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Transcriptional profile analysis of E3 ligase and hormone-related genes expressed during wheat grain development.

Capron D, Mouzeyar S, Boulaflous A, Girousse C, Rustenholz C, Laugier C, Paux E, Bouzidi MF - BMC Plant Biol. (2012)

Bottom Line: The list of the genes expressed differentially during these transitions were identified and annotated.Emphasis was placed on E3 ligase and hormone-related genes.Some E3 ligase and hormone-related genes seem to be up- or down-regulated during the early and late stages of the grain development.

View Article: PubMed Central - HTML - PubMed

Affiliation: Université Blaise Pascal, UMR 1095 GDEC, 24 avenue des Landais, F-63177 Aubière, France.

ABSTRACT

Background: Wheat grains are an important source of food, stock feed and raw materials for industry, but current production levels cannot meet world needs. Elucidation of the molecular mechanisms underlying wheat grain development will contribute valuable information to improving wheat cultivation. One of the most important mechanisms implicated in plant developmental processes is the ubiquitin-proteasome system (UPS). Among the different roles of the UPS, it is clear that it is essential to hormone signaling. In particular, E3 ubiquitin ligases of the UPS have been shown to play critical roles in hormone perception and signal transduction.

Results: A NimbleGen microarray containing 39,179 UniGenes was used to study the kinetics of gene expression during wheat grain development from the early stages of cell division to the mid-grain filling stage. By comparing 11 consecutive time-points, 9284 differentially expressed genes were identified and annotated during this study. A comparison of the temporal profiles of these genes revealed dynamic transcript accumulation profiles with major reprogramming events that occurred during the time intervals of 80-120 and 220-240°Cdays. The list of the genes expressed differentially during these transitions were identified and annotated. Emphasis was placed on E3 ligase and hormone-related genes. In total, 173 E3 ligase coding genes and 126 hormone-related genes were differentially expressed during the cell division and grain filling stages, with each family displaying a different expression profile.

Conclusions: The differential expression of genes involved in the UPS and plant hormone pathways suggests that phytohormones and UPS crosstalk might play a critical role in the wheat grain developmental process. Some E3 ligase and hormone-related genes seem to be up- or down-regulated during the early and late stages of the grain development.

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Clustering of 9284 differentially expressed genes (DEGs). (A) Hierarchical clustering of two biological replicate samples of wheat grain development. The medians of twelve expression values were used to cluster the samples (see Methods). Stages are shown as °Cdays and days after anthesis (DAA). Scale bar: 0.5 cm. A paired t-test analysis (p < 0.01, adjusted Bonferroni correction) was performed to identify the genes whose expression levels changed significantly during the transitions between [40-80] and [120-500° Cdays]. Pie chart classifications for biological processes were inferred from various sources (see Methods). Unclassified UniGenes were omitted from the pie charts: the number of GO terms is shown in bracket next to the chart. (B) Pearson's correlation coefficient matrix of the clusters in panel (A).
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Figure 1: Clustering of 9284 differentially expressed genes (DEGs). (A) Hierarchical clustering of two biological replicate samples of wheat grain development. The medians of twelve expression values were used to cluster the samples (see Methods). Stages are shown as °Cdays and days after anthesis (DAA). Scale bar: 0.5 cm. A paired t-test analysis (p < 0.01, adjusted Bonferroni correction) was performed to identify the genes whose expression levels changed significantly during the transitions between [40-80] and [120-500° Cdays]. Pie chart classifications for biological processes were inferred from various sources (see Methods). Unclassified UniGenes were omitted from the pie charts: the number of GO terms is shown in bracket next to the chart. (B) Pearson's correlation coefficient matrix of the clusters in panel (A).

Mentions: To identify the genes involved in the early stages of wheat grain development, a NimbleGen microarray analysis (with 39,179 UniGenes) was performed (ref. A-MEXP-1928). This microarray was hybridized with wheat grain cDNAs generated at early developmental stages starting approximately 2 d after anthesis (40°Cdays under our experimental conditions), and including the stages corresponding to a broad time-span of grain filling (up to 500°Cdays). As shown in Figure 1A, a total of eleven stages of grain development were screened. A LIMMA analysis of two biological replicates and a dye-swap replicate resulted in the identification of 9284 differentially expressed genes (DEGs; p < 0.01) during the eleven developmental stages (see Additional file 1).


Transcriptional profile analysis of E3 ligase and hormone-related genes expressed during wheat grain development.

Capron D, Mouzeyar S, Boulaflous A, Girousse C, Rustenholz C, Laugier C, Paux E, Bouzidi MF - BMC Plant Biol. (2012)

Clustering of 9284 differentially expressed genes (DEGs). (A) Hierarchical clustering of two biological replicate samples of wheat grain development. The medians of twelve expression values were used to cluster the samples (see Methods). Stages are shown as °Cdays and days after anthesis (DAA). Scale bar: 0.5 cm. A paired t-test analysis (p < 0.01, adjusted Bonferroni correction) was performed to identify the genes whose expression levels changed significantly during the transitions between [40-80] and [120-500° Cdays]. Pie chart classifications for biological processes were inferred from various sources (see Methods). Unclassified UniGenes were omitted from the pie charts: the number of GO terms is shown in bracket next to the chart. (B) Pearson's correlation coefficient matrix of the clusters in panel (A).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3405487&req=5

Figure 1: Clustering of 9284 differentially expressed genes (DEGs). (A) Hierarchical clustering of two biological replicate samples of wheat grain development. The medians of twelve expression values were used to cluster the samples (see Methods). Stages are shown as °Cdays and days after anthesis (DAA). Scale bar: 0.5 cm. A paired t-test analysis (p < 0.01, adjusted Bonferroni correction) was performed to identify the genes whose expression levels changed significantly during the transitions between [40-80] and [120-500° Cdays]. Pie chart classifications for biological processes were inferred from various sources (see Methods). Unclassified UniGenes were omitted from the pie charts: the number of GO terms is shown in bracket next to the chart. (B) Pearson's correlation coefficient matrix of the clusters in panel (A).
Mentions: To identify the genes involved in the early stages of wheat grain development, a NimbleGen microarray analysis (with 39,179 UniGenes) was performed (ref. A-MEXP-1928). This microarray was hybridized with wheat grain cDNAs generated at early developmental stages starting approximately 2 d after anthesis (40°Cdays under our experimental conditions), and including the stages corresponding to a broad time-span of grain filling (up to 500°Cdays). As shown in Figure 1A, a total of eleven stages of grain development were screened. A LIMMA analysis of two biological replicates and a dye-swap replicate resulted in the identification of 9284 differentially expressed genes (DEGs; p < 0.01) during the eleven developmental stages (see Additional file 1).

Bottom Line: The list of the genes expressed differentially during these transitions were identified and annotated.Emphasis was placed on E3 ligase and hormone-related genes.Some E3 ligase and hormone-related genes seem to be up- or down-regulated during the early and late stages of the grain development.

View Article: PubMed Central - HTML - PubMed

Affiliation: Université Blaise Pascal, UMR 1095 GDEC, 24 avenue des Landais, F-63177 Aubière, France.

ABSTRACT

Background: Wheat grains are an important source of food, stock feed and raw materials for industry, but current production levels cannot meet world needs. Elucidation of the molecular mechanisms underlying wheat grain development will contribute valuable information to improving wheat cultivation. One of the most important mechanisms implicated in plant developmental processes is the ubiquitin-proteasome system (UPS). Among the different roles of the UPS, it is clear that it is essential to hormone signaling. In particular, E3 ubiquitin ligases of the UPS have been shown to play critical roles in hormone perception and signal transduction.

Results: A NimbleGen microarray containing 39,179 UniGenes was used to study the kinetics of gene expression during wheat grain development from the early stages of cell division to the mid-grain filling stage. By comparing 11 consecutive time-points, 9284 differentially expressed genes were identified and annotated during this study. A comparison of the temporal profiles of these genes revealed dynamic transcript accumulation profiles with major reprogramming events that occurred during the time intervals of 80-120 and 220-240°Cdays. The list of the genes expressed differentially during these transitions were identified and annotated. Emphasis was placed on E3 ligase and hormone-related genes. In total, 173 E3 ligase coding genes and 126 hormone-related genes were differentially expressed during the cell division and grain filling stages, with each family displaying a different expression profile.

Conclusions: The differential expression of genes involved in the UPS and plant hormone pathways suggests that phytohormones and UPS crosstalk might play a critical role in the wheat grain developmental process. Some E3 ligase and hormone-related genes seem to be up- or down-regulated during the early and late stages of the grain development.

Show MeSH
Related in: MedlinePlus