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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

Biological process for up-regulated genes. Functional categorization of up regulated genes (%) in coffee genotypes (susceptible and resistant to leaf miner) without insect.
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Figure 3: Biological process for up-regulated genes. Functional categorization of up regulated genes (%) in coffee genotypes (susceptible and resistant to leaf miner) without insect.

Mentions: Regulated genes from the T0 samples were functionally characterized into three gene ontology categories – molecular function, component cellular and biological function - and grouped according their metabolic categories (Figures 1 and 2). A description of the first one hundred most variable genes, both up and down regulated, is shown on Tables 3 and 4 and illustrated in Figures 3 and 4. Several contigs had no correspondence with defined categories. A larger number of genes are up-regulated rather than down-regulated, and associated with primary and cellular metabolism, which included functions such as ion, protein and nucleic acid binding, hydrolase and transferase activities, among others. As these differences were observed in non-infested leaves, possibly a different transcriptional programming takes place in resistant leaves. This may result in a pre-defense status, enabling resistant plants to a faster defense response upon leaf-miner attack.


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)

Biological process for up-regulated genes. Functional categorization of up regulated genes (%) in coffee genotypes (susceptible and resistant to leaf miner) without insect.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Biological process for up-regulated genes. Functional categorization of up regulated genes (%) in coffee genotypes (susceptible and resistant to leaf miner) without insect.
Mentions: Regulated genes from the T0 samples were functionally characterized into three gene ontology categories – molecular function, component cellular and biological function - and grouped according their metabolic categories (Figures 1 and 2). A description of the first one hundred most variable genes, both up and down regulated, is shown on Tables 3 and 4 and illustrated in Figures 3 and 4. Several contigs had no correspondence with defined categories. A larger number of genes are up-regulated rather than down-regulated, and associated with primary and cellular metabolism, which included functions such as ion, protein and nucleic acid binding, hydrolase and transferase activities, among others. As these differences were observed in non-infested leaves, possibly a different transcriptional programming takes place in resistant leaves. This may result in a pre-defense status, enabling resistant plants to a faster defense response upon leaf-miner attack.

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