The Grape Gene Reference Catalogue as a Standard Resource for Gene Selection and Genetic Improvement

Navarro-Payá, David; Santiago, Antonio; Orduña, Luis; Zhang, Chen; Amato, Alessandra; D’Incà, Erica; Fattorini, Chiara; Pezzotti, Mario; Tornielli, Giovanni Battista; Zenoni, Sara; Rustenholz, Camille; Matus, José Tomás

doi:10.3389/fpls.2021.803977

Cited by 24 publications

(21 citation statements)

References 25 publications

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“…Most of the genes identified both by DAP‐Seq and co‐expression analyses had the MYB binding motifs identified within 5 kb upstream of TSSs. An overlap of these data with the grapevine reference gene catalogue v1.1 (Navarro‐Payá et al., 2022) available at Integrape (http://www.integrape.eu/index.php/resources/genomes/) revealed a considerable representation of secondary metabolism genes (all the provided gene symbols in this study are in accordance with the reference gene catalogue, v1.1).…”

Section: Resultssupporting

confidence: 70%

Direct regulation of shikimate, early phenylpropanoid, and stilbenoid pathways by Subgroup 2 R2R3‐MYBs in grapevine

Orduña

Navarro-Payá

et al. 2022

The Plant Journal

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The stilbenoid pathway is responsible for the production of resveratrol in grapevine (Vitis vinifera L.). A few transcription factors (TFs) have been identified as regulators of this pathway but the extent of this control has not been deeply studied. Here we show how DNA affinity purification sequencing (DAP-Seq) allows for the genome-wide TF-binding site interrogation in grape. We obtained 5190 and 4443 binding events assigned to 4041 and 3626 genes for MYB14 and MYB15, respectively (approximately 40% of peaks located within À10 kb of transcription start sites). DAP-Seq of MYB14/MYB15 was combined with aggregate gene co-expression networks (GCNs) built from more than 1400 transcriptomic datasets from leaves, fruits, and flowers to narrow down bound genes to a set of high confidence targets. The analysis of MYB14, MYB15, and MYB13, a third uncharacterized member of Subgroup 2 (S2), showed that in addition to the few previously known stilbene synthase (STS) targets, these regulators bind to 30 of 47 STS family genes. Moreover, all three MYBs bind to several PAL, C4H, and 4CL genes, in addition to shikimate pathway genes, the WRKY03 stilbenoid co-regulator and resveratrol-modifying gene candidates among which ROMT2-3 were validated enzymatically. A high proportion of DAP-Seq bound genes were induced in the activated transcriptomes of transient MYB15-overexpressing grapevine leaves, validating our methodological approach for delimiting TF targets. Overall, Subgroup 2 R2R3-MYBs appear to play a key role in binding and directly regulating several primary and secondary metabolic steps leading to an increased flux towards stilbenoid production. The integration of DAP-Seq and reciprocal GCNs offers a rapid framework for gene function characterization using genome-wide approaches in the context of non-model plant species and stands up as a valid first approach for identifying gene regulatory networks of specialized metabolism.

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Section: Resultssupporting

confidence: 70%

Direct regulation of shikimate, early phenylpropanoid, and stilbenoid pathways by Subgroup 2 R2R3‐MYBs in grapevine

Orduña

Navarro-Payá

et al. 2022

The Plant Journal

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“…The RNA-seq analysis was performed by IGA Tech (IGA Technology Services Srl, Udine, Italy), sequencing the libraries on paired-end 150-bp mode on NovaSeq 6000 (Illumina, San Diego, CA, USA), including base calling and demultiplexing, adapters masking, trimming, alignments on the reference genome (12xCHR v2.1), quality control (statistics on strandness of reads, on gene body coverage, on read distribution, and on insert size), and pairwise differential expression analysis. Functional annotations of genes were retrieved from the Integrape grapevine reference catalog ( Navarro-Payà et al., 2021 ).…”

Section: Methodsmentioning

confidence: 99%

Berry flavonoids are differently modulated by timing and intensities of water deficit in Vitis vinifera L. cv. Sangiovese

et al. 2022

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In this work, we tested the effect of different regulated deficit irrigation (RDI) regimes on berry flavonoid content and its relative biosynthetic pathways. Vines were subjected to six irrigation regimes over two consecutive years: a) full irrigation during the entire irrigation period (FI); b) moderate (RDI-1M) or c) severe (RDI-1S) water deficit between berry pea-size and veraison; d) severe water deficit during the lag-phase (RDI-LS); and e) moderate (RDI-2M) or f) severe (RDI-2S) water deficit from veraison through harvest. Berries from both RDI-1 treatments showed the highest accumulation of anthocyanins, upregulating the expression of many genes of the flavonoid pathway since the beginning of veraison until harvest, far after the water deficit was released. Although to a lesser degree than RDI-1, both post-veraison water deficit treatments increased anthocyanin concentration, particularly those of the tri-substituted forms, overexpressing the F3′5′H hydroxylases. The moderate deficit irrigation treatments enhanced anthocyanin accumulation with respect to the severe ones regardless of the period when they were applied (pre- or post-veraison). The water deficit imposed during the lag-phase downregulated many genes throughout the flavonoid pathway, showing a slight reduction in anthocyanin accumulation. The measurements of cluster temperature and light exposure highlighted that under deficit irrigation conditions, the effects induced by water stress prevailed over that of light and temperature in regulating anthocyanin biosynthesis. Flavonol concentration was higher in RDI-1S berries due to the upregulation of the flavonol synthases and the flavonol-3-O-glycosyltransferases. In this case, the higher cluster light exposure induced by water deficit in RDI-1S berries had a major role in flavonol accumulation. We conclude that the timing and intensity of water stress strongly regulate the berry flavonoid accumulation and that proper management of deficit irrigation can modulate the phenylpropanoid and flavonoid pathways.

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“…Another identified genes, all of them up regulated in PV with and with cis -eQTL associations detected in red cultivars, were Vitvi12g02292, Vitvi18g00307 and Vitvi08g01770. These genes were annotated such as ROMT (Resveratrol O -methyltransferase), flavonol synthase (FLS) and terpene synthase, respectively, by the Integrape Catalogue 2.3 47 . FLS is a key enzyme in flavonol biosynthesis that control the last step, from dihydroflavonol to flavonol 48 .…”

Section: Discussionmentioning

confidence: 99%

Bioinformatic approach for the discovery of cis-eQTL signals during fruit ripening of a woody species as grape (Vitis vinifera L.)

Martínez-García

Mas-Gómez

Wegrzyn

et al. 2022

Sci Rep

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Expression quantitative trait loci (eQTLs) are associations between genetic variants, such as Single Nucleotide Polymorphisms (SNPs), and gene expression. eQTLs are an important tool to understand the genetic variance of gene expression of complex phenotypes. eQTLs analyses are common in biomedical models but are scarce in woody crop species such as fruit trees or grapes. In this study, a comprehensive bioinformatic analysis was conducted leveraging with expression data from two different growth stages, around ripening onset, of 10 genotypes of grape (Vitis vinifera L.). A total of 2170 cis-eQTL were identified in 212 gene modulated at ripening onset. The 48% of these DEGs have a known function. Among the annotated protein-coding genes, terpene synthase, auxin-regulatory factors, GRFS, ANK_REP_REGION domain-containing protein, Kinesin motor domain-containing protein and flavonol synthase were noted. This new inventory of cis-eQTLs influencing gene expression during fruit ripening will be an important resource to examine variation for this trait and will help to elucidate the complex genetic architecture underlying this process in grape.

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The Grape Gene Reference Catalogue as a Standard Resource for Gene Selection and Genetic Improvement

Cited by 24 publications

References 25 publications

Direct regulation of shikimate, early phenylpropanoid, and stilbenoid pathways by Subgroup 2 R2R3‐MYBs in grapevine

Direct regulation of shikimate, early phenylpropanoid, and stilbenoid pathways by Subgroup 2 R2R3‐MYBs in grapevine

Berry flavonoids are differently modulated by timing and intensities of water deficit in Vitis vinifera L. cv. Sangiovese

Bioinformatic approach for the discovery of cis-eQTL signals during fruit ripening of a woody species as grape (Vitis vinifera L.)

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