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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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Patterns of gene expression during wheat grain development. Differentially expressed genes across 11 time-points of wheat grain development were grouped into 10 clusters using the K-means clustering algorithm. The ratio value (on the log2 scale) of expression is on the y-axis and the time of development in °Cdays is on the x-axis. The curve represents the mean of the expression ratio (on the log2 scale) in each cluster, and error bars represent the SD. Tick marks on the x-axis represent the 11 developmental time-points at 40, 80, 120, 160, 180, 220, 240, 260, 300, 400 and 500°Cdays. Pie chart classifications for biological process (p) and tissue category (t) are represented under the cluster. Unclassified UniGenes were omitted from the pie charts: the numbers that were classified are shown in brackets under the chart.
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Figure 2: Patterns of gene expression during wheat grain development. Differentially expressed genes across 11 time-points of wheat grain development were grouped into 10 clusters using the K-means clustering algorithm. The ratio value (on the log2 scale) of expression is on the y-axis and the time of development in °Cdays is on the x-axis. The curve represents the mean of the expression ratio (on the log2 scale) in each cluster, and error bars represent the SD. Tick marks on the x-axis represent the 11 developmental time-points at 40, 80, 120, 160, 180, 220, 240, 260, 300, 400 and 500°Cdays. Pie chart classifications for biological process (p) and tissue category (t) are represented under the cluster. Unclassified UniGenes were omitted from the pie charts: the numbers that were classified are shown in brackets under the chart.

Mentions: To gain further insight into the expression profiles of DEGs, the 40°Cdays stage was used as a common reference to compare the expression of DEGs at subsequent stages. K-means clustering of the transformed data set was carried out with 10 as the prefixed number of groups (Figure 2). The number of genes grouped into each of the ten different clusters ranged from 205 (cluster 2) to 2170 (cluster 4). Based on mRNA accumulation trends, the ten K-mean clusters of gene expression patterns were further sorted into three classes: up-regulated (clusters 1, 5, 7, 8 and 10), down-regulated (clusters 2, 4, 6 and 9) and up-down-regulated (cluster 3). The majority of DEGs were down-regulated (5393 genes), followed by up-regulated genes (3080 genes) and up-down-regulated genes (811 genes). Changes to the magnitude of gene expression levels during wheat grain development were not uniform, and the greatest changes were found in clusters 2, 5 and 7. Genes in clusters 5 and 10 were up-regulated during all the stages studied, i.e. from 40 to 500°Cdays, with expression peaks at 260 and 220°Cdays, respectively. The decrease in the expression level of genes in clusters 2 and 6 started at the early stages of wheat grain development, i.e. at 40°Cdays, but this only occurred at 80°Cdays in cluster 9 and after a small increase in expression levels at 80°Cdays in cluster 4. In clusters 1 and 8, the increase in the expression level started at 80°Cdays (Figure 2).


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)

Patterns of gene expression during wheat grain development. Differentially expressed genes across 11 time-points of wheat grain development were grouped into 10 clusters using the K-means clustering algorithm. The ratio value (on the log2 scale) of expression is on the y-axis and the time of development in °Cdays is on the x-axis. The curve represents the mean of the expression ratio (on the log2 scale) in each cluster, and error bars represent the SD. Tick marks on the x-axis represent the 11 developmental time-points at 40, 80, 120, 160, 180, 220, 240, 260, 300, 400 and 500°Cdays. Pie chart classifications for biological process (p) and tissue category (t) are represented under the cluster. Unclassified UniGenes were omitted from the pie charts: the numbers that were classified are shown in brackets under the chart.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Patterns of gene expression during wheat grain development. Differentially expressed genes across 11 time-points of wheat grain development were grouped into 10 clusters using the K-means clustering algorithm. The ratio value (on the log2 scale) of expression is on the y-axis and the time of development in °Cdays is on the x-axis. The curve represents the mean of the expression ratio (on the log2 scale) in each cluster, and error bars represent the SD. Tick marks on the x-axis represent the 11 developmental time-points at 40, 80, 120, 160, 180, 220, 240, 260, 300, 400 and 500°Cdays. Pie chart classifications for biological process (p) and tissue category (t) are represented under the cluster. Unclassified UniGenes were omitted from the pie charts: the numbers that were classified are shown in brackets under the chart.
Mentions: To gain further insight into the expression profiles of DEGs, the 40°Cdays stage was used as a common reference to compare the expression of DEGs at subsequent stages. K-means clustering of the transformed data set was carried out with 10 as the prefixed number of groups (Figure 2). The number of genes grouped into each of the ten different clusters ranged from 205 (cluster 2) to 2170 (cluster 4). Based on mRNA accumulation trends, the ten K-mean clusters of gene expression patterns were further sorted into three classes: up-regulated (clusters 1, 5, 7, 8 and 10), down-regulated (clusters 2, 4, 6 and 9) and up-down-regulated (cluster 3). The majority of DEGs were down-regulated (5393 genes), followed by up-regulated genes (3080 genes) and up-down-regulated genes (811 genes). Changes to the magnitude of gene expression levels during wheat grain development were not uniform, and the greatest changes were found in clusters 2, 5 and 7. Genes in clusters 5 and 10 were up-regulated during all the stages studied, i.e. from 40 to 500°Cdays, with expression peaks at 260 and 220°Cdays, respectively. The decrease in the expression level of genes in clusters 2 and 6 started at the early stages of wheat grain development, i.e. at 40°Cdays, but this only occurred at 80°Cdays in cluster 9 and after a small increase in expression levels at 80°Cdays in cluster 4. In clusters 1 and 8, the increase in the expression level started at 80°Cdays (Figure 2).

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