Being one of the major staple foods in the world, and an interesting model monocot plant, rice (Oryza sativa L.) has recently received attention from molecular nematologists studying the cellular and molecular aspects of the interaction between this crop and plant-parasitic nematodes. In this review, we highlight recent advances in this field, with a focus on the best-studied root-knot nematodes. Histological studies have revealed the cellular changes inside root-knot nematode–induced feeding sites, both in the compatible interaction with Oryza sativa and the incompatible interaction with the related species Oryza glaberrima. After comparing the published data from transcriptome analyses, mutant studies, and exogenous hormone applications, we provide a comprehensive model showing the role and interaction of plant hormone pathways in defense of this monocot crop against root nematodes, where jasmonate seems to play a key role. Finally, recent evidence indicates that effectors secreted from rice-infecting nematodes can suppress plant defense.

SUMMARY: Coffee ( Coffea arabica L.), one of the key export and cash crops in tropical and subtropical countries, suffers severe losses from the rust fungus Hemileia vastatrix . The transcriptome of H. vastatrix was analysed during a compatible interaction with coffee to obtain an exhaustive repertoire of the genes expressed during infection and to identify potential effector genes. Large‐scale sequencing (454‐GS‐FLEX Titanium) of mixed coffee and rust cDNAs obtained from 21‐day rust‐infected leaves generated 352 146 sequences which assembled into 22 774 contigs. In the absence of any reference genomic sequences for Coffea or Hemileia , specific trinucleotide frequencies within expressed sequence tags (ESTs) and blast homology against a set of dicots and basidiomycete genomes were used to distinguish pathogen from plant sequences. About 30% (6763) of the contigs were assigned to H. vastatrix and 61% (13 951) to C. arabica . The majority (60%) of the rust sequences did not show homology to any genomic database, indicating that they were potential novel fungal genes. In silico analyses of the 6763 H. vastatrix contigs predicted 382 secreted proteins and identified homologues of the flax rust haustorially expressed secreted proteins (HESPs) and bean rust transferred protein 1 (RTP1). These rust candidate effectors showed conserved amino‐acid domains and conserved patterns of cysteine positions suggestive of conserved functions during infection of host plants. Quantitative reverse transcription‐polymerase chain reaction profiling of selected rust genes revealed dynamic expression patterns during the time course of infection of coffee leaves . This study provides the first valuable genomic resource for the agriculturally important plant pathogen H. vastatrix and the first comprehensive C. arabica EST dataset.

SUMMARY: The beverage cash crop coffee ( Coffea arabica L.) is subject to severe losses caused by the rust fungus Hemileia vastatrix . In naturally resistant coffee plants, a specific hypersensitive reaction (HR) may be elicited early to stop fungal infection. To isolate host genes involved in HR, we undertook an expressed sequence tags (ESTs) analysis. Two cDNA libraries were constructed using suppression subtractive hybridization (SSH) and 527 non‐redundant ESTs were generated from 784 randomly picked clones. Classification of the ESTs into several functional categories showed that more than one‐quarter of the predicted proteins might encode disease resistance (R) proteins, stress‐ and defence‐proteins, and components of signal transduction pathways. Twenty‐eight differentially screened sequences (DSSs) were selected after differential hybridization of 1000 cDNA clones from each library. Investigation of the expression patterns of a subset of 13 DSSs showed higher levels of gene expression in inoculated plants compared with control plants. HR‐up‐regulation of transcript accumulation occurred for 9 out of the 13 genes 24 and 48 h after H. vastatrix challenge. Two genes encoded homologues of the Arabidopsis DND1 and NDR1 proteins, suggesting conservation of resistance signalling pathways in perennial plants. Other HR‐regulated sequences matched receptor kinases, AP2 domain‐ and WRKY transcription factors, cytochromes P450, heat shock 70 proteins, glucosyltransferases and proteins of unknown function. The ESTs reported here provide a useful resource for studying coffee resistance responses and for improving C. arabica for durable disease resistance.

Background and Aims The root-knot nematode Meloidogyne graminicola is responsible for production losses in rice (Oryza sativa) in Asia and Latin America. The accession TOG5681 of African rice, O. glaberrima, presents improved resistance to several biotic and abiotic factors, including nematodes. The aim of this study was to assess the cytological and molecular mechanisms underlying nematode resistance in this accession. Methods Penetration and development in M. graminicola in TOG5681 and the susceptible O. sativa genotype ‘Nipponbare’ were compared by microscopic observation of infected roots and histological analysis of galls. In parallel, host molecular responses to M. graminicola were assessed by root transcriptome profiling at 2, 4 and 8 d post-infection (dpi). Specific treatments with hormone inhibitors were conducted in TOG5681 to assess the impact of the jasmonic acid and salicylic acid pathways on nematode penetration and reproduction. Key Results Penetration and development of M. graminicola juveniles were reduced in the resistant TOG5681 in comparison with the susceptible accession, with degeneration of giant cells observed in the resistant genotype from 15 dpi onwards. Transcriptome changes were observed as early as 2 dpi, with genes predicted to be involved in defence responses, phenylpropanoid and hormone pathways strongly induced in TOG5681, in contrast to ‘Nipponbare’. No specific hormonal pathway could be identified as the major determinant of resistance in the rice-nematode incompatible interaction. Candidate genes proposed as involved in resistance to M. graminicola in TOG5681 were identified based on their expression pattern and quantitative trait locus (QTL) position, including chalcone synthase, isoflavone reductase, phenylalanine ammonia lyase, WRKY62 transcription factor, thionin, stripe rust resistance protein, thaumatins and ATPase3. Conclusions This study provides a novel set of candidate genes for O. glaberrima resistance to nematodes and highlights the rice-M. graminicola pathosystem as a model to study plant-nematode incompatible interactions.