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Molecular characterization of SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) gene family from Citrus and the effect of fruit load on their expression.

Shalom L, Shlizerman L, Zur N, Doron-Faigenboim A, Blumwald E, Sadka A - Front Plant Sci (2015)

Bottom Line: We showed that the Citrus SPL was able promote flowering independently of photoperiod in Arabidopsis, while miR156 repressed its flowering-promoting activity.Results showed that two additional SPL-like genes and miR172, known to be induced by SPLs in Arabidopsis, were altered by fruit load.The relationships between these factors in relation to the fruit-load effect on Citrus flowering are discussed.

View Article: PubMed Central - PubMed

Affiliation: Department of Fruit Tree Sciences, Agricultural Research Organization, The Volcani Center Bet Dagan, Israel ; The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem Rehovot, Israel.

ABSTRACT
We recently identified a Citrus gene encoding SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factor that contained a sequence complementary to miR156. Genes of the SPL family are known to play a role in flowering regulation and phase transition. In Citrus, the mRNA levels of the gene were significantly altered by fruit load in buds; under heavy fruit load (ON-Crop trees), known to suppress next year flowering, the mRNA levels were down-regulated, while fruit removal (de-fruiting), inducing next-year flowering, resulted in its up-regulation. In the current work, we set on to study the function of the gene. We showed that the Citrus SPL was able promote flowering independently of photoperiod in Arabidopsis, while miR156 repressed its flowering-promoting activity. In order to find out if fruit load affected the expression of additional genes of the SPL family, we identified and classified all SPL members in the Citrus genome, and studied their seasonal expression patterns in buds and leaves, and in response to de-fruiting. Results showed that two additional SPL-like genes and miR172, known to be induced by SPLs in Arabidopsis, were altered by fruit load. The relationships between these factors in relation to the fruit-load effect on Citrus flowering are discussed.

No MeSH data available.


miR156andmiR172levels in buds following fruit removal. (A) Expression levels of ctr-MIR156 and csi-MIR172a genes are based on transcriptomic data and are represented by FPKM-values, which normalize the read count by the length of the fragment and the total number of mapped reads. (B) Expression patterns of ctr-MIR156 and csi-MIR172a genes after fruit removal. (C) Abundance of the mature miR156 and miR172a sequences after fruit removal. For (B,C), values were determined in ON-Crop (ON), OFF-Crop (OFF), and de-fruited (DEF) trees at the indicated weeks after de-fruiting. The numbers are mean values of three independent biological replicates ± SE. Asterisks represent significant difference (P ≤ 0.05) from ON at the same time point. pri-miR, primary mRNA.
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Figure 7: miR156andmiR172levels in buds following fruit removal. (A) Expression levels of ctr-MIR156 and csi-MIR172a genes are based on transcriptomic data and are represented by FPKM-values, which normalize the read count by the length of the fragment and the total number of mapped reads. (B) Expression patterns of ctr-MIR156 and csi-MIR172a genes after fruit removal. (C) Abundance of the mature miR156 and miR172a sequences after fruit removal. For (B,C), values were determined in ON-Crop (ON), OFF-Crop (OFF), and de-fruited (DEF) trees at the indicated weeks after de-fruiting. The numbers are mean values of three independent biological replicates ± SE. Asterisks represent significant difference (P ≤ 0.05) from ON at the same time point. pri-miR, primary mRNA.

Mentions: Primary miRNAs (pri-miRs) are capped and polyadenylated non-coding RNA transcripts containing mature miRNA sequences (Voinnet, 2009). Cleavage of the primary miRNA transcript eventually results in the release of biologically active mature miRNA and ultimately, the degradation or translational repression of mRNA targets. The miRBase database (http://www.mirbase.org/) contains sequence data (precursor and mature) for 75 miRNAs from Citrus. We recently conducted an RNA deep-sequencing analysis of Citrus buds following fruit removal (Shalom et al., 2014). In the current work, we aligned the RNA deep-sequencing data to the Citrus precursor sequences from miRBase. Results of this analysis indicated that about two-thirds of them are expressed in buds; however, only a few were significantly affected by fruit load. Among these were ctr-MIR156 and csi-MIR172a, with the latter expressed to much higher levels (Figure 7A). Expression levels of ctr-MIR156 were significantly higher in ON-Crop buds as compared to OFF-Crop buds and decreased following de-fruiting (Figure 7B). In contrast, expression levels of csi-MIR172a showed the opposite trend, with OFF-Crop buds and buds after de-fruiting showing higher expression levels than ON-Crop buds. Alterations in both genes occurred as early as 1 week after de-fruiting (Figure 7B). Abundance analysis of the mature miRNA sequences was performed next. While miR156 abundance was not affected by fruit presence, miR172 was more abundant in OFF-Crop buds than ON-Crop buds, and increased significantly (two to threefold) after de-fruiting (Figure 7C).


Molecular characterization of SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) gene family from Citrus and the effect of fruit load on their expression.

Shalom L, Shlizerman L, Zur N, Doron-Faigenboim A, Blumwald E, Sadka A - Front Plant Sci (2015)

miR156andmiR172levels in buds following fruit removal. (A) Expression levels of ctr-MIR156 and csi-MIR172a genes are based on transcriptomic data and are represented by FPKM-values, which normalize the read count by the length of the fragment and the total number of mapped reads. (B) Expression patterns of ctr-MIR156 and csi-MIR172a genes after fruit removal. (C) Abundance of the mature miR156 and miR172a sequences after fruit removal. For (B,C), values were determined in ON-Crop (ON), OFF-Crop (OFF), and de-fruited (DEF) trees at the indicated weeks after de-fruiting. The numbers are mean values of three independent biological replicates ± SE. Asterisks represent significant difference (P ≤ 0.05) from ON at the same time point. pri-miR, primary mRNA.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
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Figure 7: miR156andmiR172levels in buds following fruit removal. (A) Expression levels of ctr-MIR156 and csi-MIR172a genes are based on transcriptomic data and are represented by FPKM-values, which normalize the read count by the length of the fragment and the total number of mapped reads. (B) Expression patterns of ctr-MIR156 and csi-MIR172a genes after fruit removal. (C) Abundance of the mature miR156 and miR172a sequences after fruit removal. For (B,C), values were determined in ON-Crop (ON), OFF-Crop (OFF), and de-fruited (DEF) trees at the indicated weeks after de-fruiting. The numbers are mean values of three independent biological replicates ± SE. Asterisks represent significant difference (P ≤ 0.05) from ON at the same time point. pri-miR, primary mRNA.
Mentions: Primary miRNAs (pri-miRs) are capped and polyadenylated non-coding RNA transcripts containing mature miRNA sequences (Voinnet, 2009). Cleavage of the primary miRNA transcript eventually results in the release of biologically active mature miRNA and ultimately, the degradation or translational repression of mRNA targets. The miRBase database (http://www.mirbase.org/) contains sequence data (precursor and mature) for 75 miRNAs from Citrus. We recently conducted an RNA deep-sequencing analysis of Citrus buds following fruit removal (Shalom et al., 2014). In the current work, we aligned the RNA deep-sequencing data to the Citrus precursor sequences from miRBase. Results of this analysis indicated that about two-thirds of them are expressed in buds; however, only a few were significantly affected by fruit load. Among these were ctr-MIR156 and csi-MIR172a, with the latter expressed to much higher levels (Figure 7A). Expression levels of ctr-MIR156 were significantly higher in ON-Crop buds as compared to OFF-Crop buds and decreased following de-fruiting (Figure 7B). In contrast, expression levels of csi-MIR172a showed the opposite trend, with OFF-Crop buds and buds after de-fruiting showing higher expression levels than ON-Crop buds. Alterations in both genes occurred as early as 1 week after de-fruiting (Figure 7B). Abundance analysis of the mature miRNA sequences was performed next. While miR156 abundance was not affected by fruit presence, miR172 was more abundant in OFF-Crop buds than ON-Crop buds, and increased significantly (two to threefold) after de-fruiting (Figure 7C).

Bottom Line: We showed that the Citrus SPL was able promote flowering independently of photoperiod in Arabidopsis, while miR156 repressed its flowering-promoting activity.Results showed that two additional SPL-like genes and miR172, known to be induced by SPLs in Arabidopsis, were altered by fruit load.The relationships between these factors in relation to the fruit-load effect on Citrus flowering are discussed.

View Article: PubMed Central - PubMed

Affiliation: Department of Fruit Tree Sciences, Agricultural Research Organization, The Volcani Center Bet Dagan, Israel ; The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem Rehovot, Israel.

ABSTRACT
We recently identified a Citrus gene encoding SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factor that contained a sequence complementary to miR156. Genes of the SPL family are known to play a role in flowering regulation and phase transition. In Citrus, the mRNA levels of the gene were significantly altered by fruit load in buds; under heavy fruit load (ON-Crop trees), known to suppress next year flowering, the mRNA levels were down-regulated, while fruit removal (de-fruiting), inducing next-year flowering, resulted in its up-regulation. In the current work, we set on to study the function of the gene. We showed that the Citrus SPL was able promote flowering independently of photoperiod in Arabidopsis, while miR156 repressed its flowering-promoting activity. In order to find out if fruit load affected the expression of additional genes of the SPL family, we identified and classified all SPL members in the Citrus genome, and studied their seasonal expression patterns in buds and leaves, and in response to de-fruiting. Results showed that two additional SPL-like genes and miR172, known to be induced by SPLs in Arabidopsis, were altered by fruit load. The relationships between these factors in relation to the fruit-load effect on Citrus flowering are discussed.

No MeSH data available.