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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 correlation analysis during fruit early development in Fragaria vesca. 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 9: Expression correlation analysis during fruit early development in Fragaria vesca. 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: The correlations between expressed genes in the flavonoid pathway provide an indirect image of the metabolic flux in the pathway. In our dataset, composed only of ripe fruits, genes that lead to anthocyanin synthesis were the only ones sharing positive correlations. We applied the same method to a public dataset based on the early stages of fruit development in Fragaria vesca and we found that the positive correlation patterns lead to tannin synthesis, which matches known metabolic flux observed during early expansion stages (Fig. 9; based on data from Kang et al., 2013). These analyses predict that data from a ripening series may contain evidence of tannin-directed gene expression early that realigns toward anthocyanins the fruit matures.


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 correlation analysis during fruit early development in Fragaria vesca. 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 9: Expression correlation analysis during fruit early development in Fragaria vesca. 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: The correlations between expressed genes in the flavonoid pathway provide an indirect image of the metabolic flux in the pathway. In our dataset, composed only of ripe fruits, genes that lead to anthocyanin synthesis were the only ones sharing positive correlations. We applied the same method to a public dataset based on the early stages of fruit development in Fragaria vesca and we found that the positive correlation patterns lead to tannin synthesis, which matches known metabolic flux observed during early expansion stages (Fig. 9; based on data from Kang et al., 2013). These analyses predict that data from a ripening series may contain evidence of tannin-directed gene expression early that realigns toward anthocyanins the fruit matures.

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.