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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.


Summary of the number of significant changes in transcription factors between the different families of ETH-responsive genes. Changes in the abundance of 127 TFs belonging to 15 families were identified in the FAZ-enriched pedicel of litchi. Comparison of early (Group I and Group IV) and late (Group II and Group III) stages for significantly up-regulated and down-regulated transcripts revealed differences in the families of TFs during ethephon-induced abscission. Additional information was presented in Supplementary Data Excel File 6.
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Figure 5: Summary of the number of significant changes in transcription factors between the different families of ETH-responsive genes. Changes in the abundance of 127 TFs belonging to 15 families were identified in the FAZ-enriched pedicel of litchi. Comparison of early (Group I and Group IV) and late (Group II and Group III) stages for significantly up-regulated and down-regulated transcripts revealed differences in the families of TFs during ethephon-induced abscission. Additional information was presented in Supplementary Data Excel File 6.

Mentions: Except for 58 genes putatively encoding TFs related to plant hormones, there were 127 candidate TFs belonged to diverse families including ABI3/VP1, bHLH, BLH1, bZIP, GRAS, HD-ZIP, HSF, KNOX, LBD, MADS-box, MYB, NAC, WRKY, Trihelix, and zinc finger (Figure 5, Supplementary Data Excel File 5). Of these, 51 and 76 genes were up- and down-regulated, respectively. And 78, 9, 14, and 26 belonged to Group I, Group II, Group III and Group IV, respectively. Remarkably, 71 out of 114 TFs in Group I and Group IV were down-regulated, indicating that most TFs were repressed at 1 d after the ETH treatment. There were more than 10 members in those families including bHLH, MYB, WRKY, NAC, LBD, and HD-ZIP. Most members of bHLH and HD-ZIP families were down-regulated, while 13 of 15 members in the family of WRKY were up-regulated, and all members in the families of BLH1, MADS-box, KNOX, and Trihelix were down-regulated. Moreover, 33 of the 51 up-regulated TFs were induced at 1 d after treatment, and the largest TF family was the WRKY (10 genes), followed by MYB (6 genes) and NAC (5 genes), implying that those genes from these TF families could be related with triggering the transcriptional chain reaction during ETH-induced abscission.


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)

Summary of the number of significant changes in transcription factors between the different families of ETH-responsive genes. Changes in the abundance of 127 TFs belonging to 15 families were identified in the FAZ-enriched pedicel of litchi. Comparison of early (Group I and Group IV) and late (Group II and Group III) stages for significantly up-regulated and down-regulated transcripts revealed differences in the families of TFs during ethephon-induced abscission. Additional information was presented in Supplementary Data Excel File 6.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 5: Summary of the number of significant changes in transcription factors between the different families of ETH-responsive genes. Changes in the abundance of 127 TFs belonging to 15 families were identified in the FAZ-enriched pedicel of litchi. Comparison of early (Group I and Group IV) and late (Group II and Group III) stages for significantly up-regulated and down-regulated transcripts revealed differences in the families of TFs during ethephon-induced abscission. Additional information was presented in Supplementary Data Excel File 6.
Mentions: Except for 58 genes putatively encoding TFs related to plant hormones, there were 127 candidate TFs belonged to diverse families including ABI3/VP1, bHLH, BLH1, bZIP, GRAS, HD-ZIP, HSF, KNOX, LBD, MADS-box, MYB, NAC, WRKY, Trihelix, and zinc finger (Figure 5, Supplementary Data Excel File 5). Of these, 51 and 76 genes were up- and down-regulated, respectively. And 78, 9, 14, and 26 belonged to Group I, Group II, Group III and Group IV, respectively. Remarkably, 71 out of 114 TFs in Group I and Group IV were down-regulated, indicating that most TFs were repressed at 1 d after the ETH treatment. There were more than 10 members in those families including bHLH, MYB, WRKY, NAC, LBD, and HD-ZIP. Most members of bHLH and HD-ZIP families were down-regulated, while 13 of 15 members in the family of WRKY were up-regulated, and all members in the families of BLH1, MADS-box, KNOX, and Trihelix were down-regulated. Moreover, 33 of the 51 up-regulated TFs were induced at 1 d after treatment, and the largest TF family was the WRKY (10 genes), followed by MYB (6 genes) and NAC (5 genes), implying that those genes from these TF families could be related with triggering the transcriptional chain reaction during ETH-induced abscission.

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.