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Regulation of flavonol content and composition in (Syrah×Pinot Noir) mature grapes: integration of transcriptional profiling and metabolic quantitative trait locus analyses.

Malacarne G, Costantini L, Coller E, Battilana J, Velasco R, Vrhovsek U, Grando MS, Moser C - J. Exp. Bot. (2015)

Bottom Line: Moreover, seven regions specifically associated with the fine control of flavonol biosynthesis are identified.Gene expression profiling of two groups of individuals significantly divergent for their skin flavonol content identified a large set of differentially modulated transcripts.Among these, the transcripts coding for MYB and bZIP transcription factors, methyltranferases, and glucosyltranferases specific for flavonols, proteins, and factors belonging to the UV-B signalling pathway and co-localizing with the QTL regions are proposed as candidate genes for the fine regulation of flavonol content and composition in mature grapes.

View Article: PubMed Central - PubMed

Affiliation: Genomics and Biology of Fruit Crops Department, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy giulia.malacarne@fmach.it.

No MeSH data available.


Related in: MedlinePlus

Transcriptomic analysis of high- and low-flavonol producers (HFPs and LFPs) by Affymetrix GrapeGen Chip. Assignment of the probe sets exclusively modulated in HFPs (dark grey) and in LFPs (light grey) to 84 functional categories of the third level of definition from the custom-made catalogue based on plant-related terms from the GO vocabulary and MIPS FunCat (Grimplet et al., 2012). Only the functional categories significantly enriched in HFP or LFP data sets (black and grey, respectively) compared with the GrapeGen Chip (white) according to a hypergeometric test (P<0.05) are shown.
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Figure 3: Transcriptomic analysis of high- and low-flavonol producers (HFPs and LFPs) by Affymetrix GrapeGen Chip. Assignment of the probe sets exclusively modulated in HFPs (dark grey) and in LFPs (light grey) to 84 functional categories of the third level of definition from the custom-made catalogue based on plant-related terms from the GO vocabulary and MIPS FunCat (Grimplet et al., 2012). Only the functional categories significantly enriched in HFP or LFP data sets (black and grey, respectively) compared with the GrapeGen Chip (white) according to a hypergeometric test (P<0.05) are shown.

Mentions: Differentially expressed probe sets were assigned to 84 functional categories at the third level of definition taken from the annotation of the GeneChip probe sets (Ashburner et al., 2000; Ruepp et al., 2004). Although the group of probe sets that could not be associated with any biological process (‘unknown’, ‘unclear’, and ‘unclassified’) or that could not find any significant hit (‘no hit’) was the largest in the lists of both the HFP and the LFP DEPs, 10 categories differently represented when compared with the GeneChip categories were identified (Fig. 3). In the HFP data set, the categories of the cellular process ‘Oil body organization and biogenesis’, of the primary metabolism ‘Amino acid metabolism’, ‘Carbohydrate metabolism’, ‘Lipid metabolism’, of the response to stress ‘Abiotic stress response’, and of transport ‘a-Type channels’ and ‘Lipid transport’ were significantly over-represented, while the ‘no hit’ category was somewhat surprisingly under-represented (Fig. 3). Noteworthy is the case of the 24 probe sets of the ‘Abiotic stress response’ category corresponding to genes mainly encoding dehydration- and light stress-responsive proteins, known to affect the flavonol profiles in the grape berry skin (Flamini et al., 2013; Teixeira et al., 2013): three abscisic acid (ABA)-responsive dehydration-responsive proteins 22 (Yamaguchi-Shinozaki and Shinozaki, 1993; Hanana et al., 2008) and one ELIP1 (early light-inducible protein) were identified whose activity in Arabidopsis was related to the presence of photoprotective flavonoids (Heddad et al., 2006). On the other hand, the LFP data set was significantly and exclusively enriched in two categories, ‘Cell wall organization and biogenesis’ and ‘ABA signalling’. The large fraction of differentially expressed probe sets, corresponding to genes with unknown function potentially relevant for the fine control of the flavonol pathway, highlights that knowledge of the process is still scarce and is a valuable source for further investigation. The differential expression between HFPs and LFPs was used as the main criterion to support the choice of candidates within QTLs for the genes represented on the GeneChip.


Regulation of flavonol content and composition in (Syrah×Pinot Noir) mature grapes: integration of transcriptional profiling and metabolic quantitative trait locus analyses.

Malacarne G, Costantini L, Coller E, Battilana J, Velasco R, Vrhovsek U, Grando MS, Moser C - J. Exp. Bot. (2015)

Transcriptomic analysis of high- and low-flavonol producers (HFPs and LFPs) by Affymetrix GrapeGen Chip. Assignment of the probe sets exclusively modulated in HFPs (dark grey) and in LFPs (light grey) to 84 functional categories of the third level of definition from the custom-made catalogue based on plant-related terms from the GO vocabulary and MIPS FunCat (Grimplet et al., 2012). Only the functional categories significantly enriched in HFP or LFP data sets (black and grey, respectively) compared with the GrapeGen Chip (white) according to a hypergeometric test (P<0.05) are shown.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4507773&req=5

Figure 3: Transcriptomic analysis of high- and low-flavonol producers (HFPs and LFPs) by Affymetrix GrapeGen Chip. Assignment of the probe sets exclusively modulated in HFPs (dark grey) and in LFPs (light grey) to 84 functional categories of the third level of definition from the custom-made catalogue based on plant-related terms from the GO vocabulary and MIPS FunCat (Grimplet et al., 2012). Only the functional categories significantly enriched in HFP or LFP data sets (black and grey, respectively) compared with the GrapeGen Chip (white) according to a hypergeometric test (P<0.05) are shown.
Mentions: Differentially expressed probe sets were assigned to 84 functional categories at the third level of definition taken from the annotation of the GeneChip probe sets (Ashburner et al., 2000; Ruepp et al., 2004). Although the group of probe sets that could not be associated with any biological process (‘unknown’, ‘unclear’, and ‘unclassified’) or that could not find any significant hit (‘no hit’) was the largest in the lists of both the HFP and the LFP DEPs, 10 categories differently represented when compared with the GeneChip categories were identified (Fig. 3). In the HFP data set, the categories of the cellular process ‘Oil body organization and biogenesis’, of the primary metabolism ‘Amino acid metabolism’, ‘Carbohydrate metabolism’, ‘Lipid metabolism’, of the response to stress ‘Abiotic stress response’, and of transport ‘a-Type channels’ and ‘Lipid transport’ were significantly over-represented, while the ‘no hit’ category was somewhat surprisingly under-represented (Fig. 3). Noteworthy is the case of the 24 probe sets of the ‘Abiotic stress response’ category corresponding to genes mainly encoding dehydration- and light stress-responsive proteins, known to affect the flavonol profiles in the grape berry skin (Flamini et al., 2013; Teixeira et al., 2013): three abscisic acid (ABA)-responsive dehydration-responsive proteins 22 (Yamaguchi-Shinozaki and Shinozaki, 1993; Hanana et al., 2008) and one ELIP1 (early light-inducible protein) were identified whose activity in Arabidopsis was related to the presence of photoprotective flavonoids (Heddad et al., 2006). On the other hand, the LFP data set was significantly and exclusively enriched in two categories, ‘Cell wall organization and biogenesis’ and ‘ABA signalling’. The large fraction of differentially expressed probe sets, corresponding to genes with unknown function potentially relevant for the fine control of the flavonol pathway, highlights that knowledge of the process is still scarce and is a valuable source for further investigation. The differential expression between HFPs and LFPs was used as the main criterion to support the choice of candidates within QTLs for the genes represented on the GeneChip.

Bottom Line: Moreover, seven regions specifically associated with the fine control of flavonol biosynthesis are identified.Gene expression profiling of two groups of individuals significantly divergent for their skin flavonol content identified a large set of differentially modulated transcripts.Among these, the transcripts coding for MYB and bZIP transcription factors, methyltranferases, and glucosyltranferases specific for flavonols, proteins, and factors belonging to the UV-B signalling pathway and co-localizing with the QTL regions are proposed as candidate genes for the fine regulation of flavonol content and composition in mature grapes.

View Article: PubMed Central - PubMed

Affiliation: Genomics and Biology of Fruit Crops Department, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy giulia.malacarne@fmach.it.

No MeSH data available.


Related in: MedlinePlus