Grape@GnpIS: Overview of the GnpIS grape genomics and genetics integrative resource

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HAL Id: hal-02741780

https://hal.inrae.fr/hal-02741780

Submitted on 3 Jun 2020

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Grape@GnpIS: Overview of the GnpIS grape genomics

and genetics integrative resource

Nacer Mohellibi, Nathalie Choisne, Aminah Keliet, Daphné Verdelet,

Françoise Alfama, Guillaume Merceron, Célia Michotey, Amandine Launay,

Thomas Letellier, Raphaël Flores, et al.

To cite this version:

Nacer Mohellibi, Nathalie Choisne, Aminah Keliet, Daphné Verdelet, Françoise Alfama, et al.. Grape@GnpIS: Overview of the GnpIS grape genomics and genetics integrative resource. 23. Plant and Animal Genome (PAG XXIII), Jan 2015, San Diego, Californie, United States. pp.24 slides. �hal-02741780�

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A L I M E N T A T I O N

A G R I C U L T U R E

E N V I R O N N E M E N T

Grape@GnpIS

Overview of the GnpIS Grape Genomics &

Genetics Integrative Resource

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ABOUT URGI

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Nacer Mohellibi

A bioinformatic plateform for crop

improvement

Genome

• Annotation

• Transcriptome

• SNP / Structural variant

Genetics

• Genetic maps

• Genetic markers

• Genetic resources

Phenotypes

• GxE

• QTL maps

• GWAS

URGI pipelines

Data & tools

URGI DB

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GnpIS Overview

Transversal portal

Biomart

Galaxy

Thematic portals

Global

search

GrapeMine

genome

maps

taxonomy

polymorphisms

phenotypes

Genetic resources

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Nacer Mohellibi

Transversal portal -

quicksearch

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Transversal portal

Biomart & Galaxy

Integration of Genomic and Genetics data for

Vitis markers in chr. 18

Import and

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Nacer Mohellibi

Genome

Vitis 8X

& 12X

(annotations

Genoscope

and CRIBI)

Genetic

Resources

10,459 Vitis

accessions

Phenotyping

1tria

l

Sequencing

Metadata & Files

Resequencing runs:

2 public / 13 private

Genetic Maps & Markers

27 Vitis genetic maps

Polymorphism

(genotypes of

>1100 accessions for > 14000

markers)

Thematic portals

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1 Workflow / 2 use cases

Phenotype

Accession

Variations

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Nacer Mohellibi

Use case 1: Zoom on a gene in

Flb Locus

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Vitis 12X Genome Browser

Vitis 12X.0 Generic Genome Browser @ URGI:

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Nacer Mohellibi

SNP details

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Sequence variations of the

locus

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Nacer Mohellibi

Resequencing batch

genotypes summary

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Use case 2: Enter by genome

coordinates

GrapeMine:

http://urgi.versailles.inra.fr/GrapeMine/begin.do

More details on Intermine functionnalities

Wheat3BMine Poster #654: Letellier T. et al.

and computer demo: January 13th 11:00 am

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Nacer Mohellibi

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Genes,

transcript

s, ORFs

SNPs

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Nacer Mohellibi

Zoom on a SNP

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List of the species concerned

by this marker

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Nacer Mohellibi

Diversity in V. vinifera in the chr18:

700K-800k region (1)

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Diversity in V. vinifera in the chr18:

700K-800k region (2)

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Nacer Mohellibi

Prospects

• Jbrowse based on the Vitis12X.2 assembly

Learn more about this assembly:

https://urgi.versailles.inra.fr/Species/Vitis/Data-Sequences/Genome-sequences

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Available soon: Vitis GWAS

data

More details on

GnpAsso:

Poster #1128

Computer demo

January 13th 10:30 am

GnpIS Genetic Association form:

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Acknowledgments

• URGI TEAM

• INRA PARTNERS

INRA EPGV, INRA AGAP,

INRA URGV…

• PROJECT PARTNERS

Grapereseq, Muscares,

SNPGrapeMap…

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THANK YOU FOR YOUR

ATTENTION!