Limits...
The 'PUCE CAFE' Project: the first 15K coffee microarray, a new tool for discovering candidate genes correlated to agronomic and quality traits.

Privat I, Bardil A, Gomez AB, Severac D, Dantec C, Fuentes I, Mueller L, Joët T, Pot D, Foucrier S, Dussert S, Leroy T, Journot L, de Kochko A, Campa C, Combes MC, Lashermes P, Bertrand B - BMC Genomics (2011)

Bottom Line: We have generated the first 15 K coffee array during this PUCE CAFE project, granted by Génoplante (the French consortium for plant genomics).This new tool will help study functional genomics in a wide range of experiments on various plant tissues, such as analyzing bean maturation or resistance to pathogens or drought.Furthermore, the use of this array has proven to be valid in different coffee species (diploid or tetraploid), drastically enlarging its impact for high-throughput gene expression in the community of coffee research.

View Article: PubMed Central - HTML - PubMed

Affiliation: Nestlé R&D Tours, 101 Avenue Gustave Eiffel, Notre Dame d'Oé, BP 49716, 37097 Tours Cedex 2, France. isabelle.privat@rdto.nestle.com

ABSTRACT

Background: Understanding the genetic elements that contribute to key aspects of coffee biology will have an impact on future agronomical improvements for this economically important tree. During the past years, EST collections were generated in Coffee, opening the possibility to create new tools for functional genomics.

Results: The "PUCE CAFE" Project, organized by the scientific consortium NESTLE/IRD/CIRAD, has developed an oligo-based microarray using 15,721 unigenes derived from published coffee EST sequences mostly obtained from different stages of fruit development and leaves in Coffea Canephora (Robusta). Hybridizations for two independent experiments served to compare global gene expression profiles in three types of tissue matter (mature beans, leaves and flowers) in C. canephora as well as in the leaves of three different coffee species (C. canephora, C. eugenoides and C. arabica). Microarray construction, statistical analyses and validation by Q-PCR analysis are presented in this study.

Conclusion: We have generated the first 15 K coffee array during this PUCE CAFE project, granted by Génoplante (the French consortium for plant genomics). This new tool will help study functional genomics in a wide range of experiments on various plant tissues, such as analyzing bean maturation or resistance to pathogens or drought. Furthermore, the use of this array has proven to be valid in different coffee species (diploid or tetraploid), drastically enlarging its impact for high-throughput gene expression in the community of coffee research.

Show MeSH
Transcriptome divergence between the three tissues (flower/leaf/mature bean). The total number and fraction of genes diagnosed as differentially expressed in each contrast are indicated in bold text. Also shown for each contrast is the partitioning of the total number of differentially expressed genes in the direction of up-regulation; these numbers are indicated in non-bold text. For example, 9923 genes are indicated as being differentially expressed between flowers and leaves. Of these, 5010 (32.3%) were up-regulated in flowers, and 4913 (31.6%) were up-regulated in beans. Around 58-65% of the 15,522 unigenes were differentially expressed between the three tissues.
© Copyright Policy - open-access
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3025959&req=5

Figure 4: Transcriptome divergence between the three tissues (flower/leaf/mature bean). The total number and fraction of genes diagnosed as differentially expressed in each contrast are indicated in bold text. Also shown for each contrast is the partitioning of the total number of differentially expressed genes in the direction of up-regulation; these numbers are indicated in non-bold text. For example, 9923 genes are indicated as being differentially expressed between flowers and leaves. Of these, 5010 (32.3%) were up-regulated in flowers, and 4913 (31.6%) were up-regulated in beans. Around 58-65% of the 15,522 unigenes were differentially expressed between the three tissues.

Mentions: Two statistical analyses were performed on normalized data from Experiments 1 and 2, one by the Limma Method (linear model), the other by the SAM Method (significance analysis for microarray) with two thresholds P = 0.01 and P = 0.05. For each comparison, lists of differentially-expressed genes were generated. One list was derived from the "Limma" analysis, the other from the "SAM" analysis. The files are available on BASE http://baseprod.igf.cnrs.fr/index.phtml. The Limma Method was more restrictive than the SAM Method, so the number of genes determined as being significantly differentially expressed was therefore smaller. Nevertheless, the totality of these genes was also detected by the SAM Method in the three comparisons conducted. These genes were therefore validated by two independent methods (results not shown). The lists resulting from the SAM 0.01 analysis were used to compare differentially-expressed genes for each comparison (Figure 4 for Experiment 1 and Figure 5 for Experiment 2). The lists resulting from the Limma P = 0.01 analysis was used to identify over-expressed genes in one specific tissue (bean flower or leaf) (Figure 6 Additional file 9).


The 'PUCE CAFE' Project: the first 15K coffee microarray, a new tool for discovering candidate genes correlated to agronomic and quality traits.

Privat I, Bardil A, Gomez AB, Severac D, Dantec C, Fuentes I, Mueller L, Joët T, Pot D, Foucrier S, Dussert S, Leroy T, Journot L, de Kochko A, Campa C, Combes MC, Lashermes P, Bertrand B - BMC Genomics (2011)

Transcriptome divergence between the three tissues (flower/leaf/mature bean). The total number and fraction of genes diagnosed as differentially expressed in each contrast are indicated in bold text. Also shown for each contrast is the partitioning of the total number of differentially expressed genes in the direction of up-regulation; these numbers are indicated in non-bold text. For example, 9923 genes are indicated as being differentially expressed between flowers and leaves. Of these, 5010 (32.3%) were up-regulated in flowers, and 4913 (31.6%) were up-regulated in beans. Around 58-65% of the 15,522 unigenes were differentially expressed between the three tissues.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3025959&req=5

Figure 4: Transcriptome divergence between the three tissues (flower/leaf/mature bean). The total number and fraction of genes diagnosed as differentially expressed in each contrast are indicated in bold text. Also shown for each contrast is the partitioning of the total number of differentially expressed genes in the direction of up-regulation; these numbers are indicated in non-bold text. For example, 9923 genes are indicated as being differentially expressed between flowers and leaves. Of these, 5010 (32.3%) were up-regulated in flowers, and 4913 (31.6%) were up-regulated in beans. Around 58-65% of the 15,522 unigenes were differentially expressed between the three tissues.
Mentions: Two statistical analyses were performed on normalized data from Experiments 1 and 2, one by the Limma Method (linear model), the other by the SAM Method (significance analysis for microarray) with two thresholds P = 0.01 and P = 0.05. For each comparison, lists of differentially-expressed genes were generated. One list was derived from the "Limma" analysis, the other from the "SAM" analysis. The files are available on BASE http://baseprod.igf.cnrs.fr/index.phtml. The Limma Method was more restrictive than the SAM Method, so the number of genes determined as being significantly differentially expressed was therefore smaller. Nevertheless, the totality of these genes was also detected by the SAM Method in the three comparisons conducted. These genes were therefore validated by two independent methods (results not shown). The lists resulting from the SAM 0.01 analysis were used to compare differentially-expressed genes for each comparison (Figure 4 for Experiment 1 and Figure 5 for Experiment 2). The lists resulting from the Limma P = 0.01 analysis was used to identify over-expressed genes in one specific tissue (bean flower or leaf) (Figure 6 Additional file 9).

Bottom Line: We have generated the first 15 K coffee array during this PUCE CAFE project, granted by Génoplante (the French consortium for plant genomics).This new tool will help study functional genomics in a wide range of experiments on various plant tissues, such as analyzing bean maturation or resistance to pathogens or drought.Furthermore, the use of this array has proven to be valid in different coffee species (diploid or tetraploid), drastically enlarging its impact for high-throughput gene expression in the community of coffee research.

View Article: PubMed Central - HTML - PubMed

Affiliation: Nestlé R&D Tours, 101 Avenue Gustave Eiffel, Notre Dame d'Oé, BP 49716, 37097 Tours Cedex 2, France. isabelle.privat@rdto.nestle.com

ABSTRACT

Background: Understanding the genetic elements that contribute to key aspects of coffee biology will have an impact on future agronomical improvements for this economically important tree. During the past years, EST collections were generated in Coffee, opening the possibility to create new tools for functional genomics.

Results: The "PUCE CAFE" Project, organized by the scientific consortium NESTLE/IRD/CIRAD, has developed an oligo-based microarray using 15,721 unigenes derived from published coffee EST sequences mostly obtained from different stages of fruit development and leaves in Coffea Canephora (Robusta). Hybridizations for two independent experiments served to compare global gene expression profiles in three types of tissue matter (mature beans, leaves and flowers) in C. canephora as well as in the leaves of three different coffee species (C. canephora, C. eugenoides and C. arabica). Microarray construction, statistical analyses and validation by Q-PCR analysis are presented in this study.

Conclusion: We have generated the first 15 K coffee array during this PUCE CAFE project, granted by Génoplante (the French consortium for plant genomics). This new tool will help study functional genomics in a wide range of experiments on various plant tissues, such as analyzing bean maturation or resistance to pathogens or drought. Furthermore, the use of this array has proven to be valid in different coffee species (diploid or tetraploid), drastically enlarging its impact for high-throughput gene expression in the community of coffee research.

Show MeSH