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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.


Confirmation of candidate gene-expression pattern in FAZ-enriched pedicel during ethephon-induced fruit abscission. qRT-PCR analysis (filled circles, left y-axis) of 41 selected genes at 0, 1, 2, 3 d after ethephon treatment. Relative expression values were normalized to the pre-treatment (0 d) expression value taken as 1. The data represent the mean values (±SE) of duplicate experiments from three independent biological samples. Broken lines (open circle, right y-axis) show expression profiling of genes in the FAZ-enriched pedicel from the DTA data, and indicate the total read count in RPKM for each gene after normalization across the seven samples: CK0, CK1, CK2, CK3, ETH1, ETH2, and ETH3. CK and ETH mean the untreated control and ethephon treatment, the numbers following the CK and ETH are the days after treatment.
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Figure 2: Confirmation of candidate gene-expression pattern in FAZ-enriched pedicel during ethephon-induced fruit abscission. qRT-PCR analysis (filled circles, left y-axis) of 41 selected genes at 0, 1, 2, 3 d after ethephon treatment. Relative expression values were normalized to the pre-treatment (0 d) expression value taken as 1. The data represent the mean values (±SE) of duplicate experiments from three independent biological samples. Broken lines (open circle, right y-axis) show expression profiling of genes in the FAZ-enriched pedicel from the DTA data, and indicate the total read count in RPKM for each gene after normalization across the seven samples: CK0, CK1, CK2, CK3, ETH1, ETH2, and ETH3. CK and ETH mean the untreated control and ethephon treatment, the numbers following the CK and ETH are the days after treatment.

Mentions: Forty-one randomly selected genes were analyzed by quantitative real-time PCR to verify their expression patterns (Figure 2). Among these, transcripts encoding the key enzymes involved in ethylene biosynthesis and signaling, such as ACS (L10030076), ACO (L10037576), ETR2 (U20306), EBF (U575), EIN3/EIL (U23712) and ERF (L10026303, L10050388, C2959.2, and U6276), were sharply increased at 1 d after treatment, which were consistent with the results analyzed by DTA (Figure 2). Similarly, we verified the increased expression of genes encoding those enzymes related to cell wall degradation, TFs, cytokinin metabolism and ROS production, such as BGLU (U21052), BXL (L10010659), XTH (C5711.4 and U17815), PE/PEI (C5841.2, L10049394, and U1533), PG (L10048763), HD-ZIP (U10783), NAC (U13457), WRKY (U18045 and U9115), CKX (L10048833) and Rboh (L10001757), as well as the down-regulated genes involved in auxin transport and signaling, cytokinin signaling, ROS scavenging and calcium signaling, such as PIN (U11774), AUX1 (U9940), Aux/IAA (C3897.1 and U9140), SAUR (C5333.1), ILR1 (U1508), AHK (U11693), AHP (C4349.2), ARRA (C3809.1), POD (U20379 and U15492), AO (U10993), and CML (U2171 and U4839). The expression level of one auxin early responsive gene (GH3, C4818.1) and one calcium signaling gene (CML, U1498) were increased by ETH treatment, which was identical to the DTA results. One calcium transport gene (CNGC, L10064767) showed down-regulated at 1 d after treatment and increased at 3 d after treatment (Figure 2). However, the expression level of one gene encoding auxin response factor (ARF, L10058057) was contrasted to the DTA result (Figure 2). Thus, except one ARF gene, all the other 40 genes showed similar expression patterns as detected by the DTA, indicating that the DTA analysis results were effective.


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)

Confirmation of candidate gene-expression pattern in FAZ-enriched pedicel during ethephon-induced fruit abscission. qRT-PCR analysis (filled circles, left y-axis) of 41 selected genes at 0, 1, 2, 3 d after ethephon treatment. Relative expression values were normalized to the pre-treatment (0 d) expression value taken as 1. The data represent the mean values (±SE) of duplicate experiments from three independent biological samples. Broken lines (open circle, right y-axis) show expression profiling of genes in the FAZ-enriched pedicel from the DTA data, and indicate the total read count in RPKM for each gene after normalization across the seven samples: CK0, CK1, CK2, CK3, ETH1, ETH2, and ETH3. CK and ETH mean the untreated control and ethephon treatment, the numbers following the CK and ETH are the days after treatment.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 2: Confirmation of candidate gene-expression pattern in FAZ-enriched pedicel during ethephon-induced fruit abscission. qRT-PCR analysis (filled circles, left y-axis) of 41 selected genes at 0, 1, 2, 3 d after ethephon treatment. Relative expression values were normalized to the pre-treatment (0 d) expression value taken as 1. The data represent the mean values (±SE) of duplicate experiments from three independent biological samples. Broken lines (open circle, right y-axis) show expression profiling of genes in the FAZ-enriched pedicel from the DTA data, and indicate the total read count in RPKM for each gene after normalization across the seven samples: CK0, CK1, CK2, CK3, ETH1, ETH2, and ETH3. CK and ETH mean the untreated control and ethephon treatment, the numbers following the CK and ETH are the days after treatment.
Mentions: Forty-one randomly selected genes were analyzed by quantitative real-time PCR to verify their expression patterns (Figure 2). Among these, transcripts encoding the key enzymes involved in ethylene biosynthesis and signaling, such as ACS (L10030076), ACO (L10037576), ETR2 (U20306), EBF (U575), EIN3/EIL (U23712) and ERF (L10026303, L10050388, C2959.2, and U6276), were sharply increased at 1 d after treatment, which were consistent with the results analyzed by DTA (Figure 2). Similarly, we verified the increased expression of genes encoding those enzymes related to cell wall degradation, TFs, cytokinin metabolism and ROS production, such as BGLU (U21052), BXL (L10010659), XTH (C5711.4 and U17815), PE/PEI (C5841.2, L10049394, and U1533), PG (L10048763), HD-ZIP (U10783), NAC (U13457), WRKY (U18045 and U9115), CKX (L10048833) and Rboh (L10001757), as well as the down-regulated genes involved in auxin transport and signaling, cytokinin signaling, ROS scavenging and calcium signaling, such as PIN (U11774), AUX1 (U9940), Aux/IAA (C3897.1 and U9140), SAUR (C5333.1), ILR1 (U1508), AHK (U11693), AHP (C4349.2), ARRA (C3809.1), POD (U20379 and U15492), AO (U10993), and CML (U2171 and U4839). The expression level of one auxin early responsive gene (GH3, C4818.1) and one calcium signaling gene (CML, U1498) were increased by ETH treatment, which was identical to the DTA results. One calcium transport gene (CNGC, L10064767) showed down-regulated at 1 d after treatment and increased at 3 d after treatment (Figure 2). However, the expression level of one gene encoding auxin response factor (ARF, L10058057) was contrasted to the DTA result (Figure 2). Thus, except one ARF gene, all the other 40 genes showed similar expression patterns as detected by the DTA, indicating that the DTA analysis results were effective.

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.