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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 plant hormone biosynthesis, signaling, and metabolism in the FAZ-enriched pedicel after ethylene treatment. Yellow, blue, purple, and green vertical lines indicate biosynthesis, signaling, transport and degradation genes, respectively. Gene expression levels are indicated with color bars. Additional information was presented in Supplementary Data Excel File 4.
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Figure 4: Expression profiling of genes related to plant hormone biosynthesis, signaling, and metabolism in the FAZ-enriched pedicel after ethylene treatment. Yellow, blue, purple, and green vertical lines indicate biosynthesis, signaling, transport and degradation genes, respectively. Gene expression levels are indicated with color bars. Additional information was presented in Supplementary Data Excel File 4.

Mentions: A total of 195 candidate genes were found related to plant hormone biosynthesis and signaling pathway (Figure 4, Supplementary Data Excel File 4). Of these, 124, 16, 17, and 38 genes belonged to the Group I, Group II, Group III, and Group IV, respectively. Sixty and fifty-five genes were related to auxin and ethylene, among them, 47 auxin-related genes were down-regulated and 39 ethylene-related genes were up-regulated. These genes should be closely associated with fruitlet abscission, including those encoding auxin efflux carrier component (PIN), auxin influx carrier (AUX1), AUX/IAA protein, auxin response factor (ARF), SAUR family protein, GH3 protein, 1-aminocyclopropane-1-carboxylate oxidase (ACO), 1-aminocyclopropane-1-carboxylate synthase (ACS), AP2/ERF transcription factor and ethylene receptor (ETR), et cetera. Twenty-eight gibberellins (GA) related and 18 cytokinin-related genes were found, most of them were down-regulated, such as genes encoding gibberellin 20 oxidase (GA20ox), gibberellin receptor GID1, cytokinin hydroxylase (CYP735A), histidine kinase (AHK) and two-component response regulator (AARA), etc… Eight of eighteen abscisic acid (ABA) related genes were up-regulated including those encoding zeaxanthin epoxidase (ZEP), abscisic acid receptor (PYR/PYL) and protein phosphatase 2C (PP2C), and the repressed genes mainly encoded 9-cis-epoxycarotenoid dioxygenase (NCED), carotenoid cleavage dioxygenase (CCD), and abscisic acid 8′-hydroxylase (CYP707). Moreover, six salicylic acid (SA) related genes encoded with salicylic acid-binding protein (SBP) and regulatory protein NPR1 were highly up-regulated, and five jasmonic acid (JA) related genes mainly encoded allene oxide cyclise (AOC) and jasmonate ZIM domain-containing protein (JAZ) were decreased. These results suggested that seven classes of plant hormones were involved in the process of fruitlet abscission induced by the ETH treatment. The most important hormones were ethylene and auxin, followed by GA, cytokinin and ABA. JA and SA ranked the last according to the number of DEGs.


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 plant hormone biosynthesis, signaling, and metabolism in the FAZ-enriched pedicel after ethylene treatment. Yellow, blue, purple, and green vertical lines indicate biosynthesis, signaling, transport and degradation genes, respectively. Gene expression levels are indicated with color bars. Additional information was presented in Supplementary Data Excel File 4.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 4: Expression profiling of genes related to plant hormone biosynthesis, signaling, and metabolism in the FAZ-enriched pedicel after ethylene treatment. Yellow, blue, purple, and green vertical lines indicate biosynthesis, signaling, transport and degradation genes, respectively. Gene expression levels are indicated with color bars. Additional information was presented in Supplementary Data Excel File 4.
Mentions: A total of 195 candidate genes were found related to plant hormone biosynthesis and signaling pathway (Figure 4, Supplementary Data Excel File 4). Of these, 124, 16, 17, and 38 genes belonged to the Group I, Group II, Group III, and Group IV, respectively. Sixty and fifty-five genes were related to auxin and ethylene, among them, 47 auxin-related genes were down-regulated and 39 ethylene-related genes were up-regulated. These genes should be closely associated with fruitlet abscission, including those encoding auxin efflux carrier component (PIN), auxin influx carrier (AUX1), AUX/IAA protein, auxin response factor (ARF), SAUR family protein, GH3 protein, 1-aminocyclopropane-1-carboxylate oxidase (ACO), 1-aminocyclopropane-1-carboxylate synthase (ACS), AP2/ERF transcription factor and ethylene receptor (ETR), et cetera. Twenty-eight gibberellins (GA) related and 18 cytokinin-related genes were found, most of them were down-regulated, such as genes encoding gibberellin 20 oxidase (GA20ox), gibberellin receptor GID1, cytokinin hydroxylase (CYP735A), histidine kinase (AHK) and two-component response regulator (AARA), etc… Eight of eighteen abscisic acid (ABA) related genes were up-regulated including those encoding zeaxanthin epoxidase (ZEP), abscisic acid receptor (PYR/PYL) and protein phosphatase 2C (PP2C), and the repressed genes mainly encoded 9-cis-epoxycarotenoid dioxygenase (NCED), carotenoid cleavage dioxygenase (CCD), and abscisic acid 8′-hydroxylase (CYP707). Moreover, six salicylic acid (SA) related genes encoded with salicylic acid-binding protein (SBP) and regulatory protein NPR1 were highly up-regulated, and five jasmonic acid (JA) related genes mainly encoded allene oxide cyclise (AOC) and jasmonate ZIM domain-containing protein (JAZ) were decreased. These results suggested that seven classes of plant hormones were involved in the process of fruitlet abscission induced by the ETH treatment. The most important hormones were ethylene and auxin, followed by GA, cytokinin and ABA. JA and SA ranked the last according to the number of DEGs.

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.