Considerable success has been obtained in the use of classical breeding to control economically important plant diseases, such as the coffee leaf rust and the coffee berry disease (CBD). There is a strong consensus that growing genetically resistant varieties is the most appropriate cost effective means of managing plant diseases and is one of the key components of crop improvement. It has also been recognized that a better knowledge of both, the pathogens and the plant defence mechanisms will allow the development of novel approaches to enhance the durability of resistance. After a brief description of concepts in the field of plant disease resistance, we attempt to give a view of the research progress on coffee leaf rust and CBD concerned with the pathogens infection and variability, coffee breeding for resistance and coffee resistance mechanisms.

Rust fungi (Basidiomycota, Pucciniales) are biotrophic plant pathogens which exhibit diverse complexities in their life cycles and host ranges. The completion of genome sequencing of a few rust fungi has revealed the occurrence of large genomes. Sequencing efforts for other rust fungi have been hampered by uncertainty concerning their genome sizes. Flow cytometry was recently applied to estimate the genome size of a few rust fungi, and confirmed the occurrence of large genomes in this order (averaging 151.5 Mbp, while the average for Basidiomycota was 49.9 Mbp and was 37.7 Mbp for all fungi). In this work, we have used an innovative and simple approach to simultaneously isolate nuclei from the rust and its host plant in order to estimate the genome size of 30 rust species by flow cytometry. Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome sizes of over 1,800 fungi, Gymnosporangium confusum possesses the largest fungal genome ever reported (893.2 Mbp). Moreover, even the smallest rust genome determined in this study is larger than the vast majority of fungal genomes (94 %). The average genome size of the Pucciniales is now of 305.5 Mbp, while the average Basidiomycota genome size has shifted to 70.4 Mbp and the average for all fungi reached 44.2 Mbp. Despite the fact that no correlation could be drawn between the genome sizes, the phylogenomics or the life cycle of rust fungi, it is interesting to note that rusts with Fabaceae hosts present genomes clearly larger than those with Poaceae hosts. Although this study comprises only a small fraction of the more than 7,000 rust species described, it seems already evident that the Pucciniales represent a group where genome size expansion could be a common characteristic. This is in sharp contrast to sister taxa, placing this order in a relevant position in fungal genomics research.

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.