Coffee (Coffea arabica) Molecular 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. Deep sequencing (Illumina) data obtained from resistant roots at 6 days post inoculation (dpi), inoculated with nematodes (treated) or not (control), was tested by the Trinity method for de novo assembly of transcripts without a coffee reference genome forming contigs analyzed by BlastnNR or BlastnEST. With cutoffs to adjusted p-value ≤ 0,05 and 1≤log2FC≤-1 applied to the contigs, 3519 of them were considered downregulated and 868 upregulated regarding the treated sample (inoculated). We decided to check the presence of 92 selected genes from various pathways and with different functions, reported as related to biotic stress responses in plants. We found 89% of the selected genes among the contigs, being 53 differentially expressed. In the second part of our study, we compared the in vitro sequencing results to the expression profiles generated by RT-qPCR of these genes selected from literature during the coffee roots responses to M. incognita. The same samples sequenced by Illumina were analyzed together with roots collected at 4, 5 and 6 (dpi), corresponding to the previously determined onset of HR, in three independent experiments. 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 (dpi). Many expression differences were significant at 5% and 1% to the qPCR results. 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.