# Updates on the WheatIS tools

Michael Alaux

► To cite this version:

Michael Alaux. Updates on the WheatIS tools. PAG XXVI - Plant and Animal Genome Conference, Jan 2018, San Diego, United States. [hal-04536526](https://hal.inrae.fr/hal-04536526)

HAL Id: hal-04536526

https://hal.inrae.fr/hal-04536526

Submitted on 8 Apr 2024

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# Updates on the WheatIS tools

Michael Alaux

► To cite this version:

Michael Alaux. Updates on the WheatIS tools. PAG XXVI - Plant and Animal Genome Conference, Jan 2018, San Diego, United States. hal-04536526

HAL Id: hal-04536526

https://hal.inrae.fr/hal-04536526v1

Submitted on 8 Apr 2024

HAL is a multi-disciplinary open access
archive for the deposit and dissemination of sci-
entific research documents, whether they are pub-
lished or not. The documents may come from
teaching and research institutions in France or
abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
émanant des établissements d'enseignement et de
recherche français ou étrangers, des laboratoires
publics ou privés.

<figure><img src="image_2.png" /></figure>

Distributed under a Creative Commons Attribution 4.0 International License
# Update on the WheatIS tools

Michael Alaux

<figure><img src="image_2.png" /></figure>

<figure><img src="image_3.png" /></figure>

<figure><img src="image_4.png" /></figure>

<figure><img src="image_5.png" /></figure>

<figure><img src="image_6.png" /></figure>
# Update on the WheatIS tools

Michael Alaux

<figure><img src="image_3.png" /></figure>

<figure><img src="image_4.png" /></figure>

<figure><img src="image_5.png" /></figure>

<figure><img src="image_6.png" /></figure>

<figure><img src="image_7.png" /></figure>
# WheatIS data discovery tool

<figure><img src="image_7.png" /></figure>
# WheatIS data discovery tool

<figure><img src="image_8.png" /></figure>
SolR search

About

Collaborators

Search

Data Standards

Submit Data

Tools

Links

WheatIS Nodes

WheatIS

@ PRATT J.C. / INRA

<figure><img src="image_8.png" /></figure>

About

This project aims at building an International Wheat Information System, called hereafter WheatIS, to support the wheat research community. The main objective is to provide a single-access web base system to access to the available data resources and bioinformatics tools.

This project is based on the principles listed below:

* Collective building of the WheatIS to better respond to the needs of the international wheat community;

* Incremental implementation to offer rapidly an operational information system;

* Emphasis on Quality Assurance to serve as a framework for an approach with incremental implementation;

* Promotion of an open-access model for data exchange;

* Reliance on a distributed system;

* Use of Virtual Machine and Cloud Computing technologies to facilitate sharing data and tools;

* Promotion of the visibility of each participating platform to contribute to their sustainability.

If you have questions regarding this Wheat Information System project, please contact: wheatis-contact@wheatis.org

Tweets

Follow

<figure><img src="image_9.png" /></figure>

WheatIS

@WheatIS

9 Dec

<figure><img src="image_10.png" /></figure>

WheatIS talk at next PAG conference. Book your agenda
pag.confex.com/pag/xxiv/meeti...

Expand

<figure><img src="image_11.png" /></figure>

Michael Alaux

@michaelalaux

4 Dec

Program of IWGSC Standards & Protocols workshop at PAG 2016
wheatgenome.org/Meetings-and-W... via

@wheatgenome

t Retweeted by WheatIS

Expand

<figure><img src="image_12.png" /></figure>

Michael Alaux

@michaelalaux

4 Dec

Next talk at #PAGXXIV about the IWGSC Sequence Repository

pag.confex.com/pag/xxiv/webpr...

@wheatgenome @inra_urgi @fredChoulet

t Retweeted by WheatIS

Expand

<figure><img src="image_13.png" /></figure>

Anthony Hall

@Ajwhall

9 Dec

Find out more about UK iplant

@iPlantCollab at @joyn #PAGXXIV

pag.confex.com/pag/xxiv/meeti...

Tweet to @WheatIS

http://www.wheatis.org/
About

Collaborators

Search

Data Standards

Submit Data

Tools

Links

WheatIS Nodes

WheatIS

@ PRATT J.C. / INRA

<figure><img src="image_9.png" /></figure>

About

This project aims at building an International Wheat Information System, called hereafter WheatIS, to support the wheat research community. The main objective is to provide a single-access web base system to access to the available data resources and bioinformatics tools.

This project is based on the principles listed below:

* Collective building of the WheatIS to better respond to the needs of the international wheat community;

* Incremental implementation to offer rapidly an operational information system;

* Emphasis on Quality Assurance to serve as a framework for an approach with incremental implementation;

* Promotion of an open-access model for data exchange;

* Reliance on a distributed system;

* Use of Virtual Machine and Cloud Computing technologies to facilitate sharing data and tools;

* Promotion of the visibility of each participating platform to contribute to their sustainability.

If you have questions regarding this Wheat Information System project, please contact: wheatis-contact@wheatis.org

Tweets

Follow

<figure><img src="image_10.png" /></figure>

WheatIS

@WheatIS

9 Dec

<figure><img src="image_11.png" /></figure>

WheatIS talk at next PAG conference. Book your agenda
pag.confex.com/pag/xxiv/meeti...

Expand

<figure><img src="image_12.png" /></figure>

Michael Alaux

@michaelalaux

4 Dec

Program of IWGSC Standards & Protocols workshop at PAG 2016
wheatgenome.org/Meetings-and-W... via

@wheatgenome
# Retweeted by WheatIS

4 Dec

Expand

<figure><img src="image_13.png" /></figure>

Michael Alaux

@michaelalaux

4 Dec

Next talk at #PAGXXIV about the IWGSC Sequence Repository

pag.confex.com/pag/xxiv/webpr...

@wheatgenome @inra_urgi @fredChoulet

4 Dec

Expand

<figure><img src="image_14.png" /></figure>

Anthony Hall

@Ajwhall

9 Dec

Find out more about UK iplant

@iPlantCollab at @joyn #PAGXXIV

pag.confex.com/pag/xxiv/meeti...

4 Dec
## WheatIS

<figure><img src="image_14.png" /></figure>

### Search

### How To Join

### About

### WheatIS nodes:

**transPlant-MIPS (UP):**

* CrowsNest: 13324

**transPlant-IPK (UP):**

* CR-EST: 199220

* GEBIS: 51814

* MetaCrop: 355

**transPlant-EBI (UP):**

* Ensembl Plants: 218282

**UWA (UP):**

* Wheat Pangenome: 167167

**GrainGenes (UP):**

* GrainGenes: 548

**Gramene-WheatIS (UP):**

* Gramene: 229851

**transplant-IPGPAS (UP):**

* PlantPhenoDB: 2

**T3 (UP):**

* Triticeae Toolbox: 185781

**CIMMYT (DOWN - error: 401)**

**URGI (UP):**

* IWGSC@GnpIS: 2301763

* GnpIS: 57998

* WheatIS File Repository: 6

<figure><img src="image_15.png" /></figure>

Search in all WheatIS nodes...

<figure><img src="image_16.png" /></figure>

Examples: fhb, wmc430, Triticum, TRAES3BF001000010CFD
## WheatIS

<figure><img src="image_15.png" /></figure>

Search

How To Join

About

**WheatIS nodes:**

**transPlant-MIPS (UP):**

* CrowsNest: 13324

**transPlant-IPK (UP):**

* CR-EST: 199220

* GEBIS: 51814

* MetaCrop: 355

**transPlant-EBI (UP):**

* Ensembl Plants: 218282

**UWA (UP):**

* Wheat Pangenome: 167167

**GrainGenes (UP):**

* GrainGenes: 548

**Gramene-WheatIS (UP):**

* Gramene: 229851

**transplant-IPGPAS (UP):**

* PlantPhenoDB: 2

**T3 (UP):**

* Triticeae Toolbox: 185781

**CIMMYT (DOWN - error: 401)**

**URGI (UP):**

* IWGSC@GnpIS: 2301763

* GnpIS: 57998

* WheatIS File Repository: 6

<figure><img src="image_16.png" /></figure>

Search in all WheatIS nodes...

<figure><img src="image_17.png" /></figure>

Examples: fhb, wmc430, Triticum, TRAES3BF001000010CFD
New data in 2017

transPlant-MIPS (UP):

○ CrowsNest: 13324

transPlant-IPK (UP):

○ CR-EST: 199220

○ GEBIS: 51814

○ MetaCrop: 355

transPlant-EBI (UP):

○ Ensembl Plants: 218282

transplant-IPGPAS (UP):

○ PlantPhenoDB: 2

transplant-IPGPAS (UP):

○ PlantPhenoDB: 2

T3 (UP):

○ Triticeae Toolbox: 185781

CIMMYT (UP):

- CIMMYT Dspace: 918

- CIMMYT dataverse: 37

UWA (UP):

○ Wheat Pangenome: 167167 GBrowse

GrainGenes (UP):

○ GrainGenes: 548 QTLs

Gramene-WheatIS (UP):

○ Gramene: 229851 Genes, GO, pathways, etc.
# New data in 2017

**transPlant-MIPS (UP):**

* CrowsNest: 13324

**transPlant-IPK (UP):**

* CR-EST: 199220

* GEBIS: 51814

* MetaCrop: 355

**transPlant-EBI (UP):**

* Ensembl Plants: 218282

**transplant-IPGPAS (UP):**

* PlantPhenoDB: 2

**transplant-IPGPAS (UP):**

* PlantPhenoDB: 2

**T3 (UP):**

* Triticeae Toolbox: 185781

**CIMMYT (UP):**

- CIMMYT Dspace: 918

- CIMMYT dataverse: 37

**UWA (UP):**

* Wheat Pangenome: 167167 GBrowse

**GrainGenes (UP):**

* GrainGenes: 548 QTLs

**Gramene-WheatIS (UP):**

* Gramene: 229851 Genes, GO, pathways, etc.
# UWA Wheat pangenome

<table><thead><tr><th>ID</th><th>Source</th><th>Type</th><th>Taxon</th><th>Description</th></tr></thead><tbody><tr><td>3D_g3.t1</td><td>Wheat<br>Pangenome</td><td>SEQUENCE<br>FEATURE</td><td>Triticum<br>aestivum</td><td>SEQUENCE FEATURE, Wheat Pangenome, 3D_g3.t1, Presence=1.00, Transcription factor RAX2 n:1<br>Tax: Aegilops tauschii RepID: M8D4V6_AEGTA, Triticum aestivum, mRNA, 3D_g3.t1</td></tr><tr><td>3D_g7.t1</td><td>Wheat<br>Pangenome</td><td>SEQUENCE<br>FEATURE</td><td>Triticum<br>aestivum</td><td>SEQUENCE FEATURE, Wheat Pangenome, 3D_g7.t1, Presence=1.00, Uncharacterized protein n:8<br>Tax: Triticæae RepID: A0A077S4R6_WHEAT, Triticum aestivum, mRNA, 3D_g7.t1</td></tr><tr><td>3D_g9.t1</td><td>Wheat<br>Pangenome</td><td>SEQUENCE<br>FEATURE</td><td>Triticum<br>aestivum</td><td>SEQUENCE FEATURE, Wheat Pangenome, 3D_g9.t1, Presence=1.00, Uncharacterized protein n:1<br>Tax: Triticum aestivum RepID: A0A080YUN9_WHEAT, Triticum aestivum, mRNA, 3D_g9.t1</td></tr><tr><td>3D_g9.t2</td><td>Wheat<br>Pangenome</td><td>SEQUENCE<br>FEATURE</td><td>Triticum<br>aestivum</td><td>SEQUENCE FEATURE, Wheat Pangenome, 3D_g9.t2, Presence=1.00, Uncharacterized protein n:1<br>Tax: Triticum aestivum RepID: A0A080YUN9_WHEAT, Triticum aestivum, mRNA, 3D_g9.t2</td></tr><tr><td>3D_g11.t1</td><td>Wheat<br>Pangenome</td><td>SEQUENCE<br>FEATURE</td><td>Triticum<br>aestivum</td><td>SEQUENCE FEATURE, Wheat Pangenome, 3D_g11.t1, Presence=1.00, No Hits, Triticum aestivum, mRNA, 3D_g11.t1</td></tr><tr><td>3D_g12.t1</td><td>Wheat<br>Pangenome</td><td>SEQUENCE<br>FEATURE</td><td>Triticum<br>aestivum</td><td>SEQUENCE FEATURE, Wheat Pangenome, 3D_g12.t1, Presence=1.00, Uncharacterized protein n:5<br>Tax: Triticæae RepID: W5D2X2_WHEAT, Triticum aestivum, mRNA, 3D_g12.t1</td></tr><tr><td>3D_g15.t1</td><td>Wheat<br>Pangenome</td><td>SEQUENCE<br>FEATURE</td><td>Triticum<br>aestivum</td><td>SEQUENCE FEATURE, Wheat Pangenome, 3D_g15.t1, Presence=1.00, Uncharacterized protein n:1<br>Tax: Aegilops tauschii RepID: R7WFP4_AEGTA, Triticum aestivum, mRNA, 3D_g15.t1</td></tr><tr><td>3D_g21.t1</td><td>Wheat<br>Pangenome</td><td>SEQUENCE<br>FEATURE</td><td>Triticum<br>aestivum</td><td>SEQUENCE FEATURE, Wheat Pangenome, 3D_g21.t1, Presence=1.00,<br>Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 2 n:2<br>Tax: Triticæae RepID: N1QQK4_AEGTA, Triticum aestivum, mRNA, 3D_g21.t1</td></tr><tr><td>3D_g23.t1</td><td>Wheat<br>Pangenome</td><td>SEQUENCE<br>FEATURE</td><td>Triticum<br>aestivum</td><td>SEQUENCE FEATURE, Wheat Pangenome, 3D_g23.t1, Presence=1.00, GDSL esterase/lipase n:1<br>Tax: Aegilops tauschii RepID: M8BY45_AEGTA, Triticum aestivum, mRNA, 3D_g23.t1</td></tr><tr><td>3D_g27.t1</td><td>Wheat<br>Pangenome</td><td>SEQUENCE<br>FEATURE</td><td>Triticum<br>aestivum</td><td>SEQUENCE FEATURE, Wheat Pangenome, 3D_g27.t1, Presence=1.00, Uncharacterized protein n:8<br>Tax: Triticæae RepID: M0ZDK5_HORVD, Triticum aestivum, mRNA, 3D_g27.t1</td></tr></tbody></table>

<figure><img src="image_17.png" /></figure>
UWA Wheat pangenome

<table><thead><tr><th>ID</th><th>Source</th><th>Type</th><th>Taxon</th><th>Description</th></tr></thead><tbody><tr><td>3D_g3.t1</td><td>Wheat<br>Pangenome</td><td>SEQUENCE<br>FEATURE</td><td>Triticum<br>aestivum</td><td>SEQUENCE FEATURE, Wheat Pangenome, 3D_g3.t1, Presence=1.00, Transcription factor RAX2 n:1<br>Tax:Aegilops tauschii RepID:M8D4V6_AEGTA, Triticum aestivum, mRNA, 3D_g3.t1</td></tr><tr><td>3D_g7.t1</td><td>Wheat<br>Pangenome</td><td>SEQUENCE<br>FEATURE</td><td>Triticum<br>aestivum</td><td>SEQUENCE FEATURE, Wheat Pangenome, 3D_g7.t1, Presence=1.00, Uncharacterized protein n:8<br>Tax:Triticaceae RepID:A0A077S4R6_WHEAT, Triticum aestivum, mRNA, 3D_g7.t1</td></tr><tr><td>3D_g9.t1</td><td>Wheat<br>Pangenome</td><td>SEQUENCE<br>FEATURE</td><td>Triticum<br>aestivum</td><td>SEQUENCE FEATURE, Wheat Pangenome, 3D_g9.t1, Presence=1.00, Uncharacterized protein n:1<br>Tax:Triticum aestivum RepID:A0A080YUN9_WHEAT, Triticum aestivum, mRNA, 3D_g9.t1</td></tr><tr><td>3D_g9.t2</td><td>Wheat<br>Pangenome</td><td>SEQUENCE<br>FEATURE</td><td>Triticum<br>aestivum</td><td>SEQUENCE FEATURE, Wheat Pangenome, 3D_g9.t2, Presence=1.00, Uncharacterized protein n:1<br>Tax:Triticum aestivum RepID:A0A080YUN9_WHEAT, Triticum aestivum, mRNA, 3D_g9.t2</td></tr><tr><td>3D_g11.t1</td><td>Wheat<br>Pangenome</td><td>SEQUENCE<br>FEATURE</td><td>Triticum<br>aestivum</td><td>SEQUENCE FEATURE, Wheat Pangenome, 3D_g11.t1, Presence=1.00, No Hits, Triticum aestivum,<br>mRNA, 3D_g11.t1</td></tr><tr><td>3D_g12.t1</td><td>Wheat<br>Pangenome</td><td>SEQUENCE<br>FEATURE</td><td>Triticum<br>aestivum</td><td>SEQUENCE FEATURE, Wheat Pangenome, 3D_g12.t1, Presence=1.00, Uncharacterized protein n:5<br>Tax:Triticaceae RepID:W5D2X2_WHEAT, Triticum aestivum, mRNA, 3D_g12.t1</td></tr><tr><td>3D_g15.t1</td><td>Wheat<br>Pangenome</td><td>SEQUENCE<br>FEATURE</td><td>Triticum<br>aestivum</td><td>SEQUENCE FEATURE, Wheat Pangenome, 3D_g15.t1, Presence=1.00, Uncharacterized protein n:1<br>Tax:Aegilops tauschii RepID:R7WFP4_AEGTA, Triticum aestivum, mRNA, 3D_g15.t1</td></tr><tr><td>3D_g21.t1</td><td>Wheat<br>Pangenome</td><td>SEQUENCE<br>FEATURE</td><td>Triticum<br>aestivum</td><td>SEQUENCE FEATURE, Wheat Pangenome, 3D_g21.t1, Presence=1.00,<br>Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 2 n:2<br>Tax:Triticaceae RepID:N1QQK4_AEGTA, Triticum aestivum, mRNA, 3D_g21.t1</td></tr><tr><td>3D_g23.t1</td><td>Wheat<br>Pangenome</td><td>SEQUENCE<br>FEATURE</td><td>Triticum<br>aestivum</td><td>SEQUENCE FEATURE, Wheat Pangenome, 3D_g23.t1, Presence=1.00, GDSL esterase/lipase n:1<br>Tax:Aegilops tauschii RepID:M8BY45_AEGTA, Triticum aestivum, mRNA, 3D_g23.t1</td></tr><tr><td>3D_g27.t1</td><td>Wheat<br>Pangenome</td><td>SEQUENCE<br>FEATURE</td><td>Triticum<br>aestivum</td><td>SEQUENCE FEATURE, Wheat Pangenome, 3D_g27.t1, Presence=1.00, Uncharacterized protein n:8<br>Tax:Triticaceae RepID:M0ZDK5_HORVD, Triticum aestivum, mRNA, 3D_g27.t1</td></tr></tbody></table>

<figure><img src="image_18.png" /></figure>
# Graingenes QTLs

<table><thead><tr><th>ID</th><th>Source</th><th>Type</th><th>Taxon</th><th>Description</th></tr></thead><tbody><tr><td>QAmc.ocs-4A.1</td><td>GrainGenes</td><td>QTL</td><td>Triticum aestivum</td><td>QTL, GrainGenes, QAmc.ocs-4A.1, Amylose content; Identification of genetic loci affecting amylose content and agronomic traits on chromosome 4A of wheat, Triticum aestivum</td></tr><tr><td>QCc.mst-2D</td><td>GrainGenes</td><td>QTL</td><td>Triticum aestivum</td><td>QTL, GrainGenes, QCc.mst-2D, Wheat stem sawfly attraction; Identification of Novel QTL for Sawfly Resistance in Wheat, Triticum aestivum</td></tr><tr><td>QCc.mst-4A</td><td>GrainGenes</td><td>QTL</td><td>Triticum aestivum</td><td>QTL, GrainGenes, QCc.mst-4A, Wheat stem sawfly attraction; Identification of Novel QTL for Sawfly Resistance in Wheat, Triticum aestivum</td></tr><tr><td>QCkf.ucw-7B</td><td>GrainGenes</td><td>QTL</td><td>Triticum turgidum ssp. durum</td><td>QTL, GrainGenes, QCkf.ucw-7B, Cooked firmness; QTL analysis of pasta quality using a composite microsatellite and SNP map of durum wheat, Triticum turgidum ssp. durum</td></tr><tr><td>QCol.wak-2B</td><td>GrainGenes</td><td>QTL</td><td>Triticum aestivum</td><td>QTL, GrainGenes, QCol.wak-2B, Leaf color/glaucousness; Identifying QTL for high-temperature adult-plant resistance to stripe rust (Puccinia striformis f. sp. tritici) in the spring wheat (Triticum aestivum L.) cultivar...</td></tr><tr><td>QDon.crc-3B</td><td>GrainGenes</td><td>QTL</td><td>Triticum aestivum</td><td>QTL, GrainGenes, QDon.crc-3B, Deoxynivalenol (DON) accumulation; Molecular mapping of novel genes controlling Fusarium head blight resistance and deoxynivalenol accumulation in spring wheat, Triticum aestivum</td></tr><tr><td>QDon.crc-5A</td><td>GrainGenes</td><td>QTL</td><td>Triticum aestivum</td><td>QTL, GrainGenes, QDon.crc-5A, Deoxynivalenol (DON) accumulation; Molecular mapping of novel genes controlling Fusarium head blight resistance and deoxynivalenol accumulation in spring wheat, Triticum aestivum</td></tr></tbody></table>

## GrainGenes QTL Report: QAmc.ocs-4A.1

[Printable Version] [Submit comment/correction]

<table><tr><td>QTL</td><td>QAmc.ocs-4A.1</td></tr><tr><td>Trait Affected</td><td>Amylose content</td></tr><tr><td>Ontology</td><td>TO:0000196 Planteome amylose content</td></tr><tr><td>Chromosome</td><td>4AS</td></tr><tr><td>Positive Significant Marker</td><td>Xbcd1738-4A<br/>Xcdo1387-4A</td></tr><tr><td>Species</td><td>Triticum aestivum</td></tr><tr><td>Reference</td><td>Araki E et al. (1999) Identification of genetic loci affecting amylose content in Triticum aestivum</td></tr></table>

Map based on quantitative trait

## GrainGenes Locus Report: Xbcd1738-4A

[Printable Version] [Submit comment/correction]

**Locus** Xbcd1738-4A [Marker Report]

**Type** RFLP

**Chromosome** 4A

**Chromosome Arm** 4AS

**Map**
Ta-Synthetic/Opata-4A 19.5
Ta-Synthetic/Opata-BARC-4A 18.4
Ta-Synthetic/Opata-GPW-4A 26.5

[Show Nearby Loci]

**In QTL** QAmc.ocs-4A.1
[Show all 6]

**Map Data**
Wheat, Synthetic x Opata [GBrowser]
Wheat, Synthetic x Opata, BARC
Wheat, Synthetic x Opata, GPW

**Probe** BCD1738

**Homology** CAB61839.1 e-value: 9e-37 (AJ242803) putative serine/threonine phosphatase type 2c [Sporobolus stapfianus]

**Image** BCD1738 SO autoradiogram
# Graingenes QTLs

<table><thead><tr><th>ID</th><th>Source</th><th>Type</th><th>Taxon</th><th>Description</th></tr></thead><tbody><tr><td>QAmc.ocs-4A.1</td><td>GrainGenes</td><td>QTL</td><td>Triticum aestivum</td><td>QTL, GrainGenes, QAmc.ocs-4A.1, Amylose content; Identification of genetic loci affecting amylose content and agronomic traits on chromosome 4A of wheat, Triticum aestivum</td></tr><tr><td>QCc.mst-2D</td><td>GrainGenes</td><td>QTL</td><td>Triticum aestivum</td><td>QTL, GrainGenes, QCc.mst-2D, Wheat stem sawfly attraction; Identification of Novel QTL for Sawfly Resistance in Wheat, Triticum aestivum</td></tr><tr><td>QCc.mst-4A</td><td>GrainGenes</td><td>QTL</td><td>Triticum aestivum</td><td>QTL, GrainGenes, QCc.mst-4A, Wheat stem sawfly attraction; Identification of Novel QTL for Sawfly Resistance in Wheat, Triticum aestivum</td></tr><tr><td>QCkf.ucw-7B</td><td>GrainGenes</td><td>QTL</td><td>Triticum turgidum ssp. durum</td><td>QTL, GrainGenes, QCkf.ucw-7B, Cooked firmness; QTL analysis of pasta quality using a composite microsatellite and SNP map of durum wheat, Triticum turgidum ssp. durum</td></tr><tr><td>QCol.wak-2B</td><td>GrainGenes</td><td>QTL</td><td>Triticum aestivum</td><td>QTL, GrainGenes, QCol.wak-2B, Leaf color/glaucousness; Identifying QTL for high-temperature adult-plant resistance to stripe rust (Puccinia striformis f. sp. tritici) in the spring wheat (Triticum aestivum L.) cultivar...</td></tr><tr><td>QDon.crc-3B</td><td>GrainGenes</td><td>QTL</td><td>Triticum aestivum</td><td>QTL, GrainGenes, QDon.crc-3B, Deoxynivalenol (DON) accumulation; Molecular mapping of novel genes controlling Fusarium head blight resistance and deoxynivalenol accumulation in spring wheat, Triticum aestivum</td></tr><tr><td>QDon.crc-5A</td><td>GrainGenes</td><td>QTL</td><td>Triticum aestivum</td><td>QTL, GrainGenes, QDon.crc-5A, Deoxynivalenol (DON) accumulation; Molecular mapping of novel genes controlling Fusarium head blight resistance and deoxynivalenol accumulation in spring wheat, Triticum aestivum</td></tr></tbody></table>

## GrainGenes QTL Report: QAmc.ocs-4A.1

[Printable Version] [Submit comment/correction]

<table><tr><td>QTL</td><td>QAmc.ocs-4A.1</td></tr><tr><td>Trait Affected</td><td>Amylose content</td></tr><tr><td>Ontology</td><td>TO:0000196 Planteome amylose content</td></tr><tr><td>Chromosome</td><td>4AS</td></tr><tr><td>Positive Significant Marker</td><td>Xbcd1738-4A<br/>Xcd1387-4A</td></tr><tr><td>Species</td><td>Triticum aestivum</td></tr><tr><td>Reference</td><td>Araki E et al. (1999) Identification of genetic loci affecting amylose content in Triticum aestivum</td></tr></table>

Map based on quantitative trait

## GrainGenes Locus Report: Xbcd1738-4A

[Printable Version] [Submit comment/correction]

**Locus** Xbcd1738-4A [ Marker Report ]

**Type** RFLP

**Chromosome** 4A

**Chromosome Arm** 4AS

**Map**
Ta-Synthetic/Opata-4A 19.5
Ta-Synthetic/Opata-BARC-4A 18.4
Ta-Synthetic/Opata-GPW-4A 26.5

[ Show Nearby Loci ]

**In QTL** QAmc.ocs-4A.1 [ Show all 6 ]

**Map Data**
Wheat, Synthetic x Opata [ GBrowser ]
Wheat, Synthetic x Opata, BARC
Wheat, Synthetic x Opata, GPW

**Probe** BCD1738

**Homology** CAB61839.1 e-value: 9e-37 (AJ242803) putative serine/threonine phosphatase type 2c [Sporobolus stapfianus]

**Image** BCD1738 SO autoradiogram
# Gramene

<table><thead><tr><th>ID</th><th>Source</th><th>Type</th><th>Taxon</th><th>Description</th></tr></thead><tbody><tr><td>1119260</td><td>Gramene</td><td>Pathway</td><td>Triticum aestivum, Triticum urartu, Brachypodium distachyon, Aegilops tauschii, Hordeum vulgare subsp. vulgare</td><td>Gramene, Pathway, 1119260, cardiolipin biosynthesis, Triticum aestivum, Triticum urartu, Brachypodium distachyon, Aegilops tauschii, Hordeum vulgare subsp. vulgare</td></tr><tr><td>1119261</td><td>Gramene</td><td>Pathway</td><td>Triticum aestivum, Triticum urartu, Brachypodium distachyon, Aegilops tauschii, Hordeum vulgare subsp. vulgare</td><td>Gramene, Pathway, 1119261, salicylate biosynthesis, Triticum aestivum, Triticum urartu, Brachypodium distachyon, Aegilops tauschii, Hordeum vulgare subsp. vulgare</td></tr><tr><td>1119262</td><td>Gramene</td><td>Pathway</td><td>Triticum aestivum, Triticum urartu, Brachypodium distachyon, Aegilops tauschii, Hordeum vulgare subsp. vulgare</td><td>Gramene, Pathway, 1119262, threonine biosynthesis from homoserine, Triticum aestivum, Triticum urartu, Brachypodium distachyon, Aegilops tauschii, Hordeum vulgare subsp. vulgare</td></tr></tbody></table>

1119263

Triticum
subsp.

1119265

aestivum,
vulgare

1119273

Triticum
subsp.

1119274

vulgare

1119276

vulgare

1119278

Brachypodium

1119281

vulgare

<figure><img src="image_18.png" /></figure>
# Gramene

<table><thead><tr><th>ID</th><th>Source</th><th>Type</th><th>Taxon</th><th>Description</th></tr></thead><tbody><tr><td>1119260</td><td>Gramene</td><td>Pathway</td><td>Triticum aestivum, Triticum urartu, Brachypodium distachyon, Aegilops tauschii, Hordeum vulgare subsp. vulgare</td><td>Gramene, Pathway, 1119260, cardiolipin biosynthesis, Triticum aestivum, Triticum urartu, Brachypodium distachyon, Aegilops tauschii, Hordeum vulgare subsp. vulgare</td></tr><tr><td>1119261</td><td>Gramene</td><td>Pathway</td><td>Triticum aestivum, Triticum urartu, Brachypodium distachyon, Aegilops tauschii, Hordeum vulgare subsp. vulgare</td><td>Gramene, Pathway, 1119261, salicylate biosynthesis, Triticum aestivum, Triticum urartu, Brachypodium distachyon, Aegilops tauschii, Hordeum vulgare subsp. vulgare</td></tr><tr><td>1119262</td><td>Gramene</td><td>Pathway</td><td>Triticum aestivum, Triticum urartu, Brachypodium distachyon, Aegilops tauschii, Hordeum vulgare subsp. vulgare</td><td>Gramene, Pathway, 1119262, threonine biosynthesis from homoserine, Triticum aestivum, Triticum urartu, Brachypodium distachyon, Aegilops tauschii, Hordeum vulgare subsp. vulgare</td></tr></tbody></table>

1119263

Triticum
subsp.

1119265

aestivum,
vulgare

1119273

Triticum
subsp.

1119274

vulgare

1119276

vulgare

1119278

Brachypodium

1119281

vulgare

<figure><img src="image_19.png" /></figure>
In progress at URGI

URGI (UP):

o IWGSC@GnplS: 23295514 New data from the IWGSC RefSeq v1.0

o GnplS: 58000

o OpenMinTeD: 3398 New data from publications

o WheatIS File Repository: 6
In progress at URGI

URGI (UP):

o IWGSC@GnplS: 23295514 New data from the IWGSC RefSeq v1.0

o GnplS: 58000

o OpenMinTeD: 3398 New data from publications

o WheatIS File Repository: 6
In progress at URGI

<table><thead><tr><th>ID</th><th>Source</th><th>Type</th><th>Taxon</th><th>Description</th></tr></thead><tbody><tr><td>JBrowse chr1A 100233074 100233167 miRNA</td><td>IWGSC@GnpIS</td><td>SEQUENCE FEATURE</td><td>Triticum aestivum</td><td>Start = 100233074 [...]</td></tr><tr><td>JBrowse chr1A 101106604 101106809 miRNA</td><td>IWGSC@GnpIS</td><td>SEQUENCE FEATURE</td><td>Triticum aestivum</td><td>Start = 101106604 [...]</td></tr><tr><td>JBrowse chr1A 10158696 10158807 miRNA</td><td>IWGSC@GnpIS</td><td>SEQUENCE FEATURE</td><td>Triticum aestivum</td><td>Start = 10158696 [...]</td></tr><tr><td>JBrowse chr1A 10231918 10232011 miRNA</td><td>IWGSC@GnpIS</td><td>SEQUENCE FEATURE</td><td>Triticum aestivum</td><td>Start = 10231918 [...]</td></tr><tr><td>JBrowse chr1A 102424297 102424428 miRNA</td><td>IWGSC@GnpIS</td><td>SEQUENCE FEATURE</td><td>Triticum aestivum</td><td>Start = 102424297 [...]</td></tr><tr><td>JBrowse chr1A 104839251 104839344 miRNA</td><td>IWGSC@GnpIS</td><td>SEQUENCE FEATURE</td><td>Triticum aestivum</td><td>Start = 104839251 [...]</td></tr><tr><td>JBrowse chr1A 104839691 104839784 miRNA</td><td>IWGSC@GnpIS</td><td>SEQUENCE FEATURE</td><td>Triticum aestivum</td><td>Start = 104839691 [...]</td></tr><tr><td>JBrowse chr1A 105619444 105619537 miRNA</td><td>IWGSC@GnpIS</td><td>SEQUENCE FEATURE</td><td>Triticum aestivum</td><td>Start = 105619444 [...]</td></tr><tr><td>JBrowse chr1A 107474939 107475091 miRNA</td><td>IWGSC@GnpIS</td><td>SEQUENCE FEATURE</td><td>Triticum aestivum</td><td>Start = 107474939 [...]</td></tr><tr><td>JBrowse chr1A 108071355 108071486 miRNA</td><td>IWGSC@GnpIS</td><td>SEQUENCE FEATURE</td><td>Triticum aestivum</td><td>Start = 108071355 [...]</td></tr></tbody></table>

<figure><img src="image_19.png" /></figure>
In progress at URGI

<table><thead><tr><th>ID</th><th>Source</th><th>Type</th><th>Taxon</th><th>Description</th></tr></thead><tbody><tr><td>JBrowse chr1A 100233074 100233167 miRNA</td><td>IWGSC@GnpIS</td><td>SEQUENCE FEATURE</td><td>Triticum aestivum</td><td>Start = 100233074 [...]</td></tr><tr><td>JBrowse chr1A 101106604 101106809 miRNA</td><td>IWGSC@GnpIS</td><td>SEQUENCE FEATURE</td><td>Triticum aestivum</td><td>Start = 101106604 [...]</td></tr><tr><td>JBrowse chr1A 10158696 10158807 miRNA</td><td>IWGSC@GnpIS</td><td>SEQUENCE FEATURE</td><td>Triticum aestivum</td><td>Start = 10158696 [...]</td></tr><tr><td>JBrowse chr1A 10231918 10232011 miRNA</td><td>IWGSC@GnpIS</td><td>SEQUENCE FEATURE</td><td>Triticum aestivum</td><td>Start = 10231918 [...]</td></tr><tr><td>JBrowse chr1A 102424297 102424428 miRNA</td><td>IWGSC@GnpIS</td><td>SEQUENCE FEATURE</td><td>Triticum aestivum</td><td>Start = 102424297 [...]</td></tr><tr><td>JBrowse chr1A 104839251 104839344 miRNA</td><td>IWGSC@GnpIS</td><td>SEQUENCE FEATURE</td><td>Triticum aestivum</td><td>Start = 104839251 [...]</td></tr><tr><td>JBrowse chr1A 104839691 104839784 miRNA</td><td>IWGSC@GnpIS</td><td>SEQUENCE FEATURE</td><td>Triticum aestivum</td><td>Start = 104839691 [...]</td></tr><tr><td>JBrowse chr1A 105619444 105619537 miRNA</td><td>IWGSC@GnpIS</td><td>SEQUENCE FEATURE</td><td>Triticum aestivum</td><td>Start = 105619444 [...]</td></tr><tr><td>JBrowse chr1A 107474939 107475091 miRNA</td><td>IWGSC@GnpIS</td><td>SEQUENCE FEATURE</td><td>Triticum aestivum</td><td>Start = 107474939 [...]</td></tr><tr><td>JBrowse chr1A 108071355 108071486 miRNA</td><td>IWGSC@GnpIS</td><td>SEQUENCE FEATURE</td><td>Triticum aestivum</td><td>Start = 108071355 [...]</td></tr></tbody></table>

<figure><img src="image_20.png" /></figure>
In progress at URGI

<table><thead><tr><th>ID</th><th>Source</th><th>Type</th><th>Taxon</th><th>Description</th></tr></thead><tbody><tr><td>10.1007/s10681-014-1343-6</td><td>OpenMinTeD</td><td>Bibliography</td><td>Triticum</td><td>Effects and interactions of genes Lr34, Lr68 and Sr2 on wheat leaf rust adult plant resistance in Uruguay Achieving durable resistance to leaf rust (LR), caused by Puccinia triticina, in wheat has been one of the main objectives of breeding programs [...]</td></tr><tr><td>10.1007/s10681-014-1349-0</td><td>OpenMinTeD</td><td>Bibliography</td><td>Triticum</td><td>Identification of QTL for adult plant resistance to stripe rust in Chinese wheat landrace Caoxuan 5 Yellow (or stripe) rust, caused by Puccinia striformis f [...]</td></tr><tr><td>10.1016/j.eja.2015.04.007</td><td>OpenMinTeD</td><td>Bibliography</td><td>Triticum</td><td>A simple approach to predict growth stages in winter wheat (Triticumaestivum L.) combining prediction of a crop model and marker based prediction of the deviation to a reference cultivar: A case study in France Predicting wheat growth stages using ecophysiological models is of particular interest as it allows anticipating important agricultural managements [...]</td></tr><tr><td>10.1007/s00122-015-253</td><td colspan="4">Euphytica<br/>L... August 2015, Volume 204, Issue 3, pp 599-608 | Cite as<br/>Effects and interactions of genes Lr34, Lr68 and Sr2 on wheat leaf rust adult plant resistance in Uruguay</td></tr><tr><td>10.1007/s00122-015-253</td><td>Authors</td><td colspan="3">Authors and affiliations</td></tr><tr><td>10.1007/s00122-015-253</td><td colspan="4">Paula Silva ☐, Violeta Calvo-Salazar, Federico Condón, Martin Quincke, Clara Pritsch, Lucía Gutiérrez, Ariel Castro, Sybil Herrera-Foessel, Jarislav von Zitzewitz, Silvia Germán</td></tr><tr><td>10.1016/j.cropro.2015.04.007</td><td>Article</td><td colspan="3">First Online: 20 January 2015</td></tr><tr><td>10.1371/journal.pone.013</td><td colspan="4">607 2<br/>Downloads Citations</td></tr><tr><td>10.2135/cropsci2014.10</td><td colspan="4">Abstract<br/>Achieving durable resistance to leaf rust (LR), caused by *Puccinia triticina*, in wheat has been one of the main objectives of breeding programs. Durability of LR resistance is considered to be associated with adult plant resistance (APR) genes that are quantitatively inherited and whose expression is largely influenced by environment. Our objective was to study the effects and interactions of APR genes *Lr34*, *Lr68* and *Sr2* on LR response in Uruguay using two *BC<sub>1</sub>F<sub>6</sub>* populations ('LE2304*2/Parula' and 'ORL99192*2/Parula'). The experimental material was screened for LR in three artificially inoculated environments (La Estanzuela 2012 and 2013 and Young 2012). Linked molecular markers were used to detect the presence of the genes</td></tr></tbody></table>

<figure><img src="image_20.png" /></figure>
In progress at URGI

<table><thead><tr><th>ID</th><th>Source</th><th>Type</th><th>Taxon</th><th>Description</th></tr></thead><tbody><tr><td>10.1007/s10681-014-1343-6</td><td>OpenMinTeD</td><td>Bibliography</td><td>Triticum</td><td>Effects and interactions of genes Lr34, Lr68 and Sr2 on wheat leaf rust adult plant resistance in Uruguay Achieving durable resistance to leaf rust (LR), caused by Puccinia triticina, in wheat has been one of the main objectives of breeding programs [...]</td></tr><tr><td>10.1007/s10681-014-1349-0</td><td>OpenMinTeD</td><td>Bibliography</td><td>Triticum</td><td>Identification of QTL for adult plant resistance to stripe rust in Chinese wheat landrace Caoxuan 5 Yellow (or stripe) rust, caused by Puccinia striformis f [...]</td></tr><tr><td>10.1016/j.eja.2015.04.007</td><td>OpenMinTeD</td><td>Bibliography</td><td>Triticum</td><td>A simple approach to predict growth stages in winter wheat (Triticumaestivum L.) combining prediction of a crop model and marker based prediction of the deviation to a reference cultivar: A case study in France Predicting wheat growth stages using ecophysiological models is of particular interest as it allows anticipating important agricultural managements [...]</td></tr><tr><td>10.1007/s00122-015-253</td><td colspan="4">Euphytica<br/>L... August 2015, Volume 204, Issue 3, pp 599-608 | Cite as<br/>Effects and interactions of genes Lr34, Lr68 and Sr2 on wheat leaf rust adult plant resistance in Uruguay</td></tr><tr><td>10.1007/s00122-015-253</td><td>Authors</td><td colspan="3">Authors and affiliations</td></tr><tr><td>10.1007/s00122-015-253</td><td colspan="4">Paula Silva ☐, Violeta Calvo-Salazar, Federico Condón, Martin Quincke, Clara Pritsch, Lucía Gutiérrez, Ariel Castro, Sybil Herrera-Foessel, Jarislav von Zitzewitz, Silvia Germán</td></tr><tr><td>10.1016/j.cropro.2015.04.007</td><td>Article<br/>First Online: 20 January 2015</td><td>607</td><td>2</td><td>Downloads Citations</td></tr><tr><td>10.1371/journal.pone.01315</td><td colspan="4">Abstract<br/>Achieving durable resistance to leaf rust (LR), caused by *Puccinia triticina*, in wheat has been one of the main objectives of breeding programs. Durability of LR resistance is considered to be associated with adult plant resistance (APR) genes that are quantitatively inherited and whose expression is largely influenced by environment. Our objective was to study the effects and interactions of APR genes *Lr34*, *Lr68* and *Sr2* on LR response in Uruguay using two *BC<sub>1</sub>F<sub>6</sub>* populations ('LE2304*2/Parula' and 'ORL99192*2/Parula'). The experimental material was screened for LR in three artificially inoculated environments (La Estanzuela 2012 and 2013 and Young 2012). Linked molecular markers were used to detect the presence of the genes</td></tr><tr><td>10.2135/cropsci2014.10</td><td colspan="4">S Barley (Hordeum vulgare L.)</td></tr></tbody></table>
Bug fixed

* It is now possible to find metadata containing special characters such as « . », « - », « _ »
Bug fixed

* It is now possible to find metadata containing special characters such as « . », « - », « _ »
# SolR package

You'd like to join the WheatIS federation in order to make your data discoverable through the WheatIS search tool ?

You should contact us to have support and to choose the best option that fits your needs.

* The simpler option is to extract your data in the dedicated CSV format and to provide us this file (either stored on your web server, or by any other way). We then will be able to fetch and index this file at URGI and make your data visible within the WheatIS search tool.

* If you want to keep full control over your data, you can also install and configure an on-premise Solr instance. Once installation completed, some data indexed and network opened to URGI's servers, we'll be able to add your node to our federation and you'll be visible in the WheatIS search tool.

To ease the WheatIS nodes to expose their data into the WheatIS search tool, we developed a package to help the installation, the configuration and the management of a WheatIS node, or to get primary insights about how to format your data. Download the package:

WheatIS-search-tool-sha1.solr_7fec39d8006b2c2163ddc72f294c65b17358f46f_etal script c4cb7cfb6d139b75640133ddd78b67dbdcf04866.tar.gz
(415.17 kB)

Please contact us to get support and to add your data to the WheatIS search.

Powered by

<figure><img src="image_21.png" /></figure>
# SolR package

You'd like to join the WheatIS federation in order to make your data discoverable through the WheatIS search tool ?

You should contact us to have support and to choose the best option that fits your needs.

* The simpler option is to extract your data in the dedicated CSV format and to provide us this file (either stored on your web server, or by any other way). We then will be able to fetch and index this file at URGI and make your data visible within the WheatIS search tool.

* If you want to keep full control over your data, you can also install and configure an on-premise Solr instance. Once installation completed, some data indexed and network opened to URGI's servers, we'll be able to add your node to our federation and you'll be visible in the WheatIS search tool.

To ease the WheatIS nodes to expose their data into the WheatIS search tool, we developed a package to help the installation, the configuration and the management of a WheatIS node, or to get primary insights about how to format your data. Download the package:

WheatIS-search-tool-sha1.solr_7fec39d8006b2c2163ddc72f294c65b17358f46f_etal script c4cb7cfb6d139b75640133ddd78b67dbdcf04866.tar.gz
(415.17 kB)

Please contact us to get support and to add your data to the WheatIS search.

Powered by

<figure><img src="image_21.png" /></figure>
Perspectives

<figure><img src="image_22.png" /></figure>
Perspectives

<figure><img src="image_22.png" /></figure>
# Perspectives

* Central index approach

* FTP/Web repository on each node (like Trackhub)

* Metadata harvested / indexed

* CSV Files

* Export from existing Solr with slight configuration adaptation

* Pros

* Lighter implementation for new nodes

* Easy update of the Solr engine

* Easy addition of new functionalities

* Cons / things to check

* Centralisation of queried metadata

* Description metadata only

* All content of CSV files

* Delay in index updates (day or week)
# Perspectives

* Central index approach

* FTP/Web repository on each node (like Trackhub)

* Metadata harvested / indexed

* CSV Files

* Export from existing Solr with slight configuration adaptation

* Pros

* Lighter implementation for new nodes

* Easy update of the Solr engine

* Easy addition of new functionalities

* Cons / things to check

* Centralisation of queried metadata

* Description metadata only

* All content of CSV files

* Delay in index updates (day or week)
Data standards

<figure><img src="image_23.png" /></figure>
Data standards

<figure><img src="image_23.png" /></figure>
Data standards

About

Collaborators

Search

Data Standards

Submit Data

Tools

Links

WheatIS Nodes

WheatIS

@ PRATT J.C. / INRA

<figure><img src="image_24.png" /></figure>

About

This project aims at building an International Wheat Information System, called hereafter WheatIS, to support the wheat research community. The main objective is to provide a single-access web base system to access to the available data resources and bioinformatics tools.

This project is based on the principles listed below:

* Collective building of the WheatIS to better respond to the needs of the international wheat community;

* Incremental implementation to offer rapidly an operational information system;

* Emphasis on Quality Assurance to serve as a framework for an approach with incremental implementation;

* Promotion of an open-access model for data exchange;

* Reliance on a distributed system;

* Use of Virtual Machine and Cloud Computing technologies to facilitate sharing data and tools;

* Promotion of the visibility of each participating platform to contribute to their sustainability.

If you have questions regarding this Wheat Information System project, please contact: wheatis-contact@wheatis.org

Tweets

Follow

<figure><img src="image_25.png" /></figure>

WheatIS
@WheatIS

9 Dec

WheatIS talk at next PAG conference. Book your agenda
pag.confex.com/pag/xxiv/meeti...

Expand

<figure><img src="image_26.png" /></figure>

Michael Alaux
@michaelalaux

4 Dec

Program of IWGSC Standards & Protocols workshop at PAG 2016
wheatgenome.org/Meetings-and-W... via @wheatgenome

t Retweeted by WheatIS

Expand

<figure><img src="image_27.png" /></figure>

Michael Alaux
@michaelalaux

4 Dec

Next talk at #PAGXXIV about the IWGSC Sequence Repository

pag.confex.com/pag/xxiv/webpr...
@wheatgenome @inra_urgi @fredChoulet

t Retweeted by WheatIS

Expand

<figure><img src="image_28.png" /></figure>

Anthony Hall
@Ajwhall

9 Dec

Find out more about UK iplant
@iPlantCollab at @joyn #PAGXXV
pag.confex.com/pag/xxiv/meeti...

Tweet to @WheatIS

http://www.wheatis.org/
About

Collaborators

Search

Data Standards

Submit Data

Tools

Links

WheatIS Nodes

WheatIS

@ PRATT J.C. / INRA

<figure><img src="image_24.png" /></figure>

About

This project aims at building an International Wheat Information System, called hereafter WheatIS, to support the wheat research community. The main objective is to provide a single-access web base system to access to the available data resources and bioinformatics tools.

This project is based on the principles listed below:

* Collective building of the WheatIS to better respond to the needs of the international wheat community;

* Incremental implementation to offer rapidly an operational information system;

* Emphasis on Quality Assurance to serve as a framework for an approach with incremental implementation;

* Promotion of an open-access model for data exchange;

* Reliance on a distributed system;

* Use of Virtual Machine and Cloud Computing technologies to facilitate sharing data and tools;

* Promotion of the visibility of each participating platform to contribute to their sustainability.

If you have questions regarding this Wheat Information System project, please contact: wheatis-contact@wheatis.org

Tweets

Follow

<figure><img src="image_25.png" /></figure>

WheatIS
@WheatIS

9 Dec

WheatIS talk at next PAG conference. Book your agenda
pag.confex.com/pag/xxiv/meeti...

Expand

<figure><img src="image_26.png" /></figure>

Michael Alaux
@michaelalaux

4 Dec

Program of IWGSC Standards & Protocols workshop at PAG 2016
wheatgenome.org/Meetings-and-W... via @wheatgenome

t Retweeted by WheatIS

Expand

<figure><img src="image_27.png" /></figure>

Michael Alaux
@michaelalaux

4 Dec

Next talk at #PAGXXIV about the IWGSC Sequence Repository

pag.confex.com/pag/xxiv/webpr...
@wheatgenome @inra_urgi @fredChoulet

t Retweeted by WheatIS

Expand

<figure><img src="image_28.png" /></figure>

Anthony Hall
@Ajwhall

9 Dec

Find out more about UK iplant
@iPlantCollab at @jgyn #PAGXXV
pag.confex.com/pag/xxiv/meeti...

Tweet to @WheatIS
Data standards

* News will be presented by Hadi Quesneville.

FAIRsharing.org
∞ standards, databases, policies
Data standards

* News will be presented by Hadi Quesneville.

FAIRsharing.org
∞ standards, databases, policies
WheatIS data submission

<figure><img src="image_29.png" /></figure>
WheatIS data submission

<figure><img src="image_29.png" /></figure>
About

Collaborators

Search

Data Standards

Submit Data

Tools

Links

WheatIS Nodes

WheatIS

@ PRATT J.C. / INRA

<figure><img src="image_30.png" /></figure>

## About

This project aims at building an International Wheat Information System, called hereafter WheatIS, to support the wheat research community. The main objective is to provide a single-access web base system to access to the available data resources and bioinformatics tools.

This project is based on the principles listed below:

* Collective building of the WheatIS to better respond to the needs of the international wheat community;

* Incremental implementation to offer rapidly an operational information system;

* Emphasis on Quality Assurance to serve as a framework for an approach with incremental implementation;

* Promotion of an open-access model for data exchange;

* Reliance on a distributed system;

* Use of Virtual Machine and Cloud Computing technologies to facilitate sharing data and tools;

* Promotion of the visibility of each participating platform to contribute to their sustainability.

If you have questions regarding this Wheat Information System project, please contact: wheatis-contact@wheatis.org

## Tweets

## Follow

<figure><img src="image_31.png" /></figure>

### WheatIS

9 Dec

<figure><img src="image_32.png" /></figure>

WheatIS talk at next PAG conference. Book your agenda
pag.confex.com/pag/xxiv/meeti...

Expand

<figure><img src="image_33.png" /></figure>

### Michael Alaux

4 Dec

<figure><img src="image_34.png" /></figure>

Program of IWGSC Standards & Protocols workshop at PAG 2016
wheatgenome.org/Meetings-and-W... via
@wheatgenome

t Retweeted by WheatIS

Expand

<figure><img src="image_35.png" /></figure>

### Michael Alaux

4 Dec

<figure><img src="image_36.png" /></figure>

Next talk at #PAGXXIV about the IWGSC Sequence Repository

pag.confex.com/pag/xxiv/webpr...
@wheatgenome @inra_urgi @fredChoulet

t Retweeted by WheatIS

Expand

<figure><img src="image_37.png" /></figure>

### Anthony Hall

9 Dec

<figure><img src="image_38.png" /></figure>

Find out more about UK iplant
@iPlantCollab at @joyn #PAGXXV
pag.confex.com/pag/xxiv/meeti...

Tweet to @WheatIS
About

Collaborators

Search

Data Standards

Submit Data

Tools

Links

WheatIS Nodes

WheatIS

@ PRATT J.C. / INRA

<figure><img src="image_30.png" /></figure>

About

This project aims at building an International Wheat Information System, called hereafter WheatIS, to support the wheat research community. The main objective is to provide a single-access web base system to access to the available data resources and bioinformatics tools.

This project is based on the principles listed below:

* Collective building of the WheatIS to better respond to the needs of the international wheat community;

* Incremental implementation to offer rapidly an operational information system;

* Emphasis on Quality Assurance to serve as a framework for an approach with incremental implementation;

* Promotion of an open-access model for data exchange;

* Reliance on a distributed system;

* Use of Virtual Machine and Cloud Computing technologies to facilitate sharing data and tools;

* Promotion of the visibility of each participating platform to contribute to their sustainability.

If you have questions regarding this Wheat Information System project, please contact: wheatis-contact@wheatis.org

Tweets

Follow

<figure><img src="image_31.png" /><figcaption>WheatIS
@WheatIS</figcaption></figure>

9 Dec

<figure><img src="image_32.png" /></figure>

WheatIS talk at next PAG conference. Book your agenda
pag.confex.com/pag/xxiv/meeti...

Expand

<figure><img src="image_33.png" /><figcaption>Michael Alaux
@michaelalaux</figcaption></figure>

4 Dec

Program of IWGSC Standards & Protocols workshop at PAG 2016
wheatgenome.org/Meetings-and-W... via
@wheatgenome

t Retweeted by WheatIS

Expand

<figure><img src="image_34.png" /><figcaption>Michael Alaux
@michaelalaux</figcaption></figure>

4 Dec

Next talk at #PAGXXIV about the IWGSC Sequence Repository

pag.confex.com/pag/xxiv/webpr...
@wheatgenome @inra_urgi @fredChoulet

t Retweeted by WheatIS

Expand

<figure><img src="image_35.png" /><figcaption>Anthony Hall
@Ajwhall</figcaption></figure>

9 Dec

Find out more about UK iplant
@iPlantCollab at @joyn #PAGXXV
pag.confex.com/pag/xxiv/meeti...

Tweet to @WheatIS
<figure><img src="image_39.png" /></figure>

DSpace Home

## WheatIS data repository

Laboratories and researchers can submit here their data to be shared with the whole Wheat scientific community. You can consult and download submitted data anonymously. You need to [register](#) in order to submit datasets among:

* Submit Phenotyping data (guidelines)

* Submit Genotyping data (guidelines)

* Submit SNP Discovery data (guidelines)

You may look at Wheat Data Interoperability Guidelines for recommendations on how and what to submit.

Or you can just discover what has already been submitted using browsing features below and in the right menu.

All submitted data will be in open access (publicly available). If you want to restrict their usage, you can provide a License file during the submission process.

## Communities in DSpace

Select a community to browse its collections.

* Wheat Community

## Recently Added

Fusarium head blight in spring wheat RIL population

Karolina Krystkowiak; Pawel Krajewski; pkra@igr.poznan.pl

Variations discovered by Whole Exome Capture and Genome By Sequencing approaches on

Bread wheat lines

Eduard Akhunov

Small Grain Cereals dataset

Letellier Thomas

Search DSpace

<figure><img src="image_40.png" /></figure>

Go

Advanced Search

## Browse

All of DSpace

Communities & Collections

By Issue Date

Authors

Titles

## My Account

Login

Register

## RSS Feeds

<figure><img src="image_41.png" /></figure>

RSS 1.0

<figure><img src="image_42.png" /></figure>

RSS 2.0

<figure><img src="image_43.png" /></figure>

Atom
<figure><img src="image_36.png" /></figure>

DSpace Home

## WheatIS data repository

Laboratories and researchers can submit here their data to be shared with the whole Wheat scientific community. You can consult and download submitted data anonymously. You need to [register](#) in order to submit datasets among:

* Submit Phenotyping data (guidelines)

* Submit Genotyping data (guidelines)

* Submit SNP Discovery data (guidelines)

You may look at Wheat Data Interoperability Guidelines for recommendations on how and what to submit.

Or you can just discover what has already been submitted using browsing features below and in the right menu.

All submitted data will be in open access (publicly available). If you want to restrict their usage, you can provide a License file during the submission process.

## Communities in DSpace

Select a community to browse its collections.

* Wheat Community

## Recently Added

Fusarium head blight in spring wheat RIL population

Karolina Krystkowiak; Pawel Krajewski; pkra@igr.poznan.pl

Variations discovered by Whole Exome Capture and Genome By Sequencing approaches on

Bread wheat lines

Eduard Akhunov

Small Grain Cereals dataset

Letellier Thomas

Search DSpace

<figure><img src="image_37.png" /></figure>

Advanced Search

## Browse

All of DSpace

Communities & Collections

By Issue Date

Authors

Titles

## My Account

Login

Register

## RSS Feeds

<figure><img src="image_38.png" /></figure>

RSS 1.0

<figure><img src="image_39.png" /></figure>

RSS 2.0

<figure><img src="image_40.png" /></figure>

Atom
DSpace - iRODS

* DSpace metadata are indexed in the SolR search

* We will add IWGSC public data / metadata soon
DSpace - iRODS

* DSpace metadata are indexed in the SolR search

* We will add IWGSC public data / metadata soon
Acknowledgements

<figure><img src="image_44.png" /></figure>

ZURGI

<figure><img src="image_45.png" /></figure>

<figure><img src="image_46.png" /></figure>

WHEAT
INITIATIVE

<figure><img src="image_47.png" /></figure>

RESEARCH DATA ALLIANCE

Part of the

trans

PLANT

European Plant
Genomics Infrastructure

<figure><img src="image_48.png" /></figure>

INRA
SCIENCE & IMPACT

<figure><img src="image_49.png" /></figure>
Acknowledgements

<figure><img src="image_41.png" /></figure>

ZURGI

<figure><img src="image_42.png" /></figure>

<figure><img src="image_43.png" /></figure>

WHEAT
INITIATIVE

<figure><img src="image_44.png" /></figure>

RESEARCH DATA ALLIANCE

Part of the

trans

PLANT

European Plant
Genomics Infrastructure

<figure><img src="image_45.png" /></figure>

INRA
SCIENCE & IMPACT

<figure><img src="image_46.png" /></figure>
# Questions

**WheatIS:**

http://www.wheatis.org/

**Download the SolR package to add your node in the search:**

http://wheat-urgi.versailles.inra.fr/Projects/Wheat-Information-System/SolR-tool-package

**Contacts:**

michael.alaux@inra.fr

raphael.flores@inra.fr

thomas.letellier@inra.fr

wheatis-contact@wheatis.org
Questions

WheatIS:

http://www.wheatis.org/

Download the SolR package to add your node in the search:

http://wheat-urgi.versailles.inra.fr/Projects/Wheat-Information-
System/SolR-tool-package

Contacts:

michael.alaux@inra.fr

raphael.flores@inra.fr

thomas.letellier@inra.fr

wheatis-contact@wheatis.org