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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.

Cardoso DC, Martinati JC, Giachetto PF, Vidal RO, Carazzolle MF, Padilha L, Guerreiro-Filho O, Maluf MP - BMC Genomics (2014)

Bottom Line: A successful development of herbivorous insects into plant tissues depends on coordination of metabolic processes.Expression changes (>2.00-fold) were found in resistant plants for 2137 genes (1266 up-regulated and 873 down-regulated).Our results show evidences that coffee defense responses against leaf-miner attack are balanced with other cellular functions.

View Article: PubMed Central - HTML - PubMed

Affiliation: Agronomic Institute of Campinas, Campinas, Brazil. mirian.maluf@embrapa.br.

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.

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Related in: MedlinePlus

Correlation between foldchange values obtained from microarray analysis and qRT-PCR. Blue bars indicate values for T0 interaction (T0R_T0S), red bars for T1 interaction (T1R_T1S), green bars for T2 interaction (T2R_T2S). Dark colors of each interaction indicate fold change values from microarray analysis and soft color from qRT-PCR.
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Figure 8: Correlation between foldchange values obtained from microarray analysis and qRT-PCR. Blue bars indicate values for T0 interaction (T0R_T0S), red bars for T1 interaction (T1R_T1S), green bars for T2 interaction (T2R_T2S). Dark colors of each interaction indicate fold change values from microarray analysis and soft color from qRT-PCR.

Mentions: Further qPCR analyses were performed to validate expression of selected leaf-miner resistance-associated candidate-genes (Figure 8). These included genes from pathways described above and genes with either no significant hits or similarity to unknown proteins, which may represent coffee specific genes, not yet identified or characterized.


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.

Cardoso DC, Martinati JC, Giachetto PF, Vidal RO, Carazzolle MF, Padilha L, Guerreiro-Filho O, Maluf MP - BMC Genomics (2014)

Correlation between foldchange values obtained from microarray analysis and qRT-PCR. Blue bars indicate values for T0 interaction (T0R_T0S), red bars for T1 interaction (T1R_T1S), green bars for T2 interaction (T2R_T2S). Dark colors of each interaction indicate fold change values from microarray analysis and soft color from qRT-PCR.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3924705&req=5

Figure 8: Correlation between foldchange values obtained from microarray analysis and qRT-PCR. Blue bars indicate values for T0 interaction (T0R_T0S), red bars for T1 interaction (T1R_T1S), green bars for T2 interaction (T2R_T2S). Dark colors of each interaction indicate fold change values from microarray analysis and soft color from qRT-PCR.
Mentions: Further qPCR analyses were performed to validate expression of selected leaf-miner resistance-associated candidate-genes (Figure 8). These included genes from pathways described above and genes with either no significant hits or similarity to unknown proteins, which may represent coffee specific genes, not yet identified or characterized.

Bottom Line: A successful development of herbivorous insects into plant tissues depends on coordination of metabolic processes.Expression changes (>2.00-fold) were found in resistant plants for 2137 genes (1266 up-regulated and 873 down-regulated).Our results show evidences that coffee defense responses against leaf-miner attack are balanced with other cellular functions.

View Article: PubMed Central - HTML - PubMed

Affiliation: Agronomic Institute of Campinas, Campinas, Brazil. mirian.maluf@embrapa.br.

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.

Show MeSH
Related in: MedlinePlus