Transcriptional Changes Associated to Coffee Resistance Responses to the Root-Knot Nematode Meloidogyne incognita

Root-knot nematodes (Meloidogyne spp.) are major pests damaging the coffee culture (Coffea arabica). To gain knowledge about the molecular mechanisms of plant immunity in coffee, we investigated the transcriptomic changes associated with the hypersensitive response (HR) to Meloidogyne incognita in resistant C. arabica ‘UFV 408-28’ plants.

The gene expression profiles of 88 selected genes were analyzed by real time RT-qPCR at 4, 5 and 6 days post inoculation (dpi), corresponding to the onset of HR, in three independent experiments. First, we performed statistical analysis to verify the best model to fit each gene for inoculation, genotype, and the interaction inoculation x genotype effects.

Coffee molecular responses were gradually increasing with infection time, with altered expression profiles observed for 4 (4 dpi), 12 (5 dpi) and 21 (6 dpi) genes. Interestingly, a WRKY transcription factor gene and a P450 gene were activated in incompatible interaction and supressed in compatible interaction. Second, we compared the significant qPCR expression results to deep sequencing (Illumina) data obtained from resistant roots inoculated with nematodes or not, at 6 dpi. We tested the Trinity method for de novo assembly of Illumina transcripts without a coffee reference genome.

An average of 3400 Illumina contigs were differentially expressed during coffee resistance responses to M. incognita. In particular, genes linked to the phenyl-propanoid pathway and salicylic acid biosynthesis were activated. Transcriptomic data obtained by both approaches were consistent, and some specific novel cDNA sequences may be used to unveil the resistance mechanisms acting in C. arabica.