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Overaccumulation of allelochemicals in soil from trees has a negative effect on the growth of Panax notoginseng and cause root rot. Many plant secreted phenols are water-soluble substances that can be depleted by leaching. However, comprehensive understanding of the effect of leaching of phenols in Chinese fir soil on P. notoginseng root rot disease is still lacking. Soil with high level of phenols was leached with five intensities and their effect on the root rot of P. notoginseng was assessed. Then, the relationship of root rot with changes in soil chemical properties and phenol content as well as rhizospheric microorganisms was analyzed. With increasing leaching intensity, the levels of phenols in soils and the incidence of root rot decreased significantly. Decreased phenol content could alleviate root rot by modifying the soil microbial community. Network analysis showed that root rot incidence was positively correlated with the p-hydroxybenzoic acid-enriched pathogenic fungus Ilyonectria but negatively correlated with p-hydroxybenzoic acid (HA)-, ferulic acid (FA)- or vanillic acid (VA)-suppressed bacteria, including Sphingomonas, Lysobacter, Massilia and Burkholderia. Culture experiments confirmed that individual HA, FA and VA as well as a mixture of the five phenols with increasing concentrations could stimulate the growth and sporulation of I. destructans but suppress the growth and biofilm formation of bacteria (Burkholderia and Lysobacter). Moreover, Burkholderia isolates showed antagonistic activity against the growth of I. destructans. Leaching could relieve the stimulation of pathogenic fungi by phenols and reduce the pressure on phenolic-suppressed bacteria, thereby reducing the incidence of root rot disease.

Panax notoginseng is a highly valuable herb, but root rot disease severely impairs its development and decreases the yield and quality of roots. In this study, a fungal isolate (3A‐2‐2) was obtained from P. notoginseng seedlings with root rot symptoms and was identified as Plectosphaerella plurivora based on morphological characteristics and molecular analysis. The fungal isolate 3A‐2‐2 could cause root rot disease and be re‐isolated, fulfilling Koch's postulates. This is the first study to report on root rot disease caused by P. plurivora on P. notoginseng in China.

Endophytic fungi can be beneficial to plant growth. However, the molecular mechanisms underlying colonization of Acremonium spp. remain unclear. In this study, a novel endophytic Acremonium strain was isolated from the buds of Panax notoginseng and named Acremonium sp. D212. The Acremonium sp. D212 could colonize the roots of P. notoginseng, enhance the resistance of P. notoginseng to root rot disease, and promote root growth and saponin biosynthesis in P. notoginseng. Acremonium sp. D212 could secrete indole-3-acetic acid (IAA) and jasmonic acid (JA), and inoculation with the fungus increased the endogenous levels of IAA and JA in P. notoginseng. Colonization of the Acremonium sp. D212 in the roots of the rice line Nipponbare was dependent on the concentration of methyl jasmonate (MeJA) (2-15 μmol/L) and 1-naphthalenacetic acid (NAA) (10-20 μmol/L). Moreover, the roots of the JA signaling-defective coi1-18 mutant were colonized by Acremonium sp. D212 to a lesser degree than those of the wild-type Nipponbare and miR393b-overexpressing lines, and the colonization was rescued by MeJA but not by NAA. It suggests that the cross-talk between JA signaling and the auxin biosynthetic pathway plays a crucial role in the colonization of Acremonium sp. D212 in host plants.

Long-term moderately high or low temperatures can damage economically important plants. In the present study, we treated Panax notoginseng, an important traditional Chinese medicine, with temperatures of 10, 20, and 30 °C for 30 days. We then investigated P. notoginseng glycerolipidome responses to these moderate temperature stresses using an ESI/MS-MS-based lipidomic approach. Both long-term chilling (LTC, 10 °C) and long-term heat (LTH, 30 °C) decreased photo pigment levels and photosynthetic rate. LTH-induced degradation of photo pigments and glycerolipids may further cause the decline of photosynthesis and thereafter the senescence of leaves. LTC-induced photosynthesis decline is attributed to the degradation of photosynthetic pigments rather than the degradation of chloroplastidic lipids. P. notoginseng has an especially high level of lysophosphatidylglycerol, which may indicate that either P. notoginseng phospholipase A acts in a special manner on phosphatidylglycerol (PG), or that phospholipase B acts. The ratio of sulfoquinovosyldiacylglycerol (SQDG) to PG increased significantly after LTC treatment, which may indicate that SQDG partially substitutes for PG. After LTC treatment, the increase in the degree of unsaturation of plastidic lipids was less than that of extraplastidic lipids, and the increase in the unsaturation of PG was the largest among the ten lipid classes tested. These results indicate that increasing the level of unsaturated PG may play a special role in maintaining the function and stability of P. notoginseng photosystems after LTC treatment. Keywords: Extraplastidic lipids, Glycerolipidome, Long-term chilling stress, Long-term heat stress, Panax notoginseng, Plastidic lipids

In September 2020, samples of galled roots with rhizosphere soil were collected from declining Gentiana macrophylla in Yulong County, China. The pathogenic nematodes were identified by observing morphological characteristics of females, second-stage juveniles and perineal pattern, sequence alignments, and specific amplification of sequence characterized amplified region (SCAR). The results showed that the perineal pattern of this nematode was round or oval, the dorsal arch was moderately high or low, one side or both of the lateral field extended to form a wing shape, the tail region had punctations, and the morphological characteristics and morphometric values of second-stage juveniles and females were similar to those of Meloidogyne hapla. The ITS region fragment of this nematode were highly similar to those of M. hapla in NCBI database, with a similarity of over 99.35%. Using the SCAR specific primers, a specific band with an expected size of approximately 440 bp was amplified from this nematode. Morphological and molecular identification supports the nematode species found on Gentiana macrophylla as M. hapla. This is the first report of this regulated root-knot nematode on Gentiana macrophylla in China.

The accumulation of soil-borne pathogens is the main driving factor of negative plant-soil feedbacks (NPSFs), which seriously restricts the sustainable development of agriculture. Using natural volatile organic compounds (VOCs) from plants or microorganisms as biofumigants is an emerging strategy to alleviate NPSFs in an environmentally-friendly way. Here, we identified α-terpineol from the VOCs of pine needles, confirmed the ability of α-terpineol fumigation in alleviating the NPSF of Panax notoginseng via significantly reducing seed decay rate, and also deciphered the underlying mechanism by which the soil microbial community is modified. α-Terpineol fumigation could suppress culturable fungi but enrich bacteria in a dose-dependent manner. Network analysis with high-throughput sequencing data revealed that α-terpineol could distinctly modify both fungal and bacterial communities. In detail, α-terpineol significantly suppressed the relative abundance of Ascomycota from 64.04 to 32.26%, but enriched the relative abundance of Proteobacteria, Acidobacteria and Actinobacteria. Subnetwork analysis further demonstrated that α-terpineol could directly or indirectly suppress fungal pathogens and enrich plant growth-promoting rhizobacteria (PGPRs). In vitro fumigation and co-culture experiments with culturable isolates validated these findings. The antagonism between beneficial bacteria and pathogens, and the synergistic growth promotion among α-terpineol-enriched bacteria might be involved in soil microbial community assembly. In summary, α-terpineol fumigation could directly or indirectly modify the soil microbial community to alleviate NPSFs, especially by suppressing fungal pathogens and enriching beneficial bacteria. This study suggests that VOCs from natural products are worth developing as biofumigants due to their multiple functions in modifying the soil microbial community.

Adjusting planting density is a common agricultural practice used to achieve maximum yields. However, whether the quality of medicinal herbs can be improved by implementing appropriate planting densities is still uncertain. The medicinal crop Panax notoginseng was used to analyze the effects of planting density on growth and ginsenoside accumulation, and the possible mechanisms of these effects were revealed through metabonomics. The results showed that P. notoginseng achieved high ginsenoside accumulation at high planting densities (8 × 8 and 10 × 10 cm), while simultaneously achieved high biomass and ginsenoside accumulation at moderate planting density of 15 × 15 cm. At the moderate planting density, the primary metabolism (starch and sucrose metabolism) and secondary metabolism (the biosynthesis of phytohormone IAA and ginsenoside) of the plants were significantly enhanced. However, the strong intraspecific competition at the high planting densities resulted in stress as well as the accumulation of phytohormones (SA and JA), antioxidants (gentiobiose, oxalic acid, dehydroascorbic acid) and other stress resistance-related metabolites. Interestingly, the dry biomass and ginsenoside content were significantly lower at low densities (20 × 20 and 30 × 30 cm) with low intraspecific competition, which disturbed normal carbohydrate metabolism by upregulating galactose metabolism. In summary, an appropriate planting density was benefit for the growth and accumulation of ginsenosides in P. notoginseng by balancing primary metabolism and secondary metabolism.

Transposable elements exist widely throughout plant genomes and play important roles in plant evolution. Auxin is an important regulator that is traditionally associated with root development and drought stress adaptation. The DEEPER ROOTING 1 (DRO1) gene is a key component of rice drought avoidance. Here, we identified a transposon that acts as an autonomous auxin-responsive promoter and its presence at specific genome positions conveys physiological adaptations related to drought avoidance. Rice varieties with high and auxin-mediated transcription of DRO1 in the root tip show deeper and longer root phenotypes and are thus better adapted to drought. The INDITTO2 transposon contains an auxin response element and displays auxin-responsive promoter activity; it is thus able to convey auxin regulation of transcription to genes in its proximity. In the rice Acuce, which displays DRO1-mediated drought adaptation, the INDITTO2 transposon was found to be inserted at the promoter region of the DRO1 locus. Transgenesis-based insertion of the INDITTO2 transposon into the DRO1 promoter of the non-adapted rice variety Nipponbare was sufficient to promote its drought avoidance. Our data identify an example of how transposons can act as promoters and convey hormonal regulation to nearby loci, improving plant fitness in response to different abiotic stresses. This article is protected by copyright. All rights reserved.

Negative plant-soil feedback (NPSF) frequently cause replant failure in agricultural ecosystems, which has been restricting the sustainable development of agriculture. Biochar application has appealing effects on soil improvement and potential capacity to affect NPSF, but the process is poorly understood. Here, our study demonstrated that biochar amendment can effectively alleviate the NPSF and this biochar effect is strongly linked to soil microorganism in a sanqi (Panax notoginseng) production system. High-throughput sequencing showed that the bacterial and fungal communities were altered with biochar amendment, and bacterial community is more sensitive to biochar amendment than the fungal community. Biochar amendment significantly increased the soil bacterial diversity, but the fungal diversity was not significantly different between biochar-amended and non-amended soils. Moreover, we found that biochar amendment significantly increased the soil pH, electrical conductivity, organic matter, available phosphorus, available potassium, and C/N ratio. The correlation analysis showed that these increased soil chemical variables have a significantly positive correlation with the bacterial diversity. Further analysis of the soil microbial composition demonstrated that biochar soil amendment enriched the beneficial bacterium Bacillus and Lysobacter but suppressed pathogens Fusarium and Ilyonectria. In addition, we verified that biochar had no direct effect on the pathogen Fusarium solani, but can directly enrich biocontrol bacterium Bacillus subtilis. In short, biochar application can mitigate NPSF is mostly due to the fact that biochar soil amendment modified the soil microbiome, especially inhibited pathogens by enriching beneficial bacterium with antagonistic activity against pathogen.

Interspecies interactions play a key role in soil-borne disease suppression in intercropping systems. However, there are limited data on the underlying mechanisms of soil-borne Phytophthora disease suppression. Here, a field experiment confirmed the effects of maize and soybean intercropping on Phytophthora blight of soybean caused by Phytophthora sojae. Experimentally, the roots and root exudates of maize were found to attract P. sojae zoospores and inhibit their motility and the germination of cystospores. Furthermore, five phenolic acids (p-coumaric acid, cinnamic acid, p-hydroxybenzoic acid, vanillic acid, and ferulic acid) that were consistently identified in the root exudates and rhizosphere soil of maize were found to interfere with the infection behavior of P. sojae. Among them, cinnamic acid was associated with significant chemotaxis in zoospores, and p-coumaric acid and cinnamic acid showed strong antimicrobial activity against P. sojae. However, in the rhizosphere soil of soybean, only p-hydroxybenzoic acid, low concentrations of vanillic acid, and ferulic acid were identified. Importantly, the coexistence of five phenolic acids in the maize rhizosphere compared with three phenolic acids in the soybean rhizosphere showed strong synergistic antimicrobial activity against the infection behavior of P. sojae. In summary, the types and concentrations of phenolic acids in maize and soybean rhizosphere soils were found to be crucial factors for Phytophthora disease suppression in this intercropping system.

Agricultural producers regardless of their location need to determine what strategies best fit with their local needs. In order to manage their local ecosystems in a sustainable way, three main aspects have to be considered: genetic diversity, species diversity, and ecological diversity. This chapter aims to demonstrate that biodiversity has the potential to be an effective means of disease and pest management. This chapter systematically elaborates on the key technologies and successful examples of the application of these principles of the three levels of biodiversity to disease and pest control. Rational rotation of resistant rice varieties implies to utilize diversity of resistance genes in time, that is, novel resistant variety carrying different resistance genes replaces the varieties that were susceptible to the pathogen in the field. Many studies to date have assessed the efficacy of such rotation on controlling the rice blast disease. The results of in-depth research on controlling rice blast disease by using rice genetic diversity is reported. By analyzing the genetic diversity structures of a large number of rice varieties, the optimum combination of different rice varieties was screened. These optimum combinations were deployed in the field, and to analyze the effects of combination of different varieties and different cultivating patterns on rice blast disease in an in-depth fashion. The main principles of techniques controlling rice genetic diversity are reported in this chapter. Crop species diversity can significantly increase the number of insect species that are natural enemies in a given area. The chapter further deals with intercropping patterns with different crop species to control pests and diseases, protective effects of landscape mosaic patterns on rice germplasm resources in different rice-fish systems, and chemical and resistant relationships between crops, microbes, insects and natural enemies.

Replant failure caused by negative plant-soil feedback (NPFS) in agricultural ecosystems is a critical factor restricting the development of sustainable agriculture. Soil nutrient availability has the capacity to affect plant-soil feedback. Here, we used sanqi (Panax notoginseng), which is severely threatened by NPSF, as a model plant to decipher the overall effects of nitrogen (N) rates on NPSF and the underlying mechanism. We found that a high rate of N at 450kgNha-1 (450N) aggravated the NPSF through the accumulation of pathogens in the soil compared with the optimal 250N. The increased N rates resulted in a significant increase in the soil electrical conductivity and available nitrogen but a decrease in the soil pH and C/N ratio. GeoChip 5.0 data demonstrated that these changed soil properties caused the soil to undergo stress (acidification, salinization and carbon starvation), as indicated by the enriched soil microbial gene abundances related to stress response and nutrition cycling (N, C and S). Accordingly, increased N rates reduced the richness and diversity of soil fungi and bacteria and eventually caused a shift in soil microbes from a bacterial-dominant community to a fungal-dominant community. In particular, the high 450N treatment significantly suppressed the abundance of copiotrophic bacteria, including beneficial genera Bacillus and Pseudomonas, thus weakening the antagonistic activity of these bacteria against fungal pathogens. Moreover, 450N application significantly enriched the abundance of pathogen pathogenicity-related genes. Once sanqi plants were grown in this N-stressed soil, their host-specific fungal pathogen Fusarium oxysporum significantly accumulated, which aggravated the process of NPSF. This study suggested that over-application of nitrogen is not beneficial for disease management or the reduction of fungicide application in agricultural production.

Yunmuxiang (Aucklandia lappa) is a tall, perennial herbaceous plant in the compositae family, occurring mainly in Asia and Europe. Yunmuxiang originated in India and was introduced into China in approximately 1940. Since then it has been widely cultivated in the southwest region of China for medicinal uses; it is included in the Chinese Pharmacopoeia. Yunmuxiang is used primarily as a sedative, including for anesthesia (Ting et al. 2012). Severely stunted and withered Yunmuxiang plants with rotted and galled roots were observed in a field in near the city of Lijiang (N 99°46'; E 27°18') in October 2019. These symptoms were typical of infection by root-knot nematodes.The second-stage juveniles (J2) were collected from the soil in the root zone, and adult females were dissected from roots. Population densities of J2 ranged from 325 to 645 per 100 cm3. Morphological analysis and species-specific PCR were performed on the second stage (J2) and females. Morphological characteristics are as follows: for J2 (n=20) , body length = 360.5 ± 23.4 µm, tail length = 47.2 ± 6.1 µm, and stylet length = 10.4 ± 1.9 µm, distance from dorsal esophageal gland opening to the stylet knot (DGO) = 3.96 ± 0.42 μm; females (n = 20) were pear-shaped, body length = 565.23 ± 86.68 μm, maximum body width = 407.24 ± 60.21 μm, stylet length = 9.93 ± 0.88 μm, DGO = 4.76 ± 0.32 μm, stylet median bulb width (MBW) = 29.67 ± 3.61 μm, perineum morphology is low and low dorsal arch round, with a typical inferior protrusion near the anus. These morphological characteristics are consistent with Meloidogyne hapla as described by Hunt and Handoo (2009). To confirm species identification, DNA was extracted from females (Blok, et al. 1997) and ITS region was amplified using the primers 18S/26S (Vrain et al. 1992). Furthermore, species-specific SCAR primers JMV1/JMV hapla were used as described by Adam et al. (2007). PCR produced 768 bp and 419 bp sequences. Fragments were sequenced (MW512922and MW228371, respectively) and compared with available sequences on NCBI. Sequences were 99.48% identical to the MT249016, KJ572385, and 100% identical to the GQ395574, GQ395569 M. hapla sequences, respectively. Morphological and molecular characterization supports the identification of the isolate found on Aucklandia lappa as M. hapla. Yunmuxiang seed were planted in 20 cm diameter, 10 cm deep plastic pots containing 1000 cm3 sterilized soil. Seedlings were thinned to one per pot. At the 2-3 leaf stage 10 pots were infested with 1500 M. hapla J2 per seedling, using a sterilized micropipette. Plants were maintained at 20-25°C in a greenhouse. Control plants received sterile water, and the pathogenicity test was repeated three times. After 30 days, plants were removed from pots and soil gently removed from the roots. A large number of galls (95.6 ± 2.5) and egg masses (33.5 ± 0.5) were found on each root system. Yunmuxiang was considered a good host for M. hapla in Lijiang. M. hapla is a major plant parasitic nematode with a wide geographic distribution and range of host plants and causes severe yield losses (Azevedo de Oliveira et al. 2018). Through investigation, this is the first report worldwide of M. hapla infecting Aucklandia lappa.

The roots of Panax notoginseng (Burk) F. H. Chen are used as a highly valuable Chinese herbal medicine in the prevention and treatment of cardiovascular and hematological diseases. Several aerial parts of plant are usually abandoned as the wastes. Panax notoginseng inflorescence (IFO) is commonly used as a folk medicine and dietary ingredient, its fruiting stage is referred as infructescence (IFU). Owing to high chemical complexity and structural similarity of ginsenosides, the co-eluting phenomenon, especially for the isomers, is inevitable in the chromatogram, resulting in the inaccurate quantitation. A novel LCMS method using hybrid positive full scan and multiple reaction monitoring (MRM) modes was developed to characterize ginsenoside distribution in different architectural components of IFO and IFU. MRM was performed for the quantification of G-Ra2 and NG-Fp2, a pair of co-eluting isomers with identical negative MS and MS/MS characteristics, and full scan was conducted to quantify other investigated saponins. Our data indicate that flower buds have the highest abundance of the summed saponins, fruit pedicel and fruit pericarp, commonly considered as the useless by-products of seed processing, contain the abundant saponins. Additionally, the contents of the detected ginsenosides in these architectural components significantly increased along with their growth years. Our findings will facilitate comprehensive utilization and exploitation of P. notoginseng inflorescence and infructescence.

Understanding the Vitis species at the genomic level is important for cultivar improvement of grapevine. Here we report whole-genome genetic variation at single-base resolution of 472 Vitis accessions, which cover 48 out of 60 extant Vitis species from a wide geographic distribution. The variation helps to identify a recent dramatic expansion and contraction of effective population size in the domesticated grapevines and that cultivars from the pan-Black Sea region have a unique demographic history in comparison to the other domesticated cultivars. We also find selective sweeps for berry edibility and stress resistance improvement. Furthermore, we find associations between candidate genes and important agronomic traits, such as berry shape and aromatic compounds. These results demonstrate resource value of the resequencing data for illuminating the evolutionary biology of Vitis species and providing targets for grapevine genetic improvement., Despite the importance of grapevine cultivation in human history and the economic values of cultivar improvement, large-scale genomic variation data are lacking. Here the authors resequence 472 Vitis accessions and use the identified genetic variations for domestication history, demography, and GWAS analyses.

Background Cultivation of medicinal crops, which synthesize hundreds of substances for curative functions, was focused on the synthesis of secondary metabolites rather than biomass accumulation. Nutrition is an important restrict factor for plant growth and secondary metabolites, but little attention has been given to the plasticity of nutrient uptake and secondary metabolites synthesis response to soil nitrogen (N) change. Methods Two year-field experiments of Sanqi (Panax notoginseng), which can synthesize a high level of saponin in cells, were conducted to study the effects of N application on the temporal dynamics of biomass, nutrient absorption, root architecture and the relationships between these parameters and saponin synthesis. Results Increasing N fertilizer rates could improve the dry matter yields and nutrient absorption ability through increasing the maximum daily growth (or nutrient uptake) rate. Under suitable N level (225 kg/ha N), Sanqi restricted the root length and surface and enhanced the root diameter and N uptake rate per root length (NURI) to promote nutrient absorption, but the opposite status of Sanqi root architecture and NURI was found when soil N was deficient. Furthermore, increasing N rates could promote the accumulation of saponin in roots through improving the NURI, which showed a significant positive relationship with the content of saponin in the taproots. Conclusion Appropriate N fertilizer rates could optimize both root architecture and nutrient uptake efficiency, then promote both the accumulation of dry matter and the synthesis of saponins.

Root rot caused by Cylindrocarpon destructans is one of the most devastating diseases of Panax notoginseng, and Trichoderma species are potential agents for the biocontrol of fungal diseases. Thus, we screened a total of 10 Trichoderma isolates against C. destructans and selected Trichoderma atroviride T2 as an antagonistic strain for further research. 6-Pentyl-2H-pyran-2-one (6PP) was identified as an important active metabolite in the fermentation broth of the strain and exhibited antifungal activity against C. destructans. Transcriptome and metabolome analyses showed that 6PP significantly disturbed the metabolic homeostasis of C. destructans, particularly the metabolism of amino acids. By constructing a gene coexpression network, ECHS1 was identified as the hub gene correlated with 6PP stress. 6PP significantly downregulated the expression of ECHS1 at the transcriptional level and combined with the ECHS1 protein. Autophagy occurred in C. destructans cells under 6PP stress. In conclusion, 6PP may induce autophagy in C. destructans by downregulating ECHS1 at the transcriptional level and inhibiting ECHS1 protein activity. 6PP is a potential candidate for the development of new fungicides against C. destructans.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Understanding the Vitis species at the genomic level is important for cultivar improvement of grapevine. Here we report whole-genome genetic variation at single-base resolution of 472 Vitis accessions, which cover 48 out of 60 extant Vitis species from a wide geographic distribution. The variation helps to identify a recent dramatic expansion and contraction of effective population size in the domesticated grapevines and that cultivars from the pan-Black Sea region have a unique demographic history in comparison to the other domesticated cultivars. We also find selective sweeps for berry edibility and stress resistance improvement. Furthermore, we find associations between candidate genes and important agronomic traits, such as berry shape and aromatic compounds. These results demonstrate resource value of the resequencing data for illuminating the evolutionary biology of Vitis species and providing targets for grapevine genetic improvement.

Phytophthora cactorum is a homothallic oomycete pathogen, which has a wide host range and high capability to adapt to host defense compounds and fungicides. Here we report the 121.5 Mb genome assembly of the P. cactorum using the third-generation single-molecule real-time (SMRT) sequencing technology. It is the second largest genome sequenced so far in the Phytophthora genera, which contains 27,981 protein-coding genes. Comparison with other Phytophthora genomes showed that P. cactorum had a closer relationship with P. parasitica, P. infestans and P. capsici. P. cactorum has similar gene families in the secondary metabolism and pathogenicity-related effector proteins compared with other oomycete species, but specific gene families associated with detoxification enzymes and carbohydrate-active enzymes (CAZymes) underwent expansion in P. cactorum. P. cactorum had a higher utilization and detoxification ability against ginsenosides–a group of defense compounds from Panax notoginseng–compared with the narrow host pathogen P. sojae. The elevated expression levels of detoxification enzymes and hydrolase activity-associated genes after exposure to ginsenosides further supported that the high detoxification and utilization ability of P. cactorum play a crucial role in the rapid adaptability of the pathogen to host plant defense compounds and fungicides.

Panax notoginseng is a highly valuable medicinal herb, but its culture is strongly hindered by replant failure, mainly due to autotoxicity. Deciphering the response mechanisms of plants to autotoxins is critical for overcoming the observed autotoxicity. Here, we elucidated the response of P. notoginseng to the autotoxic ginsenoside Rg1 via transcriptomic and cellular approaches. Cellular analyses demonstrated that Rg1 inhibited root growth by disrupting the cell membrane and wall. Transcriptomic analyses confirmed that genes related to the cell membrane, cell wall decomposition and reactive oxygen species (ROS) metabolism were up-regulated by Rg1 stress. Further cellular analyses revealed that Rg1 induced ROS ([Formula: see text] and H2O2) accumulation in root cells by suppressing ascorbate peroxidase (APX) and the activities of enzymes involved in the ascorbate-glutathione (ASC-GSH) cycle. Exogenous antioxidants (ASC and gentiobiose) helped cells scavenge over-accumulated ROS by promoting superoxide dismutase (SOD) activity and the ASC-GSH cycle. Collectively, the autotoxin Rg1 caused root cell death by inducing the over-accumulation of ROS, and the use of exogenous antioxidants could represent a strategy for overcoming autotoxicity.

The growing season of grapes is often associated with high levels of rainfall in the Chinese rainy regions, which leads to serious grape diseases. In this study, we sheltered grapevines from rainfall for the purpose of disease management. Experimentally (2007 and 2008), it was found that rain shelter could block the rainfall and clearly reduced the average daily leaf wetness duration and the relative humidity in the canopy compared with open field cultivation. The average severities of grape ripe rot, white rot, downy mildew, grey mould, and brown spot on the Red Globe cultivar were reduced by 85, 73, 81, 54, and 68% compared with fungicide sprays. The average severities of grape ripe rot, white rot, grey mould, and brown spot on the Shuijing cultivar were reduced by 84, 65, 100, and 73% compared with fungicide sprays. Rain shelter increased grape yields by an average of 110–176% and increased farmers' income by an average of 80–193% compared to fungicide sprays. Large-scale field monitoring from 2009 through 2012 unequivocally confirmed that rain shelter could effectively and stably control the main grape diseases. Although powdery mildew infections were more severe in plants under rain shelter cultivation than in plants under open field cultivation, this disease could be effectively controlled by one application of prochloraz and one application of difenoconazole during the growing season in vineyard trials under rain shelter from 2011 through 2013. These results demonstrated that protecting grapevines from rainfall is an efficient disease management technique with extensive application prospects in rainy regions.

In this study, the global proteomic response of Phytophthora cactorum to zoxamide was evaluated using a two-dimensional gel electrophoresis (2-DE)-based proteomic approach. Among the 21 proteins identified by matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry (MALDI-TOF/TOF MS), four cytoskeleton-related proteins were down-regulated upon addition of zoxamide. Five detoxification metabolism enzymes, seven sugar metabolism proteins and one mitochondria-related protein were up-regulated by more than 2-fold in response to zoxamide. Taken together, these results suggest that zoxamide can decrease the expression of cytoskeleton-related proteins of P. cactorum, resulting in cell death; however, the up-regulation of detoxification metabolism-related enzymes may protect P. cactorum against zoxamide, and the up-regulation of proteins related to sugar metabolism and mitochondria may lead to the generation of more energy for detoxification metabolism. These data also suggest that proteomics may be useful not only in exploring the mode of action of fungicides but also for gaining insight into the resistance mechanisms that pathogens employ against fungicides.

Understanding how fungi specialize on their plant host is crucial for developing sustainable disease control. A traditional, centuries-old rice agro-system of the Yuanyang terraces was used as a model to show that virulence effectors of the rice blast fungus Magnaporthe oryzaeh play a key role in its specialization on locally grown indica or japonica local rice subspecies. Our results have indicated that major differences in several components of basal immunity and effector-triggered immunity of the japonica and indica rice varieties are associated with specialization of M. oryzae. These differences thus play a key role in determining M. oryzae host specificity and may limit the spread of the pathogen within the Yuanyang agro-system. Specifically, the AVR-Pia effector has been identified as a possible determinant of the specialization of M. oryzae to local japonica rice. DOI: http://dx.doi.org/10.7554/eLife.19377.001, eLife digest Microbes that cause diseases in plants are a threat to food security. For example, the rice blast fungus Magnaporthe oryzae causes the loss of enough rice to feed 60 million people each year. Disease-causing microbes must overcome the plant’s first line of defense, which includes preformed barriers and antimicrobial responses that are triggered by characteristic molecules found in many different microbes. The microbes that can overcome this first line of defense typically do so with an arsenal of proteins called effectors that interfere with specific biological processes in the plant. To counteract this interference, some plants have evolved genes that encode proteins that detect these effectors and trigger stronger antimicrobial responses. For centuries, farmers and plant breeders have selected for these resistance genes when trying to breed crops that are more resistant to disease. However, over time, disease-causing microbes have lost effectors, which means that several resistance genes have rapidly become ineffective. Some researchers predicted that growing a mixture of varieties of a given crop together might be a better way of protecting crop yields. Over 16 years ago, this idea was proved successful against the rice blast fungus for rice plants grown in China. However, the exact reasons why this strategy worked and its effects on the fungus were not clear. Now Liao, Huang et al. have taken another look at rice varieties grown via the traditional method of terraces of rice paddies in Yuanyang. Some of these varieties had a strong first line of defense and few resistance genes, while others relied much more on resistance genes to protect themselves again the rice blast fungus. Liao, Huang et al. found that growing rice varieties with such different immune systems forces some of the rice blast fungi to accumulate effector proteins to combat the first line of defense, whereas other fungi had to get rid of these effectors to avoid being recognized by the major resistance genes. These two forces led to the evolution of two specialized populations of fungi that can infect specific rice varieties but not others. This means that the fungi cannot spread in the landscape, and so the fields of rice become resistant as a whole. These new findings demonstrate the importance of diversity in rice for sustainable crop protection. The next challenge will be to demonstrate if a similar approach can also protect other major crops grown in different agricultural settings. DOI: http://dx.doi.org/10.7554/eLife.19377.002

Plant disease can be effectively suppressed in intercropping systems. Our previous study demonstrated that neighbouring maize plants can restrict the spread of soil-borne pathogens of pepper plants by secreting defence compounds into the soil. However, whether maize plant can receive benefits from its neighbouring pepper plants in an intercropping system is little attention. We examined the effects of maize roots treated with elicitors from the pepper pathogen Phytophthora capsici and pepper root exudates on the synthesis of 1,4-benzoxazine-3-ones (BXs), the expression of defence-related genes in maize, and their ability to alleviate the severity of southern corn leaf blight (SCLB) caused by Bipolaris maydis. We found that SCLB was significantly reduced after the above treatments. The contents of 1,4-benzoxazine-3-ones (BXs: DIBOA, DIMBOA, and MBOA) and the expression levels of BX synthesis and defence genes in maize roots and shoots were up-regulated. DIMBOA and MBOA effectively inhibited the mycelium growth of Bipolaris maydis at physiological concentrations in maize shoots. Further studies suggested that the defence related pathways or genes in maize roots and shoots were activated by elicitors from the P. capsici or pepper root exudates. In conclusion, maize increased the levels of BXs and defence gene expression both in roots and shoots after being triggered by root exudates and pathogen from neighbouring pepper plants, eventually enhancing its resistance.

Background and Aims Sanqi ginseng (Panax notoginseng) growth is often hampered by replant failure. In this study, we aimed to examine the role of autotoxicity in Sanqi replant failures and assess the role of ginsenosides in autotoxicity. Methods The autotoxicities were measured using seedling emergence bioassays and root cell vigor staining. The ginsenosides in the roots, soils, and root exudates were identified with HPLC-MS. Results The seedling emergence and survival rate decreased significantly with the continuous number of planting years from one to three years. The root exudates, root extracts, and extracts from consecutively cultivated soils also showed significant autotoxicity against seedling emergence and growth. Ginsenosides, including R1, Rg1, Re, Rb1, Rb3, Rg2, and Rd, were identified in the roots and consecutively cultivated soil. The ginsenosides, Rg1, Re, Rg2, and Rd, were identified in the root exudates. Furthermore, the ginsenosides, R1, Rg1, Re, Rg2, and Rd, caused autotoxicity against seedling emergence and growth and root cell vigor at a concentration of 1.0 µg/mL. Conclusion Our results demonstrated that autotoxicity results in replant failure of Sanqi ginseng. While Sanqi ginseng consecutively cultivated, some ginsenosides can accumulate in rhizosphere soils through root exudates or root decomposition, which impedes seedling emergence and growth.

Nonhost resistance (NHR) pertains to the most common form of plant resistance against pathogenic microorganisms of other species. Bipolaris maydis is a non-adapted pathogen affecting soybeans, particularly of maize/soybean intercropping systems. However, no experimental evidence has described the immune response of soybeans against B. maydis. To elucidate the molecular mechanism underlying NHR in soybeans, proteomics analysis based on two-dimensional polyacrylamide gel electrophoresis (2-DE) was performed to identify proteins involved in the soybean response to B. maydis. The spread of B. maydis spores across soybean leaves induced NHR throughout the plant, which mobilized almost all organelles and various metabolic processes in response to B. maydis. Some enzymes, including ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), mitochondrial processing peptidase (MPP), oxygen evolving enhancer (OEE), and nucleoside diphosphate kinase (NDKs), were found to be related to NHR in soybeans. These enzymes have been identified in previous studies, and STRING analysis showed that most of the protein functions related to major metabolic processes were induced as a response to B. maydis, which suggested an array of complex interactions between soybeans and B. maydis. These findings suggest a systematic NHR against non-adapted pathogens in soybeans. This response was characterized by an overlap between metabolic processes and response to stimulus. Several metabolic processes provide the soybean with innate immunity to the non-adapted pathogen, B. maydis. This research investigation on NHR in soybeans may foster a better understanding of plant innate immunity, as well as the interactions between plant and non-adapted pathogens in intercropping systems.

Background: Intercropping systems could increase crop diversity and avoid vulnerability to biotic stresses. Most studies have shown that intercropping can provide relief to crops against wind-dispersed pathogens. However, there was limited data on how the practice of intercropping help crops against soil-borne Phytophthora disease. Principal Findings: Compared to pepper monoculture, a large scale intercropping study of maize grown between pepper rows reduced disease levels of the soil-borne pepper Phytophthora blight. These reduced disease levels of Phytophthora in the intercropping system were correlated with the ability of maize plants to form a ‘‘root wall’’ that restricted the movement of Phytophthora capsici across rows. Experimentally, it was found that maize roots attracted the zoospores of P. capsici and then inhibited their growth. When maize plants were grown in close proximity to each other, the roots produced and secreted larger quantities of 2,4-dihydroxy-7-methoxy-2H-1,4benzoxazin-3(4H)-one (DIMBOA) and 6-methoxy-2-benzoxazolinone (MBOA). Furthermore, MBOA, benzothiazole (BZO), and 2-(methylthio)-benzothiazole (MBZO) were identified in root exudates of maize and showed antimicrobial activity against P. capsici. Conclusions: Maize could form a ‘‘root wall’’ to restrict the spread of P. capsici across rows in maize and pepper intercropping systems. Antimicrobe compounds secreted by maize root were one of the factors that resulted in the inhibition of P. capsici. These results provide new insights into plant-plant-microbe mechanisms involved in intercropping systems.

Sanqi (Panax notoginseng (Burk.) F. H. Chen) is planted on >10,000 ha in China and is a popular Chinese medicinal material (2). Black root rot is a recently identified but worsening problem on Sanqi since 2010 in Wenshan, China. Of the plant tubers examined from 185 ha, 8.5 to 27.4% were black with necrotic lesions. The base of leaves of infected plants had brown, sunken, necrotic lesions, and symptomatic plants had one to three chlorotic leaves. A fungus was isolated consistently from the basal leaves, bulb, and tubers of symptomatic plants. Six single-spore isolates were cultured on potato sucrose agar (PSA) at 25 ± 1°C in the dark. The mycelium of each culture was white initially on PSA, and then became rust-colored. The adaxial surfaces of the plates were black. Conidiophores were 13.6 to 167.3 × 1.4 to 21.8 μm (avg. 68.6 × 2.9 μm), single or with up to four levels of branching and two to three branches (or phialides) per level. The basal branches were often divergent, whereas the terminal branches were usually more appressed. Sporodochia were not present. Microconidia were 0-septate, 4.1 to 9.5 × 2.7 to 4.1 μm (avg. 8.2 × 2.9 μm). Conidia were 1- to 3-septate and occasionally 4-septate. One- to 3-septate conidia were clavate, with a truncate or slightly protruding conidial base, 9.2 to 40.8 × 3.5 to 6.8 μm (avg. 26.7 × 5.2 μm); whereas 4-septate conidia were 32.6 to 50.3 × 5.4 to 6.8 μm (avg. 40.9 × 6.5 μm). Chlamydospores were abundant, golden to brown, single or in chains or clumps, and up to 21.8 μm in diameter. PCR amplification was carried out for one isolate, RR926, using rDNA internal transcribed spacer (ITS) primer pairs ITS1F and ITS4 (4). Sequencing of the PCR product (GenBank Accession No. KC904953) revealed 99% similarity (99% coverage) with the ITS sequence of Cylindrocarpon destructans var. destructans (AM419065). Phylogenetic analysis (MEGA 4.1) using the neighbor-joining algorithm placed the isolate in a well-supported cluster (>90% bootstrap value based on 1,000 replicates) with AM419065. Therefore, the pathogen was identified as C. destructans (Zinssm.) Scholten var. destructans (teleomorph Ilyonectria radicicola (Gerlach & L. Nilsson) P. Chaverri & C. Salgado) based on morphological characteristics and rDNA-ITS sequence analysis (1,3). Pathogenicity tests of the six isolates were conducted on five 1-year-old and five 3-year-old plants/isolate. The roots of all plants were washed with sterilized water, and then surface-sterilized with 75% ethanol. Inoculum (1 ml of 106 conidia/ml) of each isolate was brushed onto the roots of each plant with a paintbrush. Inoculated plants were planted in pots in a mixture of sterilized quartz sand:vermiculite:pearlite (2:1:1, v/v). The pots were placed under black shadecloth. The roots of five 1-year-old and five 3-year-old plants were brushed similarly with sterilized water as control treatments. After 30 days, symptoms similar to those on the original diseased plants were observed on the roots of all plants inoculated with the six isolates. The roots of non-inoculated plants remained healthy. The experiment was repeated. The same pathogen was re-isolated from the inoculated plants, but no pathogen was isolated from roots of the control plants. C. destructans var. destructans is widely distributed in soils (1), but to our knowledge, this is the first report of this fungus causing black root rot of Sanqi in China. References: (1) P. Charerri et al. Stud. Mycol. 68:57, 2011. (2) C. Y. Hu. New Rural Technol. 2:59, 2013 (in Chinese). (3) K. A. Seifert and P. E. Axelrood. Can. J. Plant Pathol. 20:115, 1998. (4) K. A. Seifert et al. Phytopathology 93:1533, 2003.

Traditional farming practices suggest that cultivation of a mixture of crop species in the same field through temporal and spatial management may be advantageous in boosting yields and preventing disease, but evidence from large-scale field testing is limited. Increasing crop diversity through intercropping addresses the problem of increasing land utilization and crop productivity. In collaboration with farmers and extension personnel, we tested intercropping of tobacco, maize, sugarcane, potato, wheat and broad bean – either by relay cropping or by mixing crop species based on differences in their heights, and practiced these patterns on 15,302 hectares in ten counties in Yunnan Province, China. The results of observation plots within these areas showed that some combinations increased crop yields for the same season between 33.2 and 84.7% and reached a land equivalent ratio (LER) of between 1.31 and 1.84. This approach can be easily applied in developing countries, which is crucial in face of dwindling arable land and increasing food demand.