Large-scale analysis of differential gene expression in coffee genotypes resistant and susceptible to leaf miner–toward the identification of candidate genes for marker assisted-selection

Abstract

BackgroundA successful development of herbivorous insects into plant tissues depends on coordination of metabolic processes. Plants have evolved complex mechanisms to recognize such attacks, and to trigger a defense response. To understand the transcriptional basis of this response, we compare gene expression profiles of two coffee genotypes, susceptible and resistant to leaf miner (Leucoptera coffella). A total of 22000 EST sequences from the Coffee Genome Database were selected for a microarray analysis. Fluorescence probes were synthesized using mRNA from the infested and non-infested coffee plants. Array hybridization, scanning and data normalization were performed using Nimble Scan® e ArrayStar® platforms. Genes with foldchange values +/-2 were considered differentially expressed. A validation of 18 differentially expressed genes was performed in infected plants using qRT-PCR approach.ResultsThe microarray analysis indicated that resistant plants differ in gene expression profile. We identified relevant transcriptional changes in defense strategies before insect attack. Expression changes (>2.00-fold) were found in resistant plants for 2137 genes (1266 up-regulated and 873 down-regulated). Up-regulated genes include those responsible for defense mechanisms, hypersensitive response and genes involved with cellular function and maintenance. Also, our analyses indicated that differential expression profiles between resistant and susceptible genotypes are observed in the absence of leaf-miner, indicating that defense is already build up in resistant plants, as a priming mechanism. Validation of selected genes pointed to four selected genes as suitable candidates for markers in assisted-selection of novel cultivars.ConclusionsOur results show evidences that coffee defense responses against leaf-miner attack are balanced with other cellular functions. Also analyses suggest a major metabolic reconfiguration that highlights the complexity of this response.

Transcriptome Analysis of Leaves, Flowers and Fruits Perisperm of Coffea arabica L. Reveals the Differential Expression of Genes Involved in Raffinose Biosynthesis

“…vinifera sequences were the most similar organism to coffee protein sequences [3, 6, 28]. Also, the conserved domains and gene ontology results were similar to those found in other large-scale trancriptome analyses, where catalytic protein, kinases, cytochrome P450 and binding sites domains were the most frequently identified categories [28, 53]. …”

Interrelated responses of tomato plants and the leaf minerTuta absolutato nitrogen supply

“…; Cardoso et al . ). Leaf mining is the ability of insect larvae to feed and develop within plant tissues, mostly leaves and stems.…”

Stage-specific reprogramming of gene expression characterizes Lr48-mediated adult plant leaf rust resistance in wheat

“…Similar results associated with APR have also been reported earlier (Century et al 1999; for a review, see Develey-Rivière and Galiana 2007). It is also apparent that among the differentially expressed genes, the upregulated genes outnumbered those which were downregulated (36) several folds, suggesting that the defense mechanisms involve activation of many, and repression of relatively fewer, specific genes/pathways (Cardoson et al 2014). Activity of most of these genes/pathways was apparently initiated during phase I (0 to 24 h after inoculation) and reached a peak during phase II (24 to 96 h after inoculation), suggesting that phase II is the most crucial stage for determining/maintaining the resistance response by host genotype.…”