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

Pillet, Jérémy; Yu, Hao; Chambers, Alan H.; Whitaker, Vance M.; Folta, Kevin M.

doi:10.1093/jxb/erv205

Cited by 95 publications

(90 citation statements)

References 30 publications

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“…The involvement of FaMADS9 in the regulatory system of flavonoid metabolism in the receptacles is supported by the number of TFs, previously reported to participate in the control of the pathway, the expression of which was altered in the FaMADS9 ‐silenced lines. These genes included MYB10 ( FvH4_1g22020 ), PCF1 ( FvH4_6g16170 ), DIV ( FvH4_6g11950 ), ZFN1 ( FvH4_6g00570 ) and ZFN2 ( FvH4_7g01060 ) (Pillet et al , ). The complex interaction among these regulatory genes in relation to flavonoid biosynthesis, as well as other developmental changes in ripening receptacles, requires the global analysis of available data sets associated with the process.…”

Section: Discussionmentioning

confidence: 99%

“…The analysis of MYB10 ( FvH4_1g22020 ), a gene involved in the regulation of the flavonoid pathway in strawberry fruits (Medina‐Puche et al , ), showed that the expression of this gene was significantly up‐regulated in the white receptacles (Table S2). Other TFs for which expression was correlated with flavonoid metabolism, such as TCP1 ( FvH4_6g16170 ), ZFN2 (FvH4_7g01060) and DIV (FvH4_6g11950) (Pillet et al , ), were down‐regulated in transgenic red receptacles (Table S2). In contrast, other genes associated with anthocyanin production in strawberry, such as the four members of the RAP family ( FvH4_1g27460 , FvH4_6g38760 , FvH4_2g25200 , FvH4_2g25210 ), encoding GST anthocyanin transporters (Luo et al , ), were up‐regulated in white receptacles of the silenced lines.…”

Section: Metabolic Changes In the Receptacles Of Famads9‐silenced Linmentioning

confidence: 99%

“…Strawberry is a non‐climacteric fruit, and several studies have analysed the metabolic (Fait et al , ) and cell wall changes (Jiménez‐Bermúdez et al , ; Quesada et al , ) that occur during fruit ripening, as well as changes in gene expression associated with this process (Aharoni and O'Connell, ; Härtl et al , ; Pillet et al , ; Sánchez‐Sevilla et al , ). Recently, a number of reports have shed light on two key elements of the strawberry fruit developmental programme of strawberry fruit: the involvement of hormones and the participation of specific transcription factors.…”

Section: Introductionmentioning

confidence: 99%

“…Additionally, studies on the three components of the complex that regulates flavonoid synthesis identified four TFs, namely FaMYB9/FaMYB11, FabHLH3 and FaTTG1, as positive regulators of the biosynthesis of proanthocyanidins (Schaart et al , ). Correlation analysis of the transcriptomes of ripening fruits also identified three TFs of the MYB, TCP and SCL families that were positively correlated with flavonoid accumulation in ripening fruits (Pillet et al , ). Recently, other TFs have been reported to regulate the gene expression of eugenol synthase2 (Medina‐Puche et al , ; Molina‐Hidalgo et al , ), which is involved in the synthesis of eugenol (Aragüez et al , ).…”

Section: Introductionmentioning

confidence: 99%

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Characterizing the involvement of FaMADS9 in the regulation of strawberry fruit receptacle development

Vallarino

Merchante

Sánchez-Sevilla

et al. 2019

Plant Biotechnology Journal

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FaMADS9 is the strawberry (Fragaria x ananassa) gene that exhibits the highest homology to the tomato (Solanum lycopersicum) RIN gene. Transgenic lines were obtained in which FaMADS9 was silenced. The fruits of these lines did not show differences in basic parameters, such as fruit firmness or colour, but exhibited lower Brix values in three of the four independent lines. The gene ontology MapMan category that was most enriched among the differentially expressed genes in the receptacles at the white stage corresponded to the regulation of transcription, including a high percentage of transcription factors and regulatory proteins associated with auxin action. In contrast, the most enriched categories at the red stage were transport, lipid metabolism and cell wall. Metabolomic analysis of the receptacles of the transformed fruits identified significant changes in the content of maltose, galactonic acid‐1,4‐lactone, proanthocyanidins and flavonols at the green/white stage, while isomaltose, anthocyanins and cuticular wax metabolism were the most affected at the red stage. Among the regulatory genes that were differentially expressed in the transgenic receptacles were several genes previously linked to flavonoid metabolism, such as MYB10, DIV, ZFN1, ZFN2, GT2, and GT5, or associated with the action of hormones, such as abscisic acid, SHP, ASR, GTE7 and SnRK2.7. The inference of a gene regulatory network, based on a dynamic Bayesian approach, among the genes differentially expressed in the transgenic receptacles at the white and red stages, identified the genes KAN1, DIV, ZFN2 and GTE7 as putative targets of FaMADS9. A MADS9‐specific CArG box was identified in the promoters of these genes.

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Section: Discussionmentioning

confidence: 99%

Section: Metabolic Changes In the Receptacles Of Famads9‐silenced Linmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Characterizing the involvement of FaMADS9 in the regulation of strawberry fruit receptacle development

Vallarino

Merchante

Sánchez-Sevilla

et al. 2019

Plant Biotechnology Journal

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“…However, among the largest and most diverse gene families, the TCP gene family has not been systematically identified in the strawberry genome. To date, only the strawberry FaTCP11 gene has been shown to play a role in ripening and in the regulation of flavan-3-ols synthesis (Pillet et al, 2015). …”

Section: Introductionmentioning

confidence: 99%

Identification and Transcript Analysis of the TCP Transcription Factors in the Diploid Woodland Strawberry Fragaria vesca

et al. 2016

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Plant-specific TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL FACTORS (TCP) transcription factors play versatile functions in multiple processes of plant growth and development. However, no systematic study has been performed in strawberry. In this study, 19 FvTCP genes were identified in the diploid woodland strawberry (Fragaria vesca) accession Heilongjiang-3. Phylogenetic analysis suggested that the FvTCP genes were classified into two main classes, with the second class further divided into two subclasses, which was supported by the exon-intron organizations and the conserved motif structures. Promoter analysis revealed various cis-acting elements related to growth and development, hormone and/or stress responses. We analyzed FvTCP gene transcript accumulation patterns in different tissues and fruit developmental stages. Among them, 12 FvTCP genes exhibited distinct tissue-specific transcript accumulation patterns. Eleven FvTCP genes were down-regulated in different fruit developmental stages, while five FvTCP genes were up-regulated. Transcripts of FvTCP genes also varied with different subcultural propagation periods and were induced by hormone treatments and biotic and abiotic stresses. Subcellular localization analysis showed that six FvTCP-GFP fusion proteins showed distinct localizations in Arabidopsis mesophyll protoplasts. Notably, transient over-expression of FvTCP9 in strawberry fruits dramatically affected the expression of a series of genes implicated in fruit development and ripening. Taken together, the present study may provide the basis for functional studies to reveal the role of this gene family in strawberry growth and development.

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Current Status of Octoploid Strawberry (Fragaria × ananassa) Genome Study

Isobe

Shirasawa

Nagano

et al. 2018

Compendium of Plant Genomes

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

Abstract: HighlightThis work in strawberry fruit predicts new genes relevant to a key metabolic pathway using correlation analysis, and then demonstrates their function in a rapid and effective transient assay.

Cited by 95 publications

References 30 publications

Characterizing the involvement of FaMADS9 in the regulation of strawberry fruit receptacle development

Characterizing the involvement of FaMADS9 in the regulation of strawberry fruit receptacle development

Identification and Transcript Analysis of the TCP Transcription Factors in the Diploid Woodland Strawberry Fragaria vesca

Current Status of Octoploid Strawberry (Fragaria × ananassa) Genome Study

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