Major Crop Plants Research Articles

Functional Characterisation of Banana (Musa spp.) 2-Oxoglutarate-Dependent Dioxygenases Involved in Flavonoid Biosynthesis

Bananas (Musa) are non-grass, monocotyledonous, perennial plants that are well known for their edible fruits. Their cultivation provides food security and employment opportunities in many countries. Banana fruits contain high levels of minerals and phytochemicals, including flavonoids, which are beneficial for human nutrition. To broaden the knowledge on flavonoid biosynthesis in this major crop plant, we aimed to identify and functionally characterise selected structural genes encoding 2-oxoglutarate-dependent dioxygenases, involved in the formation of the flavonoid aglycon. Musa candidates genes predicted to encode flavanone 3-hydroxylase (F3H), flavonol synthase (FLS) and anthocyanidin synthase (ANS) were assayed. Enzymatic functionalities of the recombinant proteins were confirmed in vivo using bioconversion assays. Moreover, transgenic analyses in corresponding Arabidopsis thaliana mutants showed that MusaF3H, MusaFLS and MusaANS were able to complement the respective loss-of-function phenotypes, thus verifying functionality of the enzymes in planta. Knowledge gained from this work provides a new aspect for further research towards genetic engineering of flavonoid biosynthesis in banana fruits to increase their antioxidant activity and nutritional value.

A single residue deletion in the barley HKT1;5 P189 variant restores plasma membrane localisation but not Na+ conductance

Leaf Na+ exclusion, mediated by plasma membrane-localised Class 1 High-affinity potassium (K+) Transporters (HKTs), is a key mechanism contributing to salinity tolerance of several major crop plants. We determined previously that the leucine to proline residue substitution at position 189 (L189P) in barley HvHKT1;5 disrupts its characteristic plasma membrane localisation and Na+ conductance. Here, we focus on a surprising observation that a single residue deletion of methionine at position 372 (M372del) within the conserved VMMYL motif in plant HKTs, restores plasma membrane localisation but not Na+ conductance in HvHKT1;5 P189. To clarify why the singular M372 deletion regains plasma membrane localisation, we built 3D models and defined α-helical assembly pathways of the P189 M372del mutant, and compared these findings to the wild-type protein, and the HvHKT1;5 L189 variant and its M372del mutant. We find that α-helical association and assembly pathways in HvHKT1;5 proteins fall in two contrasting categories. Inspections of structural flexibility through molecular dynamics simulations revealed that the conformational states of HvHKT1;5 P189 diverge from those of the L189 variant and M372del mutants. We propose that M372del in HvHKT1;5 P189 instigates structural rearrangements allowing routing to the plasma membrane, while the restoration of conductance would require further interventions. We integrate the microscopy, electrophysiology, and biocomputational data and discuss how a profound structural change in HvHKT1;5 P189 M372del impacts its α-helical protein association pathway and flexibility, and how these features underlie a delicate balance leading to restoring plasma membrane localisation but not Na+ conductance.

Structural and functional characterization of rhizosphere actinomycetes of major crop plants under shifting cultivation practice in Northeast India

Structural and functional characterization of rhizosphere actinomycetes of major crop plants under shifting cultivation practice in Northeast India

Identification of Rice Blast Loss-of-Function Mutant Alleles in the Wheat Genome as a New Strategy for Wheat Blast Resistance Breeding.

Blast is caused by the host-specific lineages of the fungus Magnaporthe oryzae and is the most important destructive disease in major crop plants, including rice and wheat. The first wheat blast outbreak that occurred in Bangladesh in 2016 and the recent epidemic in Zambia were caused by the M. oryzae Triticum (MoT) pathotype, a fungal lineage belonging to M. oryzae. Although a few reported wheat cultivars show modest resistance to MoT, the patterns of genetic variation and diversity of this pathotype make it crucial to identify additional lines of resistant wheat germplasm. Nearly 40 rice blast resistant and susceptible genes have so far been cloned. Here, we used BLAST analysis to locate two rice blast susceptible genes in the wheat reference genome, bsr-d1 and bsr-k1, and identified six identical homologous genes located on subgenomes A, B, and D. We uncovered a total of 171 single nucleotide polymorphisms (SNPs) in an ethyl methanesulfonate (EMS)-induced population, with mutation densities ranging from 1/1107.1 to 1/230.7 kb through Targeting Induced Local Lesions IN Genomes (TILLING) by sequencing. These included 81 SNPs located in exonic and promoter regions, and 13 coding alleles that are predicted to have severe effects on protein function, including two pre-mature mutants that might affect wheat blast resistance. The loss-of-function alleles identified in this study provide insights into new wheat blast resistant lines, which represent a valuable breeding resource.

Regulation of cuticular wax biosynthesis in plants under abiotic stress

Cuticular waxes are the covering of the outer layer of the plant, consist of hydrocarbon appears like whitish film or bloom in plant organs. They play a vital role like a safeguard from different stress condition in the plant. Since environmental factors are active regulators of cuticular wax biosynthesis, composition, quantity, and deposition, it is evident that cuticular wax is associated with plant stress responses. The diversity of cuticular wax compositions is a proof of the wealth of genes associated in plant wax production. Moreover, a number of wax genes were distinguished in plant/crops at abiotic stress conditions but, regulation of control of those wax genes has not been studied very well in major crop plants at abiotic conditions. A very few transcriptions factors were identified to regulate the expression level of wax genes of cuticular wax biosynthesis at abiotic stress condition. However, further study is needed to identify more candidate transcriptional regulation factors to cuticular wax production in different crop plants in diverse abiotic environments. Therefore, regulation of cuticular wax production under diverse abiotic stresses and the role of transcription factors into the plant cuticular wax accumulation will be helpful to engineer crop plants and improve transgenic crops for stress tolerance. In this review, we focused on a new perspective on transcriptional factors to regulate functional genes of cuticular wax biosynthesis in plants at abiotic stresses.

Comprehensive strategy to achieve drought tolerance in plants

In this scenario of global climate change, increasing vulnerability of plants to drought stress poses a serious threat worldwide to sustain growth, development and productivity of major crop plants. Taking it into consideration, developing plant species with greater stress tolerance capability arises to be the most sustainable solution towards enhancing crop productivity. However, to confer drought tolerance, plants evolve to undergo various biochemical and molecular changes. In line with this, many plants under drought exposure upregulate a variety of genes involved in the synthesis of several stress-induced transcription factors and protein kinases, which in turn regulate the biosynthesis and accumulation of several protective proteins and osmoprotectants, induce the activation of antioxidant defence system, help in improving photosynthesis and maintaining cellular water status by acting together with hormonal cross-talk. The current mini-review intends to provide a deep and concise understanding on stress-induced responses of plants and the transgenic approaches already been adopted to improve plant tolerance against drought.

Characterization of dwarf and narrow leaf (dnl-4) mutant in rice

ABSTRACT Height and leaf morphology are important agronomic traits of the major crop plant rice (Oryza sativa). In previous studies, the dwarf and narrow leaf genes (dnl1, dnl2 and dnl3) have identified in rice. Using the Ac/Ds knockout system, we found a new dwarf and narrow leaf (dnl) mutant and identified mutated gene. The dnl-4 mutant showed reduced plant height and leaf blade width compared to the wild type, and increased leaf inclination. The morphological defects of the mutant were caused by the suppressed expression of the DNL-4 gene, which encodes a pfkB carbohydrate kinase protein. These results suggest that DNL-4 expression is involved in modulating plant height and leaf growth. Furthermore, DNL-4 expression also affects productivity in rice: the dnl-4 mutant exhibited reduced panicle length and grain width compared with the wild type. To understand DNL-4 function in rice, we analyzed the expression levels of leaf growth-related genes, such as NAL1, NAL7, and CSLD4, in the dnl-4 mutant. Expression of NAL1 and NAL7 was downregulated in the dnl-4 mutant compared to the wild type. The observation that DNL-4 expression corresponded with that of NAL1 and NAL7 is consistent with the narrow leaf phenotype of the dnl-4 mutant. These results suggest that DNL-4 regulates plant height and leaf structure in rice.

Phosphate-Starvation-Inducible S-Like RNase Genes in Rice Are Involved in Phosphate Source Recycling by RNA Decay.

The fine-tuning of inorganic phosphate (Pi) for enhanced use efficiency has long been a challenging subject in agriculture, particularly in regard to rice as a major crop plant. Among ribonucleases (RNases), the RNase T2 family is broadly distributed across kingdoms, but little has been known on its substrate specificity compared to RNase A and RNase T1 families. Class I and class II of the RNase T2 family are defined as the S-like RNase (RNS) family and have showed the connection to Pi recycling in Arabidopsis. In this study, we first carried out a phylogenetic analysis of eight rice and five Arabidopsis RNS genes and identified mono-specific class I and dicot-specific class I RNS genes, suggesting the possibility of functional diversity between class I RNS family members in monocot and dicot species through evolution. We then compared the in silico expression patterns of all RNS genes in rice and Arabidopsis under normal and Pi-deficient conditions and further confirmed the expression patterns of rice RNS genes via qRT-PCR analysis. Subsequently, we found that most of the OsRNS genes were differentially regulated under Pi-deficient treatment. Association of Pi recycling by RNase activity in rice was confirmed by measuring total RNA concentration and ribonuclease activity of shoot and root samples under Pi-sufficient or Pi-deficient treatment during 21 days. The total RNA concentrations were decreased by < 60% in shoots and < 80% in roots under Pi starvation, respectively, while ribonuclease activity increased correspondingly. We further elucidate the signaling pathway of Pi starvation through upregulation of the OsRNS genes. The 2-kb promoter region of all OsRNS genes with inducible expression patterns under Pi deficiency contains a high frequency of P1BS cis-acting regulatory element (CRE) known as the OsPHR2 binding site, suggesting that the OsRNS family is likely to be controlled by OsPHR2. Finally, the dynamic transcriptional regulation of OsRNS genes by overexpression of OsPHR2, ospho2 mutant, and overexpression of OsPT1 lines involved in Pi signaling pathway suggests the molecular basis of OsRNS family in Pi recycling via RNA decay under Pi starvation.

An overview of recent advancement in phytohormones-mediated stress management and drought tolerance in crop plants

Plants face a continuous threat of abiotic stresses under the changing environment. Because of climate change, water scarcity has been shown to be a significant environmental constraint on plant productivity. Droughts in particular have been shown to affect plant growth and development, lead to alteration in quality and quantity of crop production, and result in global food insecurity. Phytohormones are known to play critical roles in regulating diverse processes of plant adaption to a drought environment. They regulate cellular functions at molecular levels via various cell signaling. Among various phytohormones, abscisic acid (ABA) is known for its role in drought-stress tolerance in plants. Other phytohormones such as auxins, brassinosteroids (BRs), cytokinins (CK), ethylene (ET), gibberellins (GA), jasmonic acid (JA), and salicylic acid (SA) are also crucial in plant drought tolerance. Several plant growth-promoting microbes have been reported to enhance the phytohormone levels in plants to mitigate the negative effect of drought. However, the transgenic approach appears to be a boon to engineering the genes responsible for regulating phytohormones to develop a drought-tolerant trait. Expression analyses have revealed that genes encoding transcription factors such as bZIP11, DREB2, MYB14, MYB48, WRKY2, WRKY56, WRKY108715, and RD22 play a very crucial role in phytohormone mediated drought response. Furthermore, exogenous applications of phytohormones are shown to enhance endogenous phytohormones. This review highlights the most recent advancements in phytohormone-mediated drought tolerance in major crop plants.

Molecular Marker Technology for Crop Improvement

Since the 1980s, agriculture and plant breeding have changed with the development of molecular marker technology. In recent decades, different types of molecular markers have been used for different purposes: mapping, marker-assisted selection, characterization of genetic resources, etc. These have produced effective genotyping, but the results have been costly and time-consuming, due to the small number of markers that could be tested simultaneously. Recent advances in molecular marker technologies such as the development of high-throughput genotyping platforms, genotyping by sequencing, and the release of the genome sequences of major crop plants open new possibilities for advancing crop improvement. This Special Issue collects sixteen research studies, including the application of molecular markers in eleven crop species, from the generation of linkage maps and diversity studies to the application of marker-assisted selection and genomic prediction.

Characterization of tissue specific expressed proteins and metabolites in Cenchrus polystachion (L.) Schult and their role in apomixis

Agricultural production can be aggrandized by adaptation of trending technologies or processes which focus on increase in seed production. Asexual reproduction in plants or Apomixis is such a process, but its absence in major crop plants has paved an increased research towards understanding the process of apomixis. In present study an attempt was made to understand the role of differentially expressed proteins and metabolite in plant parts like leaf, stigma, immature ovary, seed, anther sac and pollen grains of Cenchrus polystachion. 563, 936, 1188, 770, 721 and 712 proteins and 6118, 6784, 6192, 6615, 5797 and 5791 metabolites were obtained from leaf, stigma, immature ovary, seed, anther sac and pollen respectively on proteome and metabolome analysis. Some of the differentially expressed proteins and metabolites unveiled the important pathways for apomixis in Cenchrus. The top most pathways involved in apomixis are sphingolipid metabolism, glycerophospholipid metabolism, pantothenate and CoA biosynthesis, alpha linolenic acid pathway and brassinosteroid biosynthesis. The detailed analysis of the all the tissues gave an insight of the overexpression of GNDI Inhibitor (Guanosine nucleotide diphosphate dissociation inhibitor) in immature ovary. The molecular docking study further revealed that the GoLOCO motif of GNDI efficiently interacts with G alpha protein which interferes with the binding of G alpha with PLD alpha (Phospholipase D alpha). Thus, the overexpression of G alpha Inhibitor might exert their effect on PLD alpha leading to meiosis inactivation and formation of apomictic seed.

Can Alternative Metabolic Pathways and Shunts Overcome Salinity Induced Inhibition of Central Carbon Metabolism in Crops?

The annual cost of lost crop production from exposure to salinity has major impacts on food security in all parts of the world. Salinity stress disturbs energy metabolism and knowledge of the impacts on critical processes controlling plant energy production is key to successfully breeding salt tolerant crops. To date, little progress has been achieved using classic breeding approaches to develop salt tolerance. The hope of some salinity researchers is that through a better understanding of the metabolic responses and adaptation to salinity exposure, new breeding targets can be suggested to help develop salt tolerant crops. Plants sense and react to salinity through a complex system of sensors, receptor systems, transporters, signal transducers, and gene expression regulators in order to control the uptake of salts and to induce tolerant metabolism that jointly leads to changes in growth rate and biomass production. During this response, there must be a balance between supply of energy from mitochondria and chloroplasts and energy demands for water and ion transport, growth, and osmotic adjustment. The photosynthetic response to salinity has been thoroughly researched and generally we see a sharp drop in photosynthesis after exposure to salinity. However, less attention has been given to the effect of salt stress on plant mitochondrial respiration and the metabolic processes that influence respiratory rate. A further complication is the wide range of respiratory responses that have been observed in different plant species, which have included major and minor increases, decreases, and no change in respiratory rate after salt exposure. In this review, we begin by considering physiological and biochemical impacts of salinity on major crop plants. We then summarize and consider recent advances that have characterized changes in abundance of metabolites that are involved in respiratory pathways and their alternative routes and shunts in terms of energy metabolism in crop plants. We will consider the diverse molecular responses of cellular plant metabolism during salinity exposure and suggest how these metabolic responses might aid in salinity tolerance. Finally, we will consider how this commonality and diversity should influence how future research of the salinity responses of crops plants should proceed.

A collection of transcriptomic and proteomic datasets from sesame in response to salt stress.

Soil salinity is a major abiotic factor affecting the growth and development of important crops such as sesame (Sesamum indicum L.). To understand the molecular mechanisms of this oilseed crop in response to salt stress, we examined the transcriptome and proteome profiles of two sesame varieties, with contrasting tolerances to salinity. Here, RNA sequencing and quantitative proteomic analyses of 30 samples from salt-tolerant and -sensitive sesame seedlings under salt stress were carried out. These data can be used for differential gene expression and protein accumulation analyses, based on a genetic aberration or phenotypic differences in sesame responses to salt stress. Our dataset provides an extensive resource for understanding the molecular mechanisms underlying the adaptation of sesame to salt stress, and may constitute useful a resource for increasing the tolerance of major crop plants to raised salinity levels in soils.

Linking rhizosphere bacterial diversity and soil fertility in tobacco plants under different soil types and cropping pattern in Tanzania: A pilot study

Tobacco (Nicotiana tabacum L.), one of the major crop plants in Tanzania, cropping affects the level of soil fertility, but the reason has not been known. Plant rhizosphere plays an important role in affecting soil fertility through changing microbial composition. We planned a pilot study to understand the changes in microbial composition and soil nutrients in the rhizosphere soils of tobacco in three agro-ecological zone, namely Sikonge, Tabora and Urambo in Tanzania. This study assessed bacteriota composition using 16S rRNA sequencing and soil fertility in the rhizosphere of tobacco plants. The results showed that bacterial diversity in tobacco rhizosphere soils belonged to Proteobacteria phyla, associated significantly (p < 0.05) with solubilization of insoluble P, K and S. The solubilization of P, K and S in soils facilitates the availability of these nutrients to the tobacco plants (a heavy feeder crop) allows low levels of these nutrients in the soils for the subsequent crop. The Proteobacteria phyla also associated with an increase in soil N content through fixation. Therefore, bacteria diversity in tobacco rhizosphere influence solubilities of macronutrients (P, K, S) and quickly up taken by the tobacco plant and reduces their levels in soils, some bacteria involved in fixing N and increases total N in the soil.

Multigene CRISPR/Cas9 genome editing of hybrid proline rich proteins (HyPRPs) for sustainable multi-stress tolerance in crops: the review of a promising approach.

The recent global climate change has directly impacted major biotic and abiotic stress factors affecting crop productivity worldwide. Therefore, the need of the hour is to develop sustainable multiple stress tolerant crops through modern biotechnological approaches to cope with climate change. Hybrid proline rich proteins (HyPRPs) are the cell-wall structural proteins, which contain an N-terminal repetitive proline-rich domain and a C-terminal conserved eight-cysteine motif domain. HyPRPs are known to regulate multiple abiotic and biotic stress responses in plants. Recently, a few HyPRPs have been characterized as negative regulators of abiotic and biotic stress responses in different plants. Disruption of such negative regulators for desirable positive phenotypic traits has been made possible through the advent of advanced genome engineering tools. In the past few years, CRISPR/Cas9 has emerged as a novel breakthrough technology for crop improvement by target specific editing of known negative regulatory host genes. Here, we have described the mechanism of action and the role of known HyPRPs in regulating different biotic and abiotic stress responses in major crop plants. We have also discussed the importance of the CRISPR/Cas9 based genome editing system in targeting known negative regulatory HyPRPs for multi-stress crop tolerance using the tomato crop model. Application of genome editing to manipulate the HyPRPs of major crop plants holds promise in developing newer stress management methods in this rapidly changing climate and would lead in the future to sustain crop productivity.

A Potent Burkholderia Endophyte against Boxwood Blight Caused by Calonectria pseudonaviculata.

Calonectria pseudonaviculata (Cps) poses an increasing threat to boxwood, a major nursery crop and iconic landscape plant worldwide. Here, we report on a potent biocontrol agent that produces small sage green (SSG) colonies on potato dextrose agar. SSG is a bacterial strain recovered from Justin Brouwers boxwood leaves with unusual response to Cps inoculation. Water-soaked symptoms developed on leaves 2 days after inoculation then disappeared a few days later. This endophyte affected several major steps of the boxwood blight disease cycle. SSG at 107 cfu/mL lysed all conidia in mixed broth culture. SSG at 108 cfu/mL reduced blight incidence by >98% when applied one day before or 3 h after boxwood were inoculated with Cps. Its control efficacy decreased with decreasing bacterial concentration to 103 cfu/mL and increasing lead time up to 20 days. When applied on diseased leaf litter under boxwood plants, SSG reduced Cps sporulation and consequently mitigated blight incidence by 90%. SSG was identified as a new member of the Burkholderia cepacia complex with distinct characters from known clinical strains. With these protective, curative, and sanitizing properties, this Burkholderia endophyte offers great promise for sustainable blight management at production and in the landscape.

Superparamagnetic hematite nanoparticle: Cytogenetic impact on onion roots and seed germination response of major crop plants.

Augmented escape of nanostructures to the ecosystem has necessitated the comprehensive study of their impact, especially on plants. In the current study, hematite nanoparticles were prepared by employing garlic extract and checked for their cytogenetic effect on onion roots and germination characteristics of five agricultural crops (Vigna radiata, Triticum aestivum, Trigonella foenum-graecum, Cicer arietinum and Vicia faba) in the concentration range of 20-100 mg/L. Onion roots exhibited an increased mitotic index till 60 mg/L dosage, beyond which trend decreased marginally. Percentage of aberrant chromosomes reported for 100 mg/L exposure was very low (3.358 ± 0.13%) and included common defects such as clumped/sticky metaphase, ring chromosomes, laggards, spindle abnormality, chromosome bridges etc. Moreover, comet assay, DNA laddering experiment and electron micrograph study confirmed negligible damage to onion roots. Seed germination study indicated a positive response in different agronomic traits (germination index, root length, fold change in weight and vigour index) up to 60 mg/L, beyond which either negative or neutral effect was observed. However, none of the samples showed 50% inhibition in germination index; highest being 33.33% inhibition for V. faba, compared to the control. In brief, biogenic hematite nanoparticles caused insignificant phytotoxicity and were likely assimilated as iron source at lower dosage.

Genome-wide identification, characterisation and expression profile analysis of DEAD-box family genes in sweet potato wild ancestor Ipomoea trifida under abiotic stresses.

DEAD-box protein family is the largest subfamily of RNA helicases and plays an important role in RNA metabolism and plant growth, development, and stress responses. Although DEAD-box genes have been characterized in various major crop plants, their identification and characterization in Convolvulaceae is still in infancy. Sweet potato (Ipomoea batatas, in Convolvulaceae) is the seventh most important crop in the world. Ipomoea trifida is one of the ancestors of sweet potato and is an effective resource for sweet potato cross-breeding. Identification and characterisation of DEAD-box transcription factors in sweet potato wild ancestor I. trifida genome. A systematic genome-wide analysis was conducted to identify the DEAD-box transcription factors in the I. trifida genome. We identified 17 ItfDEAD-box genes which distributed unevenly on the nine chromosomes of I. trifida and encoded 29 DEAD transcripts. The phylogenetic analysis classified the DEAD-box proteins into nine groups named I-IX. Homology model prediction of ItfDEAD-box proteins obtained 14 models which lay a preliminary foundation for the further functional exploration of the ItfDEAD-box proteins. The tissue-specific and abiotic stress-responsive expression profiles of ItfDEAD-box genes were analyzed in different tissues and under abiotic stress responses by RNA-seq data and confirmed by quantitative PCR analysis. Some genes were significantly up- or down-regulated by different abiotic stress, suggesting that ItfDEAD-box plays a crucial role in stress responses in I. trifida. The identification and gene expression of the ItfDEAD-box gene family might shed light on the function exploration of DEAD-box gene in I. trifida and promote the molecular breeding of sweet potato.

Proteome Analysis of 14-3-3 Targets in Tomato Fruit Tissues.

Tomato is a major crop plant and an important constituent of the human diet. Exclusive features such as bearing fleshy fruits and undergoing a phase transition from partially photosynthetic to fully heterotrophic metabolism make tomato fruit a model system for fruit development studies. Although the tomato genome has been completely sequenced, functional proteomics studies are still at their starting stage. Proteomics technologies, especially the combination of multiple approaches, provide a very powerful tool to accurately identify functional proteins and investigate certain sets of proteins in more detail. The direct binding of plant 14-3-3 proteins to their multiple target proteins modulates the functions of the latter, suggesting that these 14-3-3 proteins are directly involved in various physiological pathways. This chapter outline methods for the identification of 14-3-3 protein complexes in tomato fruit tissues. These methods include detailed protocols for protein extraction, coimmunoprecipitation, SDS-PAGE, SYPRO Ruby staining, in-gel trypsin digestion, and LC-MS/MS analysis for 14-3-3 interactomics.

PHI-Nets: A Network Resource for Ascomycete Fungal Pathogens to Annotate and Identify Putative Virulence Interacting Proteins and siRNA Targets.

Interactions between proteins underlie all aspects of complex biological mechanisms. Therefore, methodologies based on complex network analyses can facilitate identification of promising candidate genes involved in phenotypes of interest and put this information into appropriate contexts. To facilitate discovery and gain additional insights into globally important pathogenic fungi, we have reconstructed computationally inferred interactomes using an interolog and domain-based approach for 15 diverse Ascomycete fungal species, across nine orders, specifically Aspergillus fumigatus, Bipolaris sorokiniana, Blumeria graminis f. sp. hordei, Botrytis cinerea, Colletotrichum gloeosporioides, Colletotrichum graminicola, Fusarium graminearum, Fusarium oxysporum f. sp. lycopersici, Fusarium verticillioides, Leptosphaeria maculans, Magnaporthe oryzae, Saccharomyces cerevisiae, Sclerotinia sclerotiorum, Verticillium dahliae, and Zymoseptoria tritici. Network cartography analysis was associated with functional patterns of annotated genes linked to the disease-causing ability of each pathogen. In addition, for the best annotated organism, namely F. graminearum, the distribution of annotated genes with respect to network structure was profiled using a random walk with restart algorithm, which suggested possible co-location of virulence-related genes in the protein–protein interaction network. In a second ‘use case’ study involving two networks, namely B. cinerea and F. graminearum, previously identified small silencing plant RNAs were mapped to their targets. The F. graminearum phenotypic network analysis implicates eight B. cinerea targets and 35 F. graminearum predicted interacting proteins as prime candidate virulence genes for further testing. All 15 networks have been made accessible for download at www.phi-base.org providing a rich resource for major crop plant pathogens.