Alfalfa (Medicago sativa L.) resistance to the root-lesion nematode, Pratylenchus penetrans: defense-response gene mRNA and isoflavonoid phytoalexin levels in roots

Time Course RNA-seq Reveals Soybean Responses against Root-Lesion Nematode and Resistance Players

Pratylenchus brachyurus causes serious damage to soybean production and other crops worldwide. Plant molecular responses to RLN infection remain largely unknown and no resistance genes have been identified in soybean. In this study, we analyzed molecular responses to RLN infection in moderately resistant BRSGO (Chapadões-BRS) and susceptible TMG115 RR (TMG) Glycine max genotypes. Differential expression analysis revealed two stages of response to RLN infection and a set of differentially expressed genes (DEGs) in the first stage suggested a pattern-triggered immunity (PTI) in both genotypes. The divergent time-point of DEGs between genotypes was observed four days post-infection, which included the activation of mitogen-activated protein kinase (MAPK) and plant-pathogen interaction genes in the BRS, suggesting the occurrence of an effector-triggered immunity response (ETI) in BRS. The co-expression analyses combined with single nucleotide polymorphism (SNP) uncovered a key element, a transcription factor phytochrome-interacting factor (PIF7) that is a potential regulator of moderate resistance to RLN infection. Two genes for resistance-related leucine-rich repeat (LRR) proteins were found as BRS-specific expressed genes. In addition, alternative splicing analysis revealed an intron retention in a myo-inositol oxygenase (MIOX) transcript, a gene related to susceptibility, may cause a loss of function in BRS.

Integrated Omic Approaches Reveal Molecular Mechanisms of Tolerance during Soybean and Meloidogyne incognita Interactions

The root-knot nematode (RKN), Meloidogyne incognita, is a devastating soybean pathogen worldwide. The use of resistant cultivars is the most effective method to prevent economic losses caused by RKNs. To elucidate the mechanisms involved in resistance to RKN, we determined the proteome and transcriptome profiles from roots of susceptible (BRS133) and highly tolerant (PI 595099) Glycine max genotypes 4, 12, and 30 days after RKN infestation. After in silico analysis, we described major defense molecules and mechanisms considered constitutive responses to nematode infestation, such as mTOR, PI3K-Akt, relaxin, and thermogenesis. The integrated data allowed us to identify protein families and metabolic pathways exclusively regulated in tolerant soybean genotypes. Among them, we highlighted the phenylpropanoid pathway as an early, robust, and systemic defense process capable of controlling M. incognita reproduction. Associated with this metabolic pathway, 29 differentially expressed genes encoding 11 different enzymes were identified, mainly from the flavonoid and derivative pathways. Based on differential expression in transcriptomic and proteomic data, as well as in the expression profile by RT-qPCR, and previous studies, we selected and overexpressed the GmPR10 gene in transgenic tobacco to assess its protective effect against M. incognita. Transgenic plants of the T₂ generation showed up to 58% reduction in the M. incognita reproduction factor. Finally, data suggest that GmPR10 overexpression can be effective against the plant parasitic nematode M. incognita, but its mechanism of action remains unclear. These findings will help develop new engineered soybean genotypes with higher performance in response to RKN infections.

Efficient method for isolation of high-quality RNA from Psidium guajava L. tissues

Acquiring high-quality RNA in sufficient amounts is crucial in plant molecular biology and genetic studies. Several methods for RNA extraction from plants are available in the literature, mainly due to the great biochemical diversity present in each species and tissue, which can complicate or prevent the extraction. Psidium guajava (Myrtaceae family) is a perennial fruit tree of medicinal and economic value; nevertheless, only a few molecular studies are available for the species. One reason is the difficulty in obtaining RNA due to the content of the samples, which are rich in polyphenols, polysaccharides, and secondary metabolites. Furthermore, there are few studies available for the isolation of RNA from guava or Psidium samples, which hampers advances in the study of the genus. Here, quality and yields of RNA isolates were compared using six extraction protocols: two protocols based on the application of cetyltrimethylammonium bromide (CTAB) lysis buffer, one protocol which uses the TRIzol reagent, one which applies guanidine thiocyanate lysis buffer followed by organic phase extraction, and two commercial kits (PureLink RNA Mini Kit and RNeasy Plant Mini Kit). The CTAB-based method provided the highest RNA yields and quality for five different tissues (flower bud, immature leaf, young leaf, mature leaf, and root), genotypes, and stress conditions. For the most efficient protocol, the average yield of RNA from guava leaves was 203.06 μg/g of tissue, and the A₂₆₀/A₂₈₀ and A₂₆₀/A₂₃₀ ratios were 2.1 and 2.2, respectively. RT-qPCR analysis demonstrated that the purity of the samples was sufficient for molecular biology experiments. CTAB-based methods for RNA isolation were found to be the most efficient, providing the highest RNA yields and quality for tissues from P. guajava. Additionally, they were compatible for downstream RNA-based applications, besides being simple and cost-effective.

A rice root-knot nematode Meloidogyne graminicola-resistant mutant rice line shows early expression of plant-defence genes

Resistance to rice root-knot nematode Meloidogyne graminicola in a mutant rice line is suggested to be conferred by higher expression of several genes putatively involved in damage-associated molecular pattern recognition, secondary metabolite biosynthesis including phytoalexins, and defence-related genes. Meloidogyne graminicola has emerged as the most destructive plant-parasitic nematode disease of rice (Oryza sativa L.). Genetic resistance to M. graminicola is one of the most effective methods for its management. A M. graminicola-resistant O. sativa ssp. indica mutant line-9 was previously identified through a forward genetic screen (Hatzade et al. Biologia 74:1197-1217, 2019). In the present study, we used RNA-Sequencing to investigate the molecular mechanisms conferring nematode resistance to the mutant line-9 compared to the susceptible parent JBT 36/14 at 24 h post-infection. A total of 674 transcripts were differentially expressed in line-9. Early regulation of genes putatively related to nematode damage-associated molecular pattern recognition (e.g., wall-associated receptor kinases), signalling [Nucleotide-binding, Leucine-Rich Repeat (NLRs)], pathogenesis-related (PR) genes (PR1, PR10a), defence-related genes (NB-ARC domain-containing genes), as well as a large number of genes involved in secondary metabolites including diterpenoid biosynthesis (CPS2, OsKSL4, OsKSL10, Oscyp71Z2, oryzalexin synthase, and momilactone A synthase) was observed in M. graminicola-resistant mutant line-9. It may be suggested that after the nematode juveniles penetrate the roots of line-9, early recognition of invading nematodes triggers plant immune responses mediated by phytoalexins, and other defence proteins such as PR proteins inhibit nematode growth and reproduction. Our study provides the first transcriptomic comparison of nematode-resistant and susceptible rice plants in the same genetic background and adds to the understanding of mechanisms underlying plant-nematode resistance in rice.

A Phytochemical Perspective on Plant Defense Against Nematodes

Given the large yield losses attributed to plant-parasitic nematodes and the limited availability of sustainable control strategies, new plant-parasitic nematode control strategies are urgently needed. To defend themselves against nematode attack, plants possess sophisticated multi-layered immune systems. One element of plant immunity against nematodes is the production of small molecules with anti-nematode activity, either constitutively or after nematode infection. This review provides an overview of such metabolites that have been identified to date and groups them by chemical class (e.g., terpenoids, flavonoids, glucosinolates, etc.). Furthermore, this review discusses strategies that have been used to identify such metabolites and highlights the ways in which studying anti-nematode metabolites might be of use to agriculture and crop protection. Particular attention is given to emerging, high-throughput approaches for the identification of anti-nematode metabolites, in particular the use of untargeted metabolomics techniques based on nuclear magnetic resonance (NMR) and mass spectrometry (MS).

Constitutive and Induced Expression of Total Phenol and Phenol Oxidases in Wheat Genotypes Ranging in Resistance/Susceptibility to the Root-Lesion Nematode Pratylenchus thornei

Plant-derived phenolic compounds contribute to the defense against various pathogens, including root-lesion nematodes (Pratylenchus spp.). However, there are no reports on the role of phenolic compounds in wheat (Triticum aestivum) against Pratylenchus thornei. In this study, wheat genotypes ranging from resistant to very susceptible to P. thornei were used to investigate the level of total phenols and phenol oxidases, polyphenol oxidase (PPO), and peroxidase (POD) expressed in root tissues when grown in the presence and absence of P. thornei over time (2–8 weeks). Higher constitutive levels of total phenols were found in resistant synthetic hexaploid wheats CPI133872 (576 µg gallic acid equivalent (GAE)/g root) and CPI133859 (518 µg GAE/g root) at 8 weeks after sowing, compared with moderately resistant and susceptible genotypes (192 to 390 µg GAE/g root). The activity of PPO was induced in resistant (CPI133872) and moderately resistant (GS50a and its derivate QT8343) genotypes, becoming maximal at 4 weeks after P. thornei inoculation. The activity of POD was induced in CPI133872 at 6 weeks after P. thornei inoculation. Different genetic sources of resistance to P. thornei showed diverse defense mechanisms and differences in timing responses. The combined effects of total phenols and oxidative enzymes could be important for defense against P. thornei in some resistant wheat genotypes.

Fine mapping of root lesion nematode (Pratylenchus thornei) resistance loci on chromosomes 6D and 2B of wheat

Resistance QTL to root lesion nematode (Pratylenchus thornei) in wheat (Triticum aestivum), QRlnt.sk-6D and QRlnt.sk-2B, were mapped to intervals of 3.5 cM/1.77 Mbp on chromosome 6D and 1.4 cM/2.19 Mbp on chromosome 2B, respectively. Candidate resistance genes were identified in the QTL regions and molecular markers developed for marker-assisted breeding. Two previously known resistance QTL for root lesion nematode (Pratylenchus thornei) in bread wheat (Triticum aestivum), QRlnt.sk-6D and QRlnt.sk-2B, were fine-mapped using a Sokoll (moderately resistant) by Krichauff (susceptible) doubled haploid (DH) population and six newly developed recombinant inbred line populations. Bulked segregation analysis with the 90K wheat SNP array identified linked SNPs which were subsequently converted to KASP assays for mapping in the DH and RIL populations. On chromosome 6D, 60 KASP and five SSR markers spanned a total genetic distance of 23.7 cM. QRlnt.sk-6D was delimited to a 3.5 cM interval, representing 1.77 Mbp in the bread wheat cv. Chinese Spring reference genome sequence and 2.29 Mbp in the Aegilops tauschii genome sequence. These intervals contained 42 and 43 gene models in the respective annotated genome sequences. On chromosome 2B, 41 KASP and 5 SSR markers produced a map spanning 19.9 cM. QRlnt.sk-2B was delimited to 1.4 cM, corresponding 3.14 Mbp in the durum wheat cv. Svevo reference sequence and 2.19 Mbp in Chinese Spring. The interval in Chinese Spring contained 56 high-confidence gene models. Intervals for both QTL contained genes with similarity to those previously reported to be involved in disease resistance, namely genes for phenylpropanoid biosynthetic pathway-related enzymes, NBS-LRR proteins and protein kinases. The potential roles of these candidate genes in P. thornei resistance are discussed. The KASP markers reported in this study could potentially be used for marker-assisted breeding of P. thornei-resistant wheat cultivars.

Cellular and Transcriptional Responses of Resistant and Susceptible Cultivars of Alfalfa to the Root Lesion Nematode, Pratylenchus penetrans

The root lesion nematode (RLN), Pratylenchus penetrans, is a migratory species that attacks a broad range of crops, including alfalfa. High levels of infection can reduce alfalfa forage yields and lead to decreased cold tolerance. Currently, there are no commercially certified varieties with RLN resistance. Little information on molecular interactions between alfalfa and P. penetrans, that would shed light on mechanisms of alfalfa resistance to RLN, is available. To advance our understanding of the host-pathogen interactions and to gain biological insights into the genetics and genomics of host resistance to RLN, we performed a comprehensive assessment of resistant and susceptible interactions of alfalfa with P. penetrans that included root penetration studies, ultrastructural observations, and global gene expression profiling of host plants and the nematode. Several gene-candidates associated with alfalfa resistance to P. penetrans and nematode parasitism genes encoding nematode effector proteins were identified for potential use in alfalfa breeding programs or development of new nematicides. We propose that preformed or constitutive defenses, such as significant accumulation of tannin-like deposits in root cells of the resistant cultivar, could be a key to nematode resistance, at least for the specific case of alfalfa-P. penetrans interaction.

Plant Immune Responses to Parasitic Nematodes

Plant-parasitic nematodes (PPNs), such as root-knot nematodes (RKNs) and cyst nematodes (CNs), are among the most devastating pests in agriculture. RKNs and CNs induce redifferentiation of root cells into feeding cells, which provide water and nutrients to these nematodes. Plants trigger immune responses to PPN infection by recognizing PPN invasion through several different but complementary systems. Plants recognize pathogen-associated molecular patterns (PAMPs) sderived from PPNs by cell surface-localized pattern recognition receptors (PRRs), leading to pattern-triggered immunity (PTI). Plants can also recognize tissue and cellular damage caused by invasion or migration of PPNs through PRR-based recognition of damage-associated molecular patterns (DAMPs). Resistant plants have the added ability to recognize PPN effectors via intracellular nucleotide-binding domain leucine-rich repeat (NLR)-type immune receptors, leading to NLR-triggered immunity. Some PRRs may also recognize apoplastic PPN effectors and induce PTI. Plant immune responses against PPNs include the secretion of anti-nematode enzymes, the production of anti-nematode compounds, cell wall reinforcement, production of reactive oxygen species and nitric oxide, and hypersensitive response-mediated cell death. In this review, we summarize the recognition mechanisms for PPN infection and what is known about PPN-induced immune responses in plants.

Functions of Flavonoids in Plant⁻Nematode Interactions

Most land plants can become infected by plant parasitic nematodes in the field. Plant parasitic nematodes can be free-living or endoparasitic, and they usually infect plant roots. Most damaging are endoparasites, which form feeding sites inside plant roots that damage the root system and redirect nutrients towards the parasite. This process involves developmental changes to the root in parallel with the induction of defense responses. Plant flavonoids are secondary metabolites that have roles in both root development and plant defense responses against a range of microorganisms. Here, we review our current knowledge of the roles of flavonoids in the interactions between plants and plant parasitic nematodes. Flavonoids are induced during nematode infection in plant roots, and more highly so in resistant compared with susceptible plant cultivars, but many of their functions remain unclear. Flavonoids have been shown to alter feeding site development to some extent, but so far have not been found to be essential for root–parasite interactions. However, they likely contribute to chemotactic attraction or repulsion of nematodes towards or away from roots and might help in the general plant defense against nematodes. Certain flavonoids have also been associated with functions in nematode reproduction, although the mechanism remains unknown. Much remains to be examined in this area, especially under field conditions.

Gene expression profiling describes the genetic regulation of Meloidogyne arenaria resistance in Arachis hypogaea and reveals a candidate gene for resistance

Resistance to root-knot nematode was introgressed into cultivated peanut Arachis hypogaea from a wild peanut relative, A. cardenasii and previously mapped to chromosome A09. The highly resistant recombinant inbred RIL 46 and moderately resistant RIL 48 were selected from a population with cv. Gregory (susceptible) and Tifguard (resistant) as female and male parents, respectively. RNA-seq analysis was performed on these four genotypes using root tissue harvested from root-knot nematode infected plants at 0, 3, 7 days after inoculation. Differential gene expression analysis provides evidence that root-knot nematodes modulate biological pathways involved in plant hormone, defense, cell signaling, cytoskeleton and cell wall metabolism in a susceptible reaction. Corresponding to resistance reaction, an effector-induced-immune response mediated by an R-gene was identified in Tifguard. Mapping of the introgressed region indicated that 92% of linkage group A09 was of A. cardenasii origin in Tifguard. RIL46 and RIL 48 possessed 3.6% and 83.5% of the introgression on A09, respectively. Within the small introgressed region carried by RIL 46, a constitutively expressed TIR-NBS-LRR gene was identified as the candidate for nematode resistance. Potential defense responsive pathways include effector endocytosis through clathrin-coated vesicle trafficking, defense signaling through membrane lipid metabolism and mucilage production.

Characterization of Lilium longiflorum cv. 'Nellie White' Infection with Root-lesion Nematode Pratylenchus penetrans by Bright-field and Transmission Electron Microscopy

Lilium longiflorum cv. Nellie White, commonly known as Easter lily, is an important floral crop with an annual wholesale value of over $26 million in the United States. The root-lesion nematode, Pratylenchus penetrans, is a major pest of lily due to the significant root damage it causes. In this study, we investigated the cytological aspects of this plant-nematode interaction using bright-field and transmission electron microscopy. We took advantage of an in vitro culture method to multiply lilies and follow the nematode infection over time. Phenotypic reactions of roots inoculated with P. penetrans were evaluated from 0 to 60 d after nematode infection. Symptom development progressed from initial randomly distributed discrete necrotic areas to advanced necrosis along entire roots of each inoculated plant. A major feature characterizing this susceptible host response to nematode infection was the formation of necrosis, browning, and tissue death involving both root epidermis and cortical cells. Degradation of consecutive cell walls resulted in loss of cell pressure, lack of cytoplasmic integrity, followed by cell death along the intracellular path of the nematode's migration. Pratylenchus penetrans was never seen in the vascular cylinder as the layer of collapsed endodermal cells presumably blocked the progression of nematodes into this area of the roots. This study presents the first detailed cytological characterization of P. penetrans infection of Easter lily plants.

Root-knot nematodes induce pattern-triggered immunity in Arabidopsis thaliana roots

Root-knot nematodes (RKNs; Meloidogyne spp.) are plant parasites with a broad host range causing great losses worldwide. To parasitize their hosts, RKNs establish feeding sites in roots known as giant cells. The majority of work studying plant-RKN interactions in susceptible hosts addresses establishment of the giant cells and there is limited information on the early defense responses. Here we characterized early defense or pattern-triggered immunity (PTI) against RKNs in Arabidopsis thaliana. To address PTI, we evaluated known canonical PTI signaling mutants with RKNs and investigated the expression of PTI marker genes after RKN infection using both quantitative PCR and β-glucuronidase reporter transgenic lines. We showed that PTI-compromised plants have enhanced susceptibility to RKNs, including the bak1-5 mutant. BAK1 is a common partner of distinct receptors of microbe- and damage-associated molecular patterns. Furthermore, our data indicated that nematode recognition leading to PTI responses involves camalexin and glucosinolate biosynthesis. While the RKN-induced glucosinolate biosynthetic pathway was BAK1-dependent, the camalexin biosynthetic pathway was only partially dependent on BAK1. Combined, our results indicate the presence of BAK1-dependent and -independent PTI against RKNs in A. thaliana, suggesting the existence of diverse nematode recognition mechanisms.

Stem nematode counteracts plant resistance of aphids in alfalfa, Medicago sativa

Plants are exploited by a diverse community of insect herbivores and phytopathogens that interact indirectly through plant-mediated interactions. Generally, plants are thought to respond to insects and pathogens through different defensive signaling pathways. As plants are selected for resistance to one phytophagous organism type (insect vs. pathogen) in managed systems, it is not clear how this selection may affect community interactions. This study examined the effect of nematode-resistant varieties on aphid (Acyrthosiphon pisum) suppression, and then determined how infection by the stem nematode, Ditylenchus dipsaci, mediated ecological effects on aphids and on plant defense proteins. Four alfalfa (Medicago sativa) varieties were selected with resistance to nematodes only (+,−), aphids only (−,+), nematodes and aphids (+,+), and susceptibility to nematodes and aphids (−,−). Field and greenhouse experiments were conducted to isolate the effect of nematode infection and aphid abundance on each variety. We found that varieties resistant to nematode, regardless of aphid resistance, had the lowest aphid counts, suggesting possible cross-resistance. Aphid abundance, however, increased when plants were exposed to nematodes. Resistant varieties were associated with elevated saponins but these compounds were not affected by insect or pathogen feeding. Concentrations of peroxidases and trypsin inhibitors, however, were increased in nematode resistant varieties when exposed to nematodes and aphids, respectively. The patterns of plant defense were variable, and a combination of resistance traits and changes in nutrient availability may drive positive interactions between nematodes and aphids aboveground.

Comparative QTL analysis of root lesion nematode resistance in barley

This study demonstrates for the first time that resistance to different root lesion nematodes ( P. neglectus and P. penetrans ) is controlled by a common QTL. A major resistance QTL ( Rlnnp6H ) has been mapped to chromosome 6H using two independent barley populations. Root lesion nematodes (Pratylenchus spp.) are important pests in cereal production worldwide. We selected two doubled haploid populations of barley (Igri × Franka and Uschi × HHOR 3073) and infected them with Pratylenchus penetrans and Pratylenchus neglectus. Nematode multiplication rates were measured 7 or 10 weeks after infection. In both populations, continuous phenotypic variations for nematode multiplication rates were detected indicating a quantitative inheritance of resistance. In the Igri × Franka population, four P. penetrans resistance QTLs were mapped with 857 molecular markers on four linkage groups (2H, 5H, 6H and 7H). In the Uschi × HHOR 3073 population, eleven resistance QTLs (P. penetrans and P. neglectus) were mapped with 646 molecular markers on linkage groups 1H, 3H, 4H, 5H, 6H and 7H. A major resistance QTL named Rlnnp6H (LOD score 6.42-11.19) with a large phenotypic effect (27.5-36.6 %) for both pests was mapped in both populations to chromosome 6H. Another resistance QTL for both pests was mapped on linkage group 5H (Igri × Franka population). These data provide first evidence for common resistance mechanisms against different root lesion nematode species. The molecular markers are a powerful tool for the selection of resistant barley lines among segregating populations because resistance tests are time consuming and laborious.

Natural product biosynthesis in Medicago species

The genus Medicago, a member of the legume (Fabaceae) family, comprises 87 species of flowering plants, including the forage crop M. sativa (alfalfa) and the model legume M. truncatula (barrel medic). Medicago species synthesize a variety of bioactive natural products that are used to engage into symbiotic interactions but also serve to deter pathogens and herbivores. For humans, these bioactive natural products often possess promising pharmaceutical properties. In this review, we focus on the two most interesting and well characterized secondary metabolite classes found in Medicago species, the triterpene saponins and the flavonoids, with a detailed overview of their biosynthesis, regulation, and profiling methods. Furthermore, their biological role within the plant as well as their potential utility for human health or other applications is discussed. Finally, we give an overview of the advances made in metabolic engineering in Medicago species and how the development of novel molecular and omics toolkits can influence a better understanding of this genus in terms of specialized metabolism and chemistry. Throughout, we critically analyze the current bottlenecks and speculate on future directions and opportunities for research and exploitation of Medicago metabolism.

Characterization of resistance to Pratylenchus thornei (Nematoda) in wheat (Triticum aestivum): attraction, penetration, motility, and reproduction

Lines from a cross between two wheat (Triticum aestivum) cultivars with contrasting resistance phenotypes to Pratylenchus thornei (Nematoda) were investigated to determine the stage at which resistance occurs. Host resistance was examined at nematode attraction to and penetration of roots and nematode motility, maturation, and reproduction within roots. There was no significant difference in the rate at which P. thornei was attracted toward or penetrated resistant or susceptible roots. However, suppression of migration, juvenile maturation, and reproduction in and near resistant roots was evident, suggesting that resistance acts post penetration. No preferential root penetration zone was observed in contrast to other studies. The inhibitory compounds from resistant wheat plants appeared to be constitutively expressed and water soluble because nematode migration was suppressed in roots and root exudates of unchallenged seedlings. The effects of these compounds were reversible and affected P. thornei but not P. neglectus. Apart from migration, nematode multiplication was greatly inhibited by resistance because only a few juveniles (10%) developed past stage three in roots of resistant compared with susceptible plants. Earlier in the life cycle, egg deposition and hatch of P. thornei were also significantly reduced in resistant roots and root exudates, suggesting the presence of hatching inhibitors.

Top 10 plant-parasitic nematodes in molecular plant pathology

The aim of this review was to undertake a survey of researchers working with plant-parasitic nematodes in order to determine a 'top 10' list of these pathogens based on scientific and economic importance. Any such list will not be definitive as economic importance will vary depending on the region of the world in which a researcher is based. However, care was taken to include researchers from as many parts of the world as possible when carrying out the survey. The top 10 list emerging from the survey is composed of: (1) root-knot nematodes (Meloidogyne spp.); (2) cyst nematodes (Heterodera and Globodera spp.); (3) root lesion nematodes (Pratylenchus spp.); (4) the burrowing nematode Radopholus similis; (5) Ditylenchus dipsaci; (6) the pine wilt nematode Bursaphelenchus xylophilus; (7) the reniform nematode Rotylenchulus reniformis; (8) Xiphinema index (the only virus vector nematode to make the list); (9) Nacobbus aberrans; and (10) Aphelenchoides besseyi. The biology of each nematode (or nematode group) is reviewed briefly.

Transcriptome sequencing and microarray development for the woodrat (Neotoma spp.): custom genetic tools for exploring herbivore ecology

Massively parallel sequencing has enabled the creation of novel, in-depth genetic tools for nonmodel, ecologically important organisms. We present the de novo transcriptome sequencing, analysis and microarray development for a vertebrate herbivore, the woodrat (Neotoma spp.). This genus is of ecological and evolutionary interest, especially with respect to ingestion and hepatic metabolism of potentially toxic plant secondary compounds. We generated a liver transcriptome of the desert woodrat (Neotoma lepida) using the Roche 454 platform. The assembled contigs were well annotated using rodent references (99.7% annotation), and biotransformation function was reflected in the gene ontology. The transcriptome was used to develop a custom microarray (eArray, Agilent). We tested the microarray with three experiments: one across species with similar habitat (thus, dietary) niches, one across species with different habitat niches and one across populations within a species. The resulting one-colour arrays had high technical and biological quality. Probes designed from the woodrat transcriptome performed significantly better than functionally similar probes from the Norway rat (Rattus norvegicus). There were a multitude of expression differences across the woodrat treatments, many of which related to biotransformation processes and activities. The pattern and function of the differences indicate shared ecological pressures, and not merely phylogenetic distance, play an important role in shaping gene expression profiles of woodrat species and populations. The quality and functionality of the woodrat transcriptome and custom microarray suggest these tools will be valuable for expanding the scope of herbivore biology, as well as the exploration of conceptual topics in ecology.

Flavonoids: their structure, biosynthesis and role in the rhizosphere, including allelopathy

Flavonoids are biologically active low molecular weight secondary metabolites that are produced by plants, with over 10,000 structural variants now reported. Due to their physical and biochemical properties, they interact with many diverse targets in subcellular locations to elicit various activities in microbes, plants, and animals. In plants, flavonoids play important roles in transport of auxin, root and shoot development, pollination, modulation of reactive oxygen species, and signalling of symbiotic bacteria in the legume Rhizobium symbiosis. In addition, they possess antibacterial, antifungal, antiviral, and anticancer activities. In the plant, flavonoids are transported within and between plant tissues and cells, and are specifically released into the rhizosphere by roots where they are involved in plant/plant interactions or allelopathy. Released by root exudation or tissue degradation over time, both aglycones and glycosides of flavonoids are found in soil solutions and root exudates. Although the relative role of flavonoids in allelopathic interference has been less well-characterized than that of some secondary metabolites, we present classic examples of their involvement in autotoxicity and allelopathy. We also describe their activity and fate in the soil rhizosphere in selected examples involving pasture legumes, cereal crops, and ferns. Potential research directions for further elucidation of the specific role of flavonoids in soil rhizosphere interactions are considered.

Comparative proteomic analysis of BTH and BABA-induced resistance in pea (Pisum sativum) toward infection with pea rust (Uromyces pisi)

Systemic acquired resistance (SAR) to Uromyces pisi in pea was studied by using a proteomic approach. Two-dimensional electrophoresis (2-DE) was used in order to compare the leaf proteome of two pea genotypes displaying different phenotypes (susceptible and partial resistance to the fungus), and in response to parasite infection under the effect of two inducers of SAR, BTH and BABA. Multivariate statistical analysis identified 126 differential protein spots under the experimental conditions (genotypes/treatments). All of these 126 protein spots were subjected to MALDI-TOF/TOF mass spectrometry to deduce their possible functions. A total of 50 proteins were identified using a combination of peptide mass fingerprinting (PMF) and MSMS fragmentation. Most of the identified proteins corresponded to enzymes belonging to photosynthesis, metabolism, biosynthesis, binding and defense response, whose behavior pattern was different in relation to susceptibility/resistance of the genotypes studied and to the BTH/BABA induction to pathogen response. Results obtained in this work suggested that plants could reduce their photosynthesis and other energy metabolism and enhance the production of defense-related proteins to cope the stress. On the other side, we postulated that resistance induced by the chemicals operates via different mechanisms: BABA inducer could act via phenolic biosynthesis pathway, whereas resistance provided by BTH inducer seems to be mediated by defense and stress-related proteins. The results are discussed in terms of response to rust under the effect of inducers.

Proteomic analysis by two-dimensional differential in gel electrophoresis (2D DIGE) of the early response of Pisum sativum to Orobanche crenata

Crenate broomrape (Orobanche crenata) is considered to be the major constraint for legume crops in Mediterranean countries. Strategies of control have been developed, but only marginal successes have been achieved. For the efficient control of the parasite, a better understanding of its interaction and associated resistance mechanisms at the molecular level is required. The pea response to this parasitic plant and the molecular basis of the resistance was studied using a proteomic approach based on 2D DIGE and MALDI-MSMS analysis. For this purpose, two genotypes showing different levels of resistance to O. crenata, as well as three time points (21, 25, and 30 d after inoculation) have been compared. Multivariate statistical analysis identified 43 differential protein spots under the experimental conditions (genotypes/treatments), 22 of which were identified using a combination of peptide mass fingerprinting (PMF) and MSMS fragmentation. Most of the proteins identified were metabolic and stress-related proteins and a high percentage of them (86%) matched with specific proteins of legume species. The behaviour pattern of the identified proteins suggests the existence of defence mechanisms operating during the early stages of infection that differed in both genotypes. Among these, several proteins were identified with protease activity which could play an important role in preventing the penetration and connection to the vascular system of the parasite. Our data are discussed and compared with those previously obtained in pea and Medicago truncatula.

Transcriptome analysis of resistant and susceptible genotypes of Glycine tomentella during Phakopsora pachyrhizi infection reveals novel rust resistance genes

Soybean rust, caused by Phakopsora pachyrhizi, is a destructive foliar disease in nearly all soybean-producing countries. To identify genes controlling resistance to soybean rust, transcriptome profiling was conducted in resistant and susceptible Glycine tomentella genotypes triggered by P. pachyrhizi infection. Among 38,400 genes monitored using a soybean microarray, at 5% false discovery rate, 1,342 genes were identified exhibiting significant differential expression between uninfected and P. pachyrhizi-infected leaves at 12, 24, 48, and 72 h post-inoculation (hpi) in both rust-susceptible and rust-resistant genotypes. Differentially expressed genes were grouped into 12 functional categories, and among those, large numbers relate to basic plant metabolism. Transcripts for genes involved in the phenylpropanoid pathway were up-regulated early during rust infection. Similarly, genes coding for proteins related to stress and defense responses such as glutathione-S-transferases, peroxidases, heat shock proteins, and lipoxygenases were consistently up-regulated following infection at all four time points. Whereas, subsets of genes involved in cellular transport, cellular communication, cell cycle, and DNA processing were down-regulated. Quantitative real-time reverse-transcription polymerase chain reaction (qRT-PCR) on randomly selected genes from the different categories confirmed these findings. Of differentially expressed genes, those associated with the flavonoid biosynthesis pathway as well as those coding for peroxidases and lipoxygenases were likely to be involved in rust resistance in soybean, and would serve as good candidates for functional studies. These findings provided insights into mechanisms underlying resistance and general activation of plant defense pathways in response to rust infection.

A gene expression analysis of syncytia laser microdissected from the roots of the Glycine max (soybean) genotype PI 548402 (Peking) undergoing a resistant reaction after infection by Heterodera glycines (soybean cyst nematode)

The syncytium is a nurse cell formed within the roots of Glycine max by the plant parasitic nematode Heterodera glycines. Its development and maintenance are essential for nematode survival. The syncytium appears to undergo two developmental phases during its maturation into a functional nurse cell. The first phase is a parasitism phase where the nematode establishes the molecular circuitry that during the second phase ensures a compatible interaction with the plant cell. The cytological features of syncytia undergoing susceptible or resistant reactions appear the same during the parasitism phase. Depending on the outcome of any defense response, the second phase is a period of syncytium maintenance (susceptible reaction) or failure (resistant reaction). In the analyses presented here, the localized gene expression occurring at the syncytium during the resistant reaction was studied. This was accomplished by isolating syncytial cells from Glycine max genotype Peking (PI 548402) by laser capture microdissection. Microarray analyses using the Affymetrix soybean GeneChip directly compared Peking syncytia undergoing a resistant reaction to those undergoing a susceptible reaction during the parasitism phase of the resistant reaction. Those analyses revealed lipoxygenase-9 and lipoxygenase-4 as the most highly induced genes in the resistant reaction. The analysis also identified induced levels of components of the phenylpropanoid pathway. These genes included phenylalanine ammonia lyase, chalcone isomerase, isoflavone reductase, cinnamoyl-CoA reductase and caffeic acid O-methyltransferase. The presence of induced levels of these genes implies the importance of jasmonic acid and phenylpropanoid signaling pathways locally at the site of the syncytium during the resistance phase of the resistant reaction. The analysis also identified highly induced levels of four S-adenosylmethionine synthetase genes, the EARLY-RESPONSIVE TO DEHYDRATION 2 gene and the 14-3-3 gene known as GENERAL REGULATORY FACTOR 2. Subsequent analyses studied microdissected syncytial cells at 3, 6 and 9 days post infection (dpi) during the course of the resistant reaction, resulting in the identification of signature gene expression profiles at each time point in a single G. max genotype, Peking.

Toxicity of endophyte-infected tall fescue alkaloids and grass metabolites on Pratylenchus scribneri

ABSTRACT Neotyphodium coenophialum, an endophytic fungus associated with tall fescue grass, enhances host fitness and imparts pest resistance. This symbiotum is implicated in the reduction of stresses, including plant-parasitic nematodes. To substantiate this implication, toxicological effects of root extracts, polyphenolic fraction, ergot, and loline alkaloids from endophyte-infected tall fescue were investigated using Pratylenchus scribneri, a nematode pest of tall fescue. In vitro bioassays and greenhouse studies were used as tests for effects of root fractions and compounds on motility and mortality of this lesion nematode. Greenhouse studies revealed that endophyte-infected tall fescue grasses are essentially nonhosts to P. scribneri, with root populations averaging 3 to 17 nematodes/pot, compared with 4,866 and 8,450 nematodes/pot for noninfected grasses. The in vitro assay indicated that root extracts from infected tall fescues were nematistatic. Polyphenols identified in extracts included chlorogenic acid, 3,5-dicaffeoylquinic acids, caffeic acid, and two unidentified compounds, but these were not correlated with endophyte status, qualitatively or quantitatively. Tests of several ergot alkaloids revealed that ergovaline and alpha-ergocryptine were nematicidal at 5 and 50 microg/ml, respectively, while ergocornine and ergonovine were nematistatic at most concentrations. Loline (N-formylloline), the pyrrolizidine alkaloid tested, was nematicidal (50 to 200 microg/ml). The ecological benefits of the metabolites tested here should assist in defining their role in deterring this nematode species while offering some probable mechanisms of action against plant-parasitic nematodes in general.

Differential expression proteomics to investigate responses and resistance to Orobanche crenata in Medicago truncatula

BACKGROUND

Parasitic angiosperm Orobanche crenata infection represents a major constraint for the cultivation of legumes worldwide. The level of protection achieved to date is either incomplete or ephemeral. Hence, an efficient control of the parasite requires a better understanding of its interaction and associated resistance mechanisms at molecular levels.

RESULTS

In order to study the plant response to this parasitic plant and the molecular basis of the resistance we have used a proteomic approach. The root proteome of two accessions of the model legume Medicago truncatula displaying differences in their resistance phenotype, in control as well as in inoculated plants, over two time points (21 and 25 days post infection), has been compared. We report quantitative as well as qualitative differences in the 2-DE maps between early- (SA 27774) and late-resistant (SA 4087) genotypes after Coomassie and silver-staining: 69 differential spots were observed between non-inoculated genotypes, and 42 and 25 spots for SA 4087 and SA 27774 non-inoculated and inoculated plants, respectively. In all, 49 differential spots were identified by peptide mass fingerprinting (PMF) following MALDI-TOF/TOF mass spectrometry. Many of the proteins showing significant differences between genotypes and after parasitic infection belong to the functional category of defense and stress-related proteins. A number of spots correspond to proteins with the same function, and might represent members of a multigenic family or post-transcriptional forms of the same protein.

CONCLUSION

The results obtained suggest the existence of a generic defense mechanism operating during the early stages of infection and differing in both genotypes. The faster response to the infection observed in the SA 27774 genotype might be due to the action of proteins targeted against key elements needed for the parasite's successful infection, such as protease inhibitors. Our data are discussed and compared with those previously obtained with pea 1 and transcriptomic analysis of other plant-pathogen and plant-parasitic plant systems.

Structure and function of enzymes involved in the biosynthesis of phenylpropanoids

As a major component of plant specialized metabolism, phenylpropanoid biosynthetic pathways provide anthocyanins for pigmentation, flavonoids such as flavones for protection against UV photodamage, various flavonoid and isoflavonoid inducers of Rhizobium nodulation genes, polymeric lignin for structural support and assorted antimicrobial phytoalexins. As constituents of plant-rich diets and an assortment of herbal medicinal agents, the phenylpropanoids exhibit measurable cancer chemopreventive, antimitotic, estrogenic, antimalarial, antioxidant and antiasthmatic activities. The health benefits of consuming red wine, which contains significant amounts of 3,4',5-trihydroxystilbene (resveratrol) and other phenylpropanoids, highlight the increasing awareness in the medical community and the public at large as to the potential dietary importance of these plant derived compounds. As recently as a decade ago, little was known about the three-dimensional structure of the enzymes involved in these highly branched biosynthetic pathways. Ten years ago, we initiated X-ray crystallographic analyses of key enzymes of this pathway, complemented by biochemical and enzyme engineering studies. We first investigated chalcone synthase (CHS), the entry point of the flavonoid pathway, and its close relative stilbene synthase (STS). Work soon followed on the O-methyl transferases (OMTs) involved in modifications of chalcone, isoflavonoids and metabolic precursors of lignin. More recently, our groups and others have extended the range of phenylpropanoid pathway structural investigations to include the upstream enzymes responsible for the initial recruitment of phenylalanine and tyrosine, as well as a number of reductases, acyltransferases and ancillary tailoring enzymes of phenylpropanoid-derived metabolites. These structure-function studies collectively provide a comprehensive view of an important aspect of phenylpropanoid metabolism. More specifically, these atomic resolution insights into the architecture and mechanistic underpinnings of phenylpropanoid metabolizing enzymes contribute to our understanding of the emergence and on-going evolution of specialized phenylpropanoid products, and underscore the molecular basis of metabolic biodiversity at the chemical level. Finally, the detailed knowledge of the structure, function and evolution of these enzymes of specialized metabolism provide a set of experimental templates for the enzyme and metabolic engineering of production platforms for diverse novel compounds with desirable dietary and medicinal properties.

Inducible Flavone in Oats (Avena sativa) Is a Novel Defense Against Plant-Parasitic Nematodes

ABSTRACT The induction of defense compounds in oats (Avena sativa) in response to invasion by parasitic nematodes and to application of the wound hormone methyl jasmonate was examined. Oats cv. Quoll seedlings were challenged with Pratylenchus neglectus, Heterodera avenae, and Ditylenchus dipsaci and treated with 1 x 10(-4) M methyl jasmonate. Three compounds, isolated in methanolic root and shoot extracts of oats, exhibiting an absorbance spectrum typical of flavone glycosides, were induced by nematode invasion and methyl jasmonate. These were identified as flavone-C-glycosides by mass spectrometry. The effect of the flavone-C-glycosides on the invasion by and development of cereal cyst nematode H. avenae was assessed using methanolic extracts of shoots and roots from methyl jasmonate-treated plants. Both extracts impaired nematode invasion and development. When the extracts were fractionated by high voltage paper electrophoresis, only one flavone-C-glycoside, O-methyl-apigenin-C-deoxyhexoside-O-hexoside, inhibited nematode invasion. The protective effect of the induction of flavone-C-glycosides in oats by methyl jasmonate was evaluated against H. avenae and P. neglectus. Treatment with methyl jasmonate reduced invasion of both nematodes and increased plant mass, compensating for damage caused by the nematodes, and is attributed to the active flavone-C-glycoside. The active compound, O-methyl-apigenin-C-deoxyhexoside-O-hexoside, has not been implicated previously in plant defense against any pest or pathogen, and appears to provide protection against the major cereal nematodes Heterodera and Pratylenchus.

Grape berry biochemistry revisited upon proteomic analysis of the mesocarp

Major soluble proteins of grapevine ripe berries were extracted from six different cultivars including non vinifera, with trichloroacetic acid acetone and resolved in two-dimensional electrophoresis (2-DE) gels. About three hundred spots were detected on the 2-DE map after colloidal blue staining. From 2-DE map of cv. Gamay mesocarp, 67 proteins were identified (p > 0.95) using matrix-assisted laser desorption/ionization-mass spectrometry analysis. About 34%, 19%, and 13% of identified proteins play, respectively, a role in energy metabolism, defense, and stress response and primary metabolism. 2-DE analysis revealed considerable accumulation of dehydrin, invertase, and a putative transcription factor in the ripe fruit, in addition to pathogenesis-related proteins such as chitinase and thaumatin-like proteins previously documented as prevalent proteins in ripe berries. Actual translation of redundant transcripts of unclear function such as Grip31, Grip32, and Grip61 recently cloned in ripe grape berries was confirmed. The relative abundance of UDP-glucose pyrophosphorylase and vacuolar invertase strongly supported a key role of the apoplastic pathway of sugar loading during ripening. Comparative analysis shows that differences between cultivars were low, but different isoforms of alcohol dehydrogenase and of a transcription factor of hexose transporter were obvious in the six cultivars. Peptide mass fingerprinting suggests that the Adh isoforms would be Adh2/Adh6 or Adh2/Adh7 dimers and unambiguously shows that considerable deletion/insertion inside Adh7 are not cloning artifacts.

Expression of Oryzacystatin I and II in Alfalfa Increases Resistance to the Root-Lesion Nematode

ABSTRACT Digestive cysteine proteinases have been isolated from plant-parasitic nematodes as well as coleopteran and hemipteran insects. Phytocystatins, inhibitors of cysteine proteinases, are found in a number of plants where they may play a role in defense against pathogens and pests. The cDNAs of the phytocystatins from rice, oryzacystatin I (OC-I) and oryzacystatin II (OC-II), were expressed in alfalfa (Medicago sativa) plants under the control of the potato protease inhibitor II (PinII) promoter and the plants were evaluated for resistance to the root-lesion nematode (Pratylenchus penetrans). A PinII-beta-glucuronidase (GUS) gene was introduced into alfalfa to determine the pattern of gene expression from this promoter. Constitutive GUS expression was observed in leaf and root vascular tissue, and in some plants, expression was observed in leaf mesophyll cells. Mechanical wounding of leaves increased GUS expression approximately twofold over 24 h. Inoculation with root-lesion nematodes resulted in localized GUS expression. Populations of root-lesion nematodes in alfalfa roots from one line containing the PinII::OC-I transgene and one line containing the PinII::OC-II transgene were reduced 29 and 32%, respectively, compared with a transgenic control line. These results suggest that oryzacystatins have the potential to confer increased resistance to the root-lesion nematode in alfalfa.

Phytochemical based strategies for nematode control

This review examines the discovery of naturally occurring phytochemicals antagonistic toward plant-parasitic and other nematodes. Higher plants have yielded a broad spectrum of active compounds, including polythienyls, isothiocyanates, glucosinolates, cyanogenic glycosides, polyacetylenes, alkaloids, lipids, terpenoids, sesquiterpenoids, diterpenoids, quassinoids, steroids, triterpenoids, simple and complex phenolics, and several other classes. Many other antinematodal compounds have been isolated from biocontrol and other fungi. Natural products active against mammalian parasites can serve as useful sources of compounds for examination of activity against plant parasites. The agricultural utilization of phytochemicals, although currently uneconomic in many situations, offers tremendous potential.

Investigations into the biochemical basis for nematode resistance in roots of three musa cultivars in response to Radopholus similis infection

The Musa cultivars, Dwarf Cavendish, Yangambi Km5 and Kunnan, exhibit considerable differences in resistance to Radopholus similis. Infection resulted in significant increases in condensed tannins and flavan-3,4-diols in roots (P < 0.001). The highly resistant cultivar Kunnan had the highest levels of condensed tannins before and after infection. The preinfection levels were similar to the postinfection levels of the two other cultivars. Tannins had mostly procyanidin character, but Kunnan also contained propelargonidins; these compounds may be involved in the resistance mechanism. It is suggested that the butanol/HCl assay be used as a rapid test in screening for resistance to R. similis.