can serve to verify their classification or to relate the variation of toxigenic potential within a species. Strains of Fusarium graminearum (55), Fusarium crookwellense (16), and Fusarium culmorum (3) were grown in three liquid media and on rice. The toxins produced in the various media were assessed by analyzing the metabolites by gas chromatography/mass spectrometry. These data are used to propose a number of chemotypes. The metabolic profiles of Fusarium graminearum were similar, having chemotype I (deoxynivalenol) in common. In Chinese strains, chemotype IA (deoxynivalenol, 3-acetyl) predominated while the Mexican strains, as with other North American strains, were chemotype IB (deoxynivalenol, 15-acetyl). The Fusarium culmorum strains tested had a chemotype similar to that of chemotype IA of Fusarium graminearum. The Fusarium crookwellense strains, which were collected from eight countries, had a chemotype II (nivalenol, diacetyl) in common, regardless of their source. A similar chemotype II has been reported for Fusarium graminearum strains but it is rare. The Fusarium crookwellense strains also showed the presence of chemotype IA (isotrichodermin, 8-hydroxy) and chemotype IB (isotrichodermin, 7-hydroxy).

Ustilaginoidea virens (Cooke) Takah is an ascomycetous fungus that causes rice false smut, a devastating emerging disease worldwide. Here we report a 39.4 Mb draft genome sequence of U. virens that encodes 8,426 predicted genes. The genome has ~25% repetitive sequences that have been affected by repeat-induced point mutations. Evolutionarily, U. virens is close to the entomopathogenic Metarhizium spp., suggesting potential host jumping across kingdoms. U. virens possesses reduced gene inventories for polysaccharide degradation, nutrient uptake and secondary metabolism, which may result from adaptations to the specific floret infection and biotrophic lifestyles. Consistent with their potential roles in pathogenicity, genes for secreted proteins and secondary metabolism and the pathogen–host interaction database genes are highly enriched in the transcriptome during early infection. We further show that 18 candidate effectors can suppress plant hypersensitive responses. Together, our analyses offer new insights into molecular mechanisms of evolution, biotrophy and pathogenesis of U. virens. Rice false smut, caused by the pathogenic ascomycete fungus Ustilaginoidea virens (Cooke) Takah, has a significant economic impact on crop production. Here, Zhang et al. report the draft genome sequence of U. virensand provide insight into the evolution of genes involved in pathogenicity and adaptation to a biotrophic and floret-infecting lifestyle.

concentrations. However, the mechanisms underlying changes in soil C storage are not well understood, hampering long-term predictions of climate C-feedbacks. The activity of the extracellular enzymes ligninase and cellulase can be used to track changes in the predominant C sources of soil microbes and can thus provide mechanistic insights into soil C loss pathways. Here we show, using meta-analysis, that reductions in soil C stocks with warming are associated with increased ratios of ligninase to cellulase activity. Furthermore, whereas long-term (≥5 years) warming reduced the soil recalcitrant C pool by 14%, short-term warming had no significant effect. Together, these results suggest that warming stimulates microbial utilization of recalcitrant C pools, possibly exacerbating long-term climate-C feedbacks.

Charcoal derived from the partial combustion of vegetation is ubiquitous in soils and sediments and can potentially sequester organic contaminants. To examine the role of charcoal in the sorption and desorption behaviors of diuron pesticide in soil, synthetic charcoals were produced through carbonization of red gum (Eucalyptus spp.) wood chips at 450 and 850 degrees C (referred to as charcoals BC450 and BC850, respectively, in this paper). Pore size distribution analyses revealed that BC850 contained mainly micropores (pores approximately 0.49 nm mean width), whereas BC450 was essentially not a microporous material. Short-term equilibration (< 24 h) tests were conducted to measure sorption and desorption of diuron in a soil amended with various amounts of charcoals of both types. The sorption coefficients, isotherm nonlinearity, and apparent sorption-desorption hysteresis markedly increased with increasing content of charcoal in the soil, more prominently in the case of BC850, presumably due to the presence of micropores and its relatively higher specific surface area. The degree of apparent sorption-desorption hystersis (hysteresis index) showed a good correlation with the micropore volume of the charcoal-amended soils. This study indicates that the presence of small amounts of charcoal produced at high temperatures (e.g., interior of wood logs during a fire) in soil can have a marked effect on the release behavior of organic compounds. Mechanisms of this apparent hysteretic behavior need to be further investigated.