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Open Access Research article

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

Danielle C Cardoso1, Juliana C Martinati1, Poliana F Giachetto2, Ramon O Vidal3, Marcelo F Carazzolle3, Lilian Padilha14, Oliveiro Guerreiro-Filho1 and Mirian P Maluf14*

Author Affiliations

1 Agronomic Institute of Campinas, Campinas, Brazil

2 Embrapa Agriculture Informatics, Campinas, Brazil

3 LNBio-Unicamp, Campinas, Brazil

4 Embrapa Coffee, Brasilia, Brazil

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BMC Genomics 2014, 15:66  doi:10.1186/1471-2164-15-66

Published: 24 January 2014

Abstract

Background

A 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.

Results

The 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.

Conclusions

Our 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.

Keywords:
Coffea arabica; Leaf miner; Microarray; Plant defense