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Identification of candidate flavonoid pathway genes using transcriptome correlation network analysis in ripe strawberry (Fragaria × ananassa) fruits.

Pillet J, Yu HW, Chambers AH, Whitaker VM, Folta KM - J. Exp. Bot. (2015)

Bottom Line: The results suggest that two of the newly-identified regulators likely contribute to discrete nodes of the flavonoid pathway.The third putative transcription factor appears to be a universal regulator of flavonoid-pathway genes, as many pathway transcripts decrease in abundance when this gene is silenced.This report demonstrates that such systems-level approaches may be especially powerful when connected to an effective transient expression system, helping to provide rapid and strong evidence of gene function in key fruit-ripening processes.

View Article: PubMed Central - PubMed

Affiliation: Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA.

No MeSH data available.


Expression profile correlation analysis of the flavonoid biosynthetic pathway in the ‘Mara des Bois’ × ‘Elyana’ F1 population. Correlations are considered positive when Pearson’s r>0.65 (P<0.05). The thicker the line the more close to 1 the correlation is. PAL, phenylalanine ammonia lyase; C4H, cinnamate-4-hydroxylase; 4CL, 4-coumaroyl:CoA-ligase; CHS, chalcone synthase; CHI, chalcone isomerase; F3H, flavanone 3 hydrolase; F3’H, flavanone 3’ hydrolase; FLS, flavonol synthase; DFR, dihydroflavanol reductase; LAR, leucoanthocyanidin reductase; ANR, anthocyanidin reductase; ANS, anthocyanidin synthase; UFGT, UDP-glucose flavonoid glycosyl transferase.
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Figure 2: Expression profile correlation analysis of the flavonoid biosynthetic pathway in the ‘Mara des Bois’ × ‘Elyana’ F1 population. Correlations are considered positive when Pearson’s r>0.65 (P<0.05). The thicker the line the more close to 1 the correlation is. PAL, phenylalanine ammonia lyase; C4H, cinnamate-4-hydroxylase; 4CL, 4-coumaroyl:CoA-ligase; CHS, chalcone synthase; CHI, chalcone isomerase; F3H, flavanone 3 hydrolase; F3’H, flavanone 3’ hydrolase; FLS, flavonol synthase; DFR, dihydroflavanol reductase; LAR, leucoanthocyanidin reductase; ANR, anthocyanidin reductase; ANS, anthocyanidin synthase; UFGT, UDP-glucose flavonoid glycosyl transferase.

Mentions: Correlations in the expression profiles within this set of genes were calculated, and positive correlations between genes (Pearson’s r>0.65, P<0.05) were identified (Fig. 2). This analysis reveals that transcript levels for each of the genes in this pathway seem to share strong correlation with at least three or four other genes in the pathway. These findings suggest a strongly connected and co-regulated pathway, consistent with what is already known about the relationships between these genes in other plants, including Arabidopsis (Yonekura-Sakakibara et al., 2008) and tomato (Ozaki et al., 2010). Some key genes can also be identified, including two CHS isoforms (CHS1, CHS2) and CHI (CHALCONE ISOMERASE). These transcripts share six, seven and six positive correlations with other genes, respectively. Even when positive correlations were found between either PAL1 and PAL2 and the same other genes, no correlation between the two PAL isoforms was detected, suggesting different roles or, more likely, different regulation processes for the two isoforms. Furthermore, the global correlation pattern is in agreement with the metabolic flux occurring in the ripe fruit. Indeed, positive correlations are only found between genes that are involved in the anthocyanin pathway and no correlation were established with genes like LAR and ANR that are specific for the synthesis of tannins or FLS for the flavonols. No correlation was found for the F3’H gene suggesting the implication of this enzyme in processes other than anthocyanin synthesis in ripening strawberry fruit.


Identification of candidate flavonoid pathway genes using transcriptome correlation network analysis in ripe strawberry (Fragaria × ananassa) fruits.

Pillet J, Yu HW, Chambers AH, Whitaker VM, Folta KM - J. Exp. Bot. (2015)

Expression profile correlation analysis of the flavonoid biosynthetic pathway in the ‘Mara des Bois’ × ‘Elyana’ F1 population. Correlations are considered positive when Pearson’s r>0.65 (P<0.05). The thicker the line the more close to 1 the correlation is. PAL, phenylalanine ammonia lyase; C4H, cinnamate-4-hydroxylase; 4CL, 4-coumaroyl:CoA-ligase; CHS, chalcone synthase; CHI, chalcone isomerase; F3H, flavanone 3 hydrolase; F3’H, flavanone 3’ hydrolase; FLS, flavonol synthase; DFR, dihydroflavanol reductase; LAR, leucoanthocyanidin reductase; ANR, anthocyanidin reductase; ANS, anthocyanidin synthase; UFGT, UDP-glucose flavonoid glycosyl transferase.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4507756&req=5

Figure 2: Expression profile correlation analysis of the flavonoid biosynthetic pathway in the ‘Mara des Bois’ × ‘Elyana’ F1 population. Correlations are considered positive when Pearson’s r>0.65 (P<0.05). The thicker the line the more close to 1 the correlation is. PAL, phenylalanine ammonia lyase; C4H, cinnamate-4-hydroxylase; 4CL, 4-coumaroyl:CoA-ligase; CHS, chalcone synthase; CHI, chalcone isomerase; F3H, flavanone 3 hydrolase; F3’H, flavanone 3’ hydrolase; FLS, flavonol synthase; DFR, dihydroflavanol reductase; LAR, leucoanthocyanidin reductase; ANR, anthocyanidin reductase; ANS, anthocyanidin synthase; UFGT, UDP-glucose flavonoid glycosyl transferase.
Mentions: Correlations in the expression profiles within this set of genes were calculated, and positive correlations between genes (Pearson’s r>0.65, P<0.05) were identified (Fig. 2). This analysis reveals that transcript levels for each of the genes in this pathway seem to share strong correlation with at least three or four other genes in the pathway. These findings suggest a strongly connected and co-regulated pathway, consistent with what is already known about the relationships between these genes in other plants, including Arabidopsis (Yonekura-Sakakibara et al., 2008) and tomato (Ozaki et al., 2010). Some key genes can also be identified, including two CHS isoforms (CHS1, CHS2) and CHI (CHALCONE ISOMERASE). These transcripts share six, seven and six positive correlations with other genes, respectively. Even when positive correlations were found between either PAL1 and PAL2 and the same other genes, no correlation between the two PAL isoforms was detected, suggesting different roles or, more likely, different regulation processes for the two isoforms. Furthermore, the global correlation pattern is in agreement with the metabolic flux occurring in the ripe fruit. Indeed, positive correlations are only found between genes that are involved in the anthocyanin pathway and no correlation were established with genes like LAR and ANR that are specific for the synthesis of tannins or FLS for the flavonols. No correlation was found for the F3’H gene suggesting the implication of this enzyme in processes other than anthocyanin synthesis in ripening strawberry fruit.

Bottom Line: The results suggest that two of the newly-identified regulators likely contribute to discrete nodes of the flavonoid pathway.The third putative transcription factor appears to be a universal regulator of flavonoid-pathway genes, as many pathway transcripts decrease in abundance when this gene is silenced.This report demonstrates that such systems-level approaches may be especially powerful when connected to an effective transient expression system, helping to provide rapid and strong evidence of gene function in key fruit-ripening processes.

View Article: PubMed Central - PubMed

Affiliation: Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA.

No MeSH data available.