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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.


Expression profiling of genes related to cell wall modification, ROS response, calcium signaling transduction, and protein ubiquitination in the FAZ-enriched pedicel after ethylene treatment. Up-regulated genes involved in cell wall degradation, cell wall loosening and ROS response, and down-regulated genes related to cell wall biosynthesis were showed. All genes involved in calcium signaling transduction and protein ubiquitination were exhibited. Gene expression levels were indicated with color bars. Additional information was presented in Supplementary Data Excel File 4.
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Figure 6: Expression profiling of genes related to cell wall modification, ROS response, calcium signaling transduction, and protein ubiquitination in the FAZ-enriched pedicel after ethylene treatment. Up-regulated genes involved in cell wall degradation, cell wall loosening and ROS response, and down-regulated genes related to cell wall biosynthesis were showed. All genes involved in calcium signaling transduction and protein ubiquitination were exhibited. Gene expression levels were indicated with color bars. Additional information was presented in Supplementary Data Excel File 4.

Mentions: A total of 208 genes including 56, 104, 21, and 27 genes related to cell wall biosynthesis, degradation, loosing and modification were found, respectively (Supplementary Data Excel File 6). Of these, 72 and 136 genes were up- and down-regulated, respectively. Of the up-regulated genes, there were 51 cell wall degradation, loosing and modification related transcripts (Figure 6). Among them, 4 genes were related to callose degradation, like endo-1,3-β-glucosidases (ENGs) and β-1,3-glucanases (BGN13s); 5 genes were involved in cellulose degradation, such as endo-1,4-β-D-glucanases (CELs) and β-glucosidases (BGLUs); 11 genes like endo-1,4-β-mannosidase (MAN), xyloglucan endotransglucosylase/hydrolases (XTHs) and β-D-xylosidases (BXLs) were related to hemicellulose degradation; 13 genes such as polygalacturonases (PGs) and pectate lyase (PLs) were associated with pectin degradation; 12 expansins (EXPs) related to cell wall loosening and 6 pectinesterase/pectinesterase inhibitors (PE/PEIs) genes were involved in cell wall modification. Of the down-regulated genes, there were 35 cell wall biosynthesis-related genes (Figure 6), including those encoding cellulose synthase, extensin, glycine-rich cell wall structural protein, UDP-glucuronate 4-epimerase and xyloglucan glycosyltransferase. There were not surprised that those genes encoding enzymes mentioned above may be involved in the process of fruitlet abscission induced by ethephon. However, 101 down-regulated genes related to cell wall degradation, loosening and modification, and 21 up-regulated genes related to cell wall biosynthesis were also found in our study.


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)

Expression profiling of genes related to cell wall modification, ROS response, calcium signaling transduction, and protein ubiquitination in the FAZ-enriched pedicel after ethylene treatment. Up-regulated genes involved in cell wall degradation, cell wall loosening and ROS response, and down-regulated genes related to cell wall biosynthesis were showed. All genes involved in calcium signaling transduction and protein ubiquitination were exhibited. Gene expression levels were indicated with color bars. Additional information was presented in Supplementary Data Excel File 4.
© Copyright Policy
Related In: Results  -  Collection

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Figure 6: Expression profiling of genes related to cell wall modification, ROS response, calcium signaling transduction, and protein ubiquitination in the FAZ-enriched pedicel after ethylene treatment. Up-regulated genes involved in cell wall degradation, cell wall loosening and ROS response, and down-regulated genes related to cell wall biosynthesis were showed. All genes involved in calcium signaling transduction and protein ubiquitination were exhibited. Gene expression levels were indicated with color bars. Additional information was presented in Supplementary Data Excel File 4.
Mentions: A total of 208 genes including 56, 104, 21, and 27 genes related to cell wall biosynthesis, degradation, loosing and modification were found, respectively (Supplementary Data Excel File 6). Of these, 72 and 136 genes were up- and down-regulated, respectively. Of the up-regulated genes, there were 51 cell wall degradation, loosing and modification related transcripts (Figure 6). Among them, 4 genes were related to callose degradation, like endo-1,3-β-glucosidases (ENGs) and β-1,3-glucanases (BGN13s); 5 genes were involved in cellulose degradation, such as endo-1,4-β-D-glucanases (CELs) and β-glucosidases (BGLUs); 11 genes like endo-1,4-β-mannosidase (MAN), xyloglucan endotransglucosylase/hydrolases (XTHs) and β-D-xylosidases (BXLs) were related to hemicellulose degradation; 13 genes such as polygalacturonases (PGs) and pectate lyase (PLs) were associated with pectin degradation; 12 expansins (EXPs) related to cell wall loosening and 6 pectinesterase/pectinesterase inhibitors (PE/PEIs) genes were involved in cell wall modification. Of the down-regulated genes, there were 35 cell wall biosynthesis-related genes (Figure 6), including those encoding cellulose synthase, extensin, glycine-rich cell wall structural protein, UDP-glucuronate 4-epimerase and xyloglucan glycosyltransferase. There were not surprised that those genes encoding enzymes mentioned above may be involved in the process of fruitlet abscission induced by ethephon. However, 101 down-regulated genes related to cell wall degradation, loosening and modification, and 21 up-regulated genes related to cell wall biosynthesis were also found in our study.

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.