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Genome-wide digital transcript analysis of putative fruitlet abscission related genes regulated by ethephon in litchi.

Li C, Wang Y, Ying P, Ma W, Li J - Front Plant Sci (2015)

Bottom Line: Of these, there were 1867 early-responsive genes whose expressions were up- or down-regulated from 0 to 1 d after treatment.The most affected genes included those related to ethylene biosynthesis and signaling, auxin transport and signaling, transcription factors (TFs), protein ubiquitination, ROS response, calcium signal transduction, and cell wall modification.These genes could be clustered into four groups and 13 subgroups according to their similar expression patterns. qRT-PCR displayed the expression pattern of 41 selected candidate genes, which proved the accuracy of our DTA data.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, China Litchi Research Center, South China Agricultural University Guangzhou, China ; Physiological Laboratory for South China Fruits, College of Horticulture, South China Agricultural University Guangzhou, China.

ABSTRACT
The high level of physiological fruitlet abscission in litchi (Litchi chinensis Sonn.) causes severe yield loss. Cell separation occurs at the fruit abscission zone (FAZ) and can be triggered by ethylene. However, a deep knowledge of the molecular events occurring in the FAZ is still unknown. Here, genome-wide digital transcript abundance (DTA) analysis of putative fruit abscission related genes regulated by ethephon in litchi were studied. More than 81 million high quality reads from seven ethephon treated and untreated control libraries were obtained by high-throughput sequencing. Through DTA profile analysis in combination with Gene Ontology and KEGG pathway enrichment analyses, a total of 2730 statistically significant candidate genes were involved in the ethephon-promoted litchi fruitlet abscission. Of these, there were 1867 early-responsive genes whose expressions were up- or down-regulated from 0 to 1 d after treatment. The most affected genes included those related to ethylene biosynthesis and signaling, auxin transport and signaling, transcription factors (TFs), protein ubiquitination, ROS response, calcium signal transduction, and cell wall modification. These genes could be clustered into four groups and 13 subgroups according to their similar expression patterns. qRT-PCR displayed the expression pattern of 41 selected candidate genes, which proved the accuracy of our DTA data. Ethephon treatment significantly increased fruit abscission and ethylene production of fruitlet. The possible molecular events to control the ethephon-promoted litchi fruitlet abscission were prompted out. The increased ethylene evolution in fruitlet would suppress the synthesis and polar transport of auxin and trigger abscission signaling. To the best of our knowledge, it is the first time to monitor the gene expression profile occurring in the FAZ-enriched pedicel during litchi fruit abscission induced by ethephon on the genome-wide level. This study will contribute to a better understanding for the molecular regulatory mechanism of fruit abscission in litchi.

No MeSH data available.


Ethephon-responsive genes expression pattern obtained by kinetics-based clustering analysis. Group I, cluster of genes with early and transient changes; group II, clusters of genes modified in their expression until 2 d after treatment; group III, cluster of genes with expression kinetics exhibiting late changes; group IV, cluster of genes with persistent changes during the whole abscission process. The + and − signs in bracket represent up- and down-regulated of genes, respectively, while 0 represents no change. The numbers on the right of bracket indicate the total numbers of genes in each cluster. All of these changes were based on a four-fold change criterion (log2 ratio) indicated by blue dotted line. Gray dotted line indicates the gene-expression levels and the average values of gene-expression level in clusters is shown by the red solid lines.
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Figure 3: Ethephon-responsive genes expression pattern obtained by kinetics-based clustering analysis. Group I, cluster of genes with early and transient changes; group II, clusters of genes modified in their expression until 2 d after treatment; group III, cluster of genes with expression kinetics exhibiting late changes; group IV, cluster of genes with persistent changes during the whole abscission process. The + and − signs in bracket represent up- and down-regulated of genes, respectively, while 0 represents no change. The numbers on the right of bracket indicate the total numbers of genes in each cluster. All of these changes were based on a four-fold change criterion (log2 ratio) indicated by blue dotted line. Gray dotted line indicates the gene-expression levels and the average values of gene-expression level in clusters is shown by the red solid lines.

Mentions: Based on their patterns of expression, these candidate genes could be classified into four groups, which consisted of genes with similar temporal patterns of expression kinetics (Figure 3). Group I included 1867 early-responsive genes whose expression were up- or down-regulated early at 1 d after treatment; Group II had 148 middle-responsive genes whose expression were not induced or suppressed until 2 d after treatment; Group III contained 258 late-responsive genes that were not regulated until 3 d after treatment; Group IV consisted of 457 constant-responsive genes that up- or down-regulated early and whose expression was maintained constant during the treatment. By hierarchical cluster analysis, each group could be subsequently divided into two to six clusters, for example, Group I included cluster 1A, 1B, 1C, 1D, 1E, and 1F which had 172, 261, 55, 776, 434, and 169 genes, respectively. In total, 723 up-regulated and 1601 down-regulated genes were found at 1 d after treatment, and 299 up-regulated and 107 down-regulated genes were found at 2 d or 3 d after treatment. These results showed that the majority (85.13%) of those candidate genes made a quick response to the ETH treatment in 24 h when no significant difference on fruit abscission rate was found between the control and the ETH treatment.


Genome-wide digital transcript analysis of putative fruitlet abscission related genes regulated by ethephon in litchi.

Li C, Wang Y, Ying P, Ma W, Li J - Front Plant Sci (2015)

Ethephon-responsive genes expression pattern obtained by kinetics-based clustering analysis. Group I, cluster of genes with early and transient changes; group II, clusters of genes modified in their expression until 2 d after treatment; group III, cluster of genes with expression kinetics exhibiting late changes; group IV, cluster of genes with persistent changes during the whole abscission process. The + and − signs in bracket represent up- and down-regulated of genes, respectively, while 0 represents no change. The numbers on the right of bracket indicate the total numbers of genes in each cluster. All of these changes were based on a four-fold change criterion (log2 ratio) indicated by blue dotted line. Gray dotted line indicates the gene-expression levels and the average values of gene-expression level in clusters is shown by the red solid lines.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4493771&req=5

Figure 3: Ethephon-responsive genes expression pattern obtained by kinetics-based clustering analysis. Group I, cluster of genes with early and transient changes; group II, clusters of genes modified in their expression until 2 d after treatment; group III, cluster of genes with expression kinetics exhibiting late changes; group IV, cluster of genes with persistent changes during the whole abscission process. The + and − signs in bracket represent up- and down-regulated of genes, respectively, while 0 represents no change. The numbers on the right of bracket indicate the total numbers of genes in each cluster. All of these changes were based on a four-fold change criterion (log2 ratio) indicated by blue dotted line. Gray dotted line indicates the gene-expression levels and the average values of gene-expression level in clusters is shown by the red solid lines.
Mentions: Based on their patterns of expression, these candidate genes could be classified into four groups, which consisted of genes with similar temporal patterns of expression kinetics (Figure 3). Group I included 1867 early-responsive genes whose expression were up- or down-regulated early at 1 d after treatment; Group II had 148 middle-responsive genes whose expression were not induced or suppressed until 2 d after treatment; Group III contained 258 late-responsive genes that were not regulated until 3 d after treatment; Group IV consisted of 457 constant-responsive genes that up- or down-regulated early and whose expression was maintained constant during the treatment. By hierarchical cluster analysis, each group could be subsequently divided into two to six clusters, for example, Group I included cluster 1A, 1B, 1C, 1D, 1E, and 1F which had 172, 261, 55, 776, 434, and 169 genes, respectively. In total, 723 up-regulated and 1601 down-regulated genes were found at 1 d after treatment, and 299 up-regulated and 107 down-regulated genes were found at 2 d or 3 d after treatment. These results showed that the majority (85.13%) of those candidate genes made a quick response to the ETH treatment in 24 h when no significant difference on fruit abscission rate was found between the control and the ETH treatment.

Bottom Line: Of these, there were 1867 early-responsive genes whose expressions were up- or down-regulated from 0 to 1 d after treatment.The most affected genes included those related to ethylene biosynthesis and signaling, auxin transport and signaling, transcription factors (TFs), protein ubiquitination, ROS response, calcium signal transduction, and cell wall modification.These genes could be clustered into four groups and 13 subgroups according to their similar expression patterns. qRT-PCR displayed the expression pattern of 41 selected candidate genes, which proved the accuracy of our DTA data.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, China Litchi Research Center, South China Agricultural University Guangzhou, China ; Physiological Laboratory for South China Fruits, College of Horticulture, South China Agricultural University Guangzhou, China.

ABSTRACT
The high level of physiological fruitlet abscission in litchi (Litchi chinensis Sonn.) causes severe yield loss. Cell separation occurs at the fruit abscission zone (FAZ) and can be triggered by ethylene. However, a deep knowledge of the molecular events occurring in the FAZ is still unknown. Here, genome-wide digital transcript abundance (DTA) analysis of putative fruit abscission related genes regulated by ethephon in litchi were studied. More than 81 million high quality reads from seven ethephon treated and untreated control libraries were obtained by high-throughput sequencing. Through DTA profile analysis in combination with Gene Ontology and KEGG pathway enrichment analyses, a total of 2730 statistically significant candidate genes were involved in the ethephon-promoted litchi fruitlet abscission. Of these, there were 1867 early-responsive genes whose expressions were up- or down-regulated from 0 to 1 d after treatment. The most affected genes included those related to ethylene biosynthesis and signaling, auxin transport and signaling, transcription factors (TFs), protein ubiquitination, ROS response, calcium signal transduction, and cell wall modification. These genes could be clustered into four groups and 13 subgroups according to their similar expression patterns. qRT-PCR displayed the expression pattern of 41 selected candidate genes, which proved the accuracy of our DTA data. Ethephon treatment significantly increased fruit abscission and ethylene production of fruitlet. The possible molecular events to control the ethephon-promoted litchi fruitlet abscission were prompted out. The increased ethylene evolution in fruitlet would suppress the synthesis and polar transport of auxin and trigger abscission signaling. To the best of our knowledge, it is the first time to monitor the gene expression profile occurring in the FAZ-enriched pedicel during litchi fruit abscission induced by ethephon on the genome-wide level. This study will contribute to a better understanding for the molecular regulatory mechanism of fruit abscission in litchi.

No MeSH data available.