# Preliminary Results from the IWGSC Wheat Diversity Project

Joshua C Stein, Kevin Fengler, Victor Llaca, Elodie Belmonte, Vincent Pailler, Hugo Zalzalé, Leonardo I Pereyra-Bistraín, Clément Debiton, Véronique Gautier, Pauline Lasserre-Zuber, et al.

<figure><img src="image_1.png" /></figure>

► To cite this version:

Joshua C Stein, Kevin Fengler, Victor Llaca, Elodie Belmonte, Vincent Pailler, et al. Preliminary Results from the IWGSC Wheat Diversity Project. PAG 33, Jan 2026, San diego, United States. hal-05518160

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

International Wheat Genome
Sequencing Consortium

# Preliminary Results from the IWGSC Wheat Diversity Project

Joshua Stein
IWGSC

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

Plant and Animal Genome Conference

San Diego, CA, USA

10 January 2026
Bread Wheat is a Global Food Security Crop

50 million metric tons per year
Global production
Provides ~20% human dietary
Calories and protein
More nutritionally complete than
Other cereal grains: Protein, B
vitamins, and iron.

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

M.A., H.J. Braun, T.S. Payne, R.P. Singh, K. Sonder, M. Baum, M. van Ginkel, and O. 2016. Impacts of International Wheat Improvement Research, 1994-2014. Mexico, D.F.: CIMMYT.

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

https://upload.wikimedia.org/wikipedia/ commons/c/c7/Korb_mit_Brötchen.

This file is licensed under the [Creative Commons Attribution-Share Alike 3.0 Un](https://creativecommons.org/licenses/by-sa/3.0/de).
# IWGSC History & Scientific Impacts

IWGSC's vision: high quality bread wheat genome sequence to empower all aspects of bread wheat science.

* The hexaploid genome (16-Gb)

* Human genome; 42x Rice genome

* 100,000 protein-coding genes

<figure><img src="image_7.png" /></figure>

Country of Corresponding Author in 440 Citations (2020 & 2021)

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

* Access to the first bread wheat IWGSC RefSeq - Chinese Spring

* Publication/release of IWGSC RefSeq v2.1 and annotation

* Publication and analysis of IWGSC RefSeq v1.0

* Pre-publication release of IWGSC RefSeq v1.0

* Chromosome-based whole genome shotgun assembly (IWGSC WGA v0.4).

* Physical maps for all chromosomes completed

* Publication of first chromosome based draft genome sequence

* IWGSC formed by wheat growers, plant scientists, and public and private breeders

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

<figure><img src="image_10.png" /></figure>
Breeder's Dilemma

ear-over-year increase production is required.

limate change promising to destabilize production trends.

roision of genetic diversity.

enetic gains are sluggish; TFP is .7% vs. annual target of 2.03%

on J. Wheat Facts and Futures: CIMMYT; 2009. p. 1-19; Rosegrant Global Food Demand, Supply, and Price Prospects to 2010: International Food Policy Research Institute; 2010.)

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

World wheat yield, production and area from 1961 to 2016 (FAO,

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

Tadesse et al. 2019. Crop Breed Genet Genom. 2019;1:e190005.
# Landraces as a Foundational Source of Wheat Diversity

ally-adapted and farmed for
thousands of years before
placement by modern varieties
risk of extinction, preserved
NRAE.

etic diversity is mostly absent
modern varieties, making these
draces valuable trait
ervoirs.

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

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

ERGE7966 (Northwest Europe)

Resistance to leaf rust
(Puccinia triticina)

INRAE Small Grains BRC

Y., Kang, L. et al. Population genomics unravels the Holocene history of bread wheat and its relatives. *Nat. Plants* 9, 403–419 (2023). https://doi.org/10.1038/s41477-023-01367-9

1. Dispersed Emergence and Protracted Domestication of Polyploid Wheat Uncovered by Mosaic Ancestral Haploblock Inference. *Nat. Commun.* 2022, 13 (1), 3891.
# IWGSC Wheat Diversity Project

Reserve, discover, and mobilize genetic resources by sequencing landrace genomes that encompass the worldwide diversity of bread wheat.

* **Goal 1:** Generate platinum quality genome assemblies for 12 maximally diverse bread wheat landrace accessions and the community reference cv. Chinese Spring (CS).

* **Goal 2:** Establish transcriptome data and gene annotations for these accessions and update the IWGSC CS RefSeq annotation in a manner that sustains its role as a community-curated resource.

* **Goal 3:** Construct a Practical Haplotype Graph (PHG) to catalog all genetic diversity within bread wheat and enable community-driven discoveries across the species.

* **Goal 4:** Increase STEM educator training, public scientific literacy, and adoption of project resources through partnerships in education, outreach, and training (EOT).

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

Investigator

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

Pierre Sourdille

INRAO

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

GDEC

Genetique Université Zo谱biologie - Cérèles

Biological Resources, Genome Production, Annotation

<figure><img src="image_18.png" /><figcaption>Pierre Sourdille</figcaption></figure>

<figure><img src="image_19.png" /><figcaption>Frédéric Choulet</figcaption></figure>

<figure><img src="image_20.png" /><figcaption>Hélène Rimbert</figcaption></figure>

<figure><img src="image_21.png" /><figcaption>Véronique Gautier</figcaption></figure>

INRAO

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

IWGSC Data Repository

<figure><img src="image_23.png" /><figcaption>Michael Alaux</figcaption></figure>

université
PARIS-SACLAY

Transcriptome

<figure><img src="image_24.png" /><figcaption>Moussa Benhamed</figcaption></figure>

GEORGE
Practical Haplotype

<figure><img src="image_25.png" /><figcaption>C. Robin</figcaption></figure>

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

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

Funded by
the European Union

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

INRAO

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

A project supported by the National Science Foundation under grant #2322957, the European Research Council ERC (project 3Dwheat #101044), INRAE Plant Biology and Breeding department, and the International Wheat Genome Sequencing Consortium
# Selection of Foundational Phylogeographic Haplotypes

ScienceAdvances

AAAS

SIGNIFICANT RESEARCH, GLOBAL IMPACT

(5): eaav0536. Published online 2019 May 29. doi: 10.1126/sciadv.aav0536

1 | PMID: 31149630

geography and history of wheat genetic diversity

† Sophie Bouchet,¹,† Sandra Robert,¹ Romain De Oliveira,¹ Hélène Rimbert,¹

Eric Choulet,¹ International Wheat Genome Sequencing Consortium,²,‡ BreedWheat
Tienne Paux¹,∗

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

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

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TaBW280K SNP array

4,506 wheat lines

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

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

* Sampled 4506 wheat lines from 18 countries, including 632 Landrace preserved at the INRAE Small Group Biological Research Centre.

* Identified 8 Phylogeographic Haplogroups among landraces.

* Selected 12 maximally diverse 1 showing minimal admixture.

<table><thead><tr><th>Haplogroup</th><th>Country</th><th>Habit</th><th>Assign-8†</th></tr></thead><tbody><tr><td>CAA</td><td>Iraq</td><td>Spring</td><td>0.994</td></tr><tr><td>CAU</td><td>Palestine</td><td>Winter</td><td>1</td></tr><tr><td>INP</td><td>India</td><td>Spring</td><td>1</td></tr><tr><td>SEA</td><td>China</td><td>Winter</td><td>1</td></tr><tr><td>NWE</td><td>France</td><td>Winter</td><td>1</td></tr><tr><td>MED</td><td>Tunisia</td><td>Spring</td><td>1</td></tr><tr><td>IBP</td><td>Portugal</td><td>Spring</td><td>1</td></tr><tr><td>SEE</td><td>Ukraine</td><td>Winter</td><td>1</td></tr><tr><td>NWE</td><td>Turkey</td><td>Spring</td><td>0.676</td></tr><tr><td>*NWE</td><td>France</td><td>Winter</td><td>0.506</td></tr><tr><td>SEE</td><td>Morocco</td><td>Spring</td><td>0.714</td></tr><tr><td>NA</td><td>Colombia</td><td>Spring</td><td>NA</td></tr></tbody></table>

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

erc

INRAE

European Research Council
Funded by the European Union

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

A project supported by the National Science Foundation under grant #2322957, the European Research Council ERC (project 3Dwheat #101044399), INRAE Plant Bi
Breeding department, and the International Wheat Genome Sequencing Consortium
<figure><img src="image_39.png" /><figcaption>12 Selected Landraces from 8 Phylogeographic Haplotypes</figcaption></figure>
Project Strategy & Data Generation

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

or Llaca & Kevin Fengler (Corteva Agriscience)

12 Landraces + Chinese Spring

1. PacBio HiFi sequencing: 25-30X

2. Bionano Optical Maps: 80-100X

3. Hi-C Illumina: 25-55X

Chinese Spring only:
ONT sequencing: 35X
# Primary Contig Assemblies

## Hifiasm assembly (excluding contigs <70-kb)

<table><thead><tr><th>Sample Name</th><th>Read-N50 (kb)</th><th>Total Yield (Gb)</th><th>Fold Coverage</th><th>Contig #</th><th>Max. Contig (Mb)</th><th>Contig N50 (Mb)</th><th>Total Length (Gb)</th></tr></thead><tbody><tr><td>CHINESESPRING (ONT)**</td><td>49.1</td><td>542.5</td><td>35</td><td>380</td><td>582</td><td>238.8</td><td>14.56</td></tr><tr><td>CHINESESPRING</td><td>17.9</td><td>593.1</td><td>38</td><td>897</td><td>403</td><td>69.6</td><td>14.52</td></tr><tr><td>9676</td><td>18.2</td><td>429.1</td><td>28</td><td>968</td><td>231</td><td>43.3</td><td>14.47</td></tr><tr><td>BANATKA</td><td>18.3</td><td>461.5</td><td>30</td><td>977</td><td>292</td><td>43.0</td><td>14.47</td></tr><tr><td>BARBELA</td><td>17.4</td><td>487.5</td><td>31</td><td>934</td><td>405</td><td>49.4</td><td>14.49</td></tr><tr><td>BINTANE*</td><td>17</td><td>418.4</td><td>31</td><td>2,630</td><td>254</td><td>35.1</td><td>15.54</td></tr><tr><td>BLANC DE HAUTE SAONE*</td><td>18</td><td>446.7</td><td>30</td><td>1,499</td><td>418</td><td>51.6</td><td>14.90</td></tr><tr><td>HURMA</td><td>17.6</td><td>492.1</td><td>32</td><td>979</td><td>339</td><td>45.2</td><td>14.52</td></tr><tr><td>LANDRACE</td><td>18.3</td><td>509.9</td><td>33</td><td>906</td><td>415</td><td>48.8</td><td>14.50</td></tr><tr><td>MAHOR</td><td>17.8</td><td>431.9</td><td>28</td><td>988</td><td>245</td><td>47.7</td><td>14.45</td></tr><tr><td>NANKINGNO25</td><td>18.9</td><td>461.6</td><td>30</td><td>877</td><td>329</td><td>62.1</td><td>14.49</td></tr><tr><td>POCHO*</td><td>18.8</td><td>487.4</td><td>27</td><td>1,718</td><td>335</td><td>49.5</td><td>15.17</td></tr><tr><td>PRINCEALBERT</td><td>18.8</td><td>494.3</td><td>32</td><td>887</td><td>322</td><td>52.9</td><td>14.46</td></tr><tr><td>SBEI*</td><td>19.1</td><td>487.3</td><td>31</td><td>1,507</td><td>389</td><td>50.3</td><td>14.83</td></tr></tbody></table>

<footnote>* Four genomes were produced at Gentyane/GDEC (INRAE, France); remaining genomes were produced at Corteva Agriscience (Johnston, IA, USA). ** ONT reads assembled with Hifiasm using "--ont" flag; all others are PacBio HiFi read assemblies.</footnote>
Advantage Using Bionano Maps

<figure><img src="image_41.png" /><figcaption>➤ Hybrid assembly provides greater contiguity and allows calculation of gap-sizes.</figcaption></figure>

<figure><img src="image_42.png" /></figure>
# Chromosome-scale Reconstruction of 13 Wheat Genomes

<table><thead><tr><th rowspan="2"></th><th rowspan="2">Sequence Length (Mb)</th><th rowspan="2">% Sequence Placed</th><th rowspan="2">Gap Length (Mb)</th><th rowspan="2">Gap Counts</th><th colspan="3">Gaps by Subgenome**</th></tr><tr><th>% A</th><th>% B</th><th>% D</th></tr></thead><tbody><tr><td>SPRING (ONT)</td><td>14.56</td><td>99.96</td><td>4.4</td><td>299</td><td>9</td><td>89</td><td>2</td></tr><tr><td>SPRING</td><td>14.52</td><td>99.9</td><td>15.0</td><td>775</td><td>15</td><td>65</td><td>7</td></tr><tr><td></td><td>14.47</td><td>99.9</td><td>14.5</td><td>903</td><td>18</td><td>64</td><td>12</td></tr><tr><td></td><td>14.47</td><td>99.94</td><td>25.7</td><td>861</td><td>17</td><td>63</td><td>14</td></tr><tr><td></td><td>14.49</td><td>99.91</td><td>18.1</td><td>835</td><td>19</td><td>65</td><td>9</td></tr><tr><td></td><td>15.54</td><td>99.96</td><td>121.5</td><td>1000</td><td>19</td><td>65</td><td>15</td></tr><tr><td>CHAUTE SAONE*</td><td>14.90</td><td>99.88</td><td>20.9</td><td>770</td><td>21</td><td>66</td><td>11</td></tr><tr><td></td><td>14.52</td><td>99.91</td><td>14.1</td><td>888</td><td>18</td><td>61</td><td>12</td></tr><tr><td></td><td>14.50</td><td>99.96</td><td>10.1</td><td>799</td><td>18</td><td>67</td><td>11</td></tr><tr><td></td><td>14.45</td><td>99.86</td><td>19.7</td><td>906</td><td>19</td><td>59</td><td>11</td></tr><tr><td>025</td><td>14.49</td><td>99.91</td><td>15.6</td><td>786</td><td>14</td><td>62</td><td>13</td></tr><tr><td></td><td>15.17</td><td>99.76</td><td>5.5</td><td>756</td><td>18</td><td>66</td><td>13</td></tr><tr><td>BERT</td><td>14.46</td><td>99.94</td><td>16.9</td><td>810</td><td>17</td><td>65</td><td>10</td></tr><tr><td></td><td>14.83</td><td>99.86</td><td>169.1</td><td>839</td><td>18</td><td>64</td><td>15</td></tr></tbody></table>

and assembly performed at Gentyane and GDEC (INRAE, France); all others genomes were at Corteva Agriscience (Johnston, IA, USA). **Remainder of gaps are in unplaced contigs.

A

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

B

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

D

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

<figure><img src="image_46.png" /></figure>
# BUSCO Gene Complement Analysis

BUSCO (Poales) > 99.9% for all genomes

Overall, 85% of BUSCOs are found in 3 copies.

<figure><img src="image_47.png" /></figure>
View into Structural Variation

comparative genomic views show value in revealing conserved and novel struct
ion

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

<figure><img src="image_49.png" /></figure>
# Transcriptome Data Generation

## Transcriptome sequencing

5 Tissues X
13 wheat
accessions

shoot

root

grain
spike

<figure><img src="image_50.png" /></figure>

stem

<figure><img src="image_51.png" /></figure>

<figure><img src="image_52.png" /></figure>

<table><tr><td>Stage:</td><td>3-leaf</td><td>2 DAA</td></tr><tr><td>days scale:</td><td>13</td><td>71</td></tr><tr><td>Age (weeks):</td><td>3-4</td><td>8-12</td></tr></table>

<table><thead><tr><th></th><th>Shoot</th><th>Root</th></tr></thead><tbody><tr><td>Read count (M)</td><td>1.5 - 13.2 (ave = 8.7)</td><td>5.1 - 14.9 (ave = 9.9)</td></tr><tr><td>Yield (Gb)</td><td>0.85 - 8.71 (ave = 5.0)</td><td>2.5 - 8.6 (ave = 5.3)</td></tr><tr><td>Ave read length (nt)</td><td>486 - 670 (ave = 587)</td><td>449 - 606 (ave = 529)</td></tr></tbody></table>

<figure><img src="image_53.png" /></figure>

<figure><img src="image_54.png" /></figure>

<figure><img src="image_55.png" /></figure>

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<figure><img src="image_58.png" /></figure>

<figure><img src="image_59.png" /></figure>

A project supported by the National Science Foundation under grant #2322957, the European Research Council ERC (project 3Dwheat #101044) INRAE Plant Biology and Breeding department, and the International Wheat Genome Sequencing Consortium
# IWGSC CS RefSeq v3.0 – Annotation pipeline

## Annotated Genes:

11,044 High Confidence
00,190 Low Confidence

EggNog v.5

* Gene Ontology
* KEGG Pathways
* PFAM domains
* Ortholog assignment

Dagchainer

Synteny maps

<figure><img src="image_60.png" /></figure>

Chromosome scaled by physical position

## Structural Annotation

**Transposon annotation:**

* CLARITE_smk pipeline

**Transfer annotations from IWGSC CS RefSeq v2.1:**

* MAGATT

* LiftOn

**Ab initio prediction:**

* FgenesH

* Augustus

* Helixer

**Protein evidence:**

* Ensembl Plants (Triticum durum, Triticum urartu, Aegilops tauschii, Hordeum vulgare, Oryza sativa, Brachypodium distachyon, Zea mays, and Arabidopsis thaliana)

* Uniprot/SwissProt clade Poales (taxid:38820)

* Aligned with Miniprot.

**cDNA evidence:**

* Public FLcDNA (PacBio Iso-Seq) of 14 conditions in Chinese Spring (SRR28004282-SRR28004295, SRR28004297).

* Aligned with Minimap2 and assembled with Stringtie2.

## EvidenceModeler
D version cross-reference for ~178,000 annotations

A04G105300 TraesCS1A01G072300,TraesCS1A02G072300,TraesCS1A03G0176800,Traes_1AS_160541C8C.1,Traes_1AS_D8E37233E.1

A04G105400 TraesCS1A01G102200LC,TraesCS1A02G102200LC,TraesCS1A03G0177000LC

A04G105500 TraesCS1A01G072500,TraesCS1A02G072500,TraesCS1A03G0177400

A04G105600 TraesCS1A01G072700,TraesCS1A02G072700,TraesCS1A03G0177600,Traes_1AS_306BB8CFE.1

A04G105700 TraesCS1A01G072800,TraesCS1A02G072800,TraesCS1A03G0177700,Traes_1AS_1B1587F7D.1,Traes_1AS_D67B5B3FB.1

A04G105800 TraesCS1A01G102500LC,TraesCS1A02G102500LC,TraesCS1A03G0177900LC

## Genomic mapping

<figure><img src="image_61.png" /></figure>

~28,500 groups containing at least 1 copy in each subgenome

~19,200 groups with strict 1:1:1 triplets

et al. Theor Appl Genet. 2018 Nov;131(11):2451-2462.
# Data Availability

## WGSC Data Repository, hosted at INRAE-URGI (FR)

* All genome assemblies and annotation

* Ad hoc data sets not supported by NCBI

* Public release at a future date

## NCBI GenBank

* All genome assemblies

* Public release at a future date

BrainGenes, Ensembl Plants, Wheat Information System (WheatIS) : future
Take Homes

ad wheat landraces are a rich source genetic diversity largely absent in modern breeding materials & reservoir for adaptive traits.

Awardship of the updated Chinese Spring RefSeq + Annotation will sustain this scientific resource into the future.

Landrace germplasm publicly available through INRAE small grains BRC future analyses and generation of a Practical Haplotype Graph is in progress.
# Project Contributors

ICO

## U. Paris-Saclay/IPS2

Ge Sourdille
Éric Choulet
Étonique Gautier
Étienne Rimbert
Éline Lasserre-Zuber
Ge Belmonte
Ant Pailler
Ant Debiton
Ge Marin
Lie Bouchet
Ge Saintenac

## Corteva Agriscience

* Victor Llaca
* Kevin Fengler

## IWGSC

Kellye Eversole
Joshua Stein
Catalina Johnson

## INRAE-URGI

Michael Alaux

Moussa Benhamed
Hugo Zalzale
* Leonardo Pereyra-Bis

## U. Georgia, Athens

Robin Buell
* John P. Hamilton
IC0 highlighted names are not authors of the PAG abstract - please double echeck

Isabelle Caugant; 2025-11-17T19:29:06.162
Funding Acknowledgements

<figure><img src="image_62.png" /></figure>

National Science Foundation grant #2322957

<figure><img src="image_63.png" /></figure>

Funded by
European Union

<figure><img src="image_64.png" /></figure>

European Research Council
Established by the European Commission

European Research Council ERC (project 3Dwheat #1010443)

<figure><img src="image_65.png" /></figure>

INRAE Plant Biology and Breeding Department

<figure><img src="image_66.png" /></figure>

International Wheat Genome Sequencing Consortium
<figure><img src="image_67.png" /></figure>

<figure><img src="image_68.png" /></figure>

<figure><img src="image_69.png" /></figure>

# The IWGSC Wheat Diversity Project:
## Foundational Genome Resources to Advance a Global Food Security Crop

The International Wheat Genome Sequencing Consortium¹, Joshua Stein¹, Gina Zastrow-Hayes², Victor Llaca², Hélène Rimbert³, Frédéric Choulet³, Clément Debiton³, Charles Poncet³, Michael Alaux⁴, Pierre Sourdille³, Moussa Benhamed⁵, C. Robin Buell⁶, and Kellye Eversole¹

(1) IWGSC, Eau Claire, WI, (2)Corteva Agriscience, Johnston, IA, (3)INRAE UMR 1095 GDEC, Clermont-Ferrand, France, (4)URGI, INRAE, Université Paris-Saclay, Versailles, France, (5)Institute of Plant Sciences - Paris-Saclay, Orsay, France, (6)Department of Crop & Soil Sciences, Institute of Plant Breeding, Genetics, & Genomics, University of Georgia, Athens, GA

> This project addresses the critical need to preserve, discover, and mobilize genetic resources by sequencing landrace genomes that encompass the worldwide diversity of bread wheat.

### ABSTRACT:

Crop diversity is essential to drive the future adaptive capacity of agriculture. In bread wheat (Triticum aestivum L. 2n = 6x = 42, AABBD), a significant amount of diversity is held within landraces traditionally farmed across Northern Africa, Europe, and Asia for thousands of years, and, while the varieties are no longer grown today, they remain a key reservoir for adaptive traits. Today's high-yielding varieties contain only a small fraction of this available gene pool, however, raising concerns that genetic erosion within modern stocks could limit future gains in wheat production. Further, this resource could contain traits that would help modern varieties meet the challenges of production in changing climates and the accompanying disease and pest pressures. This International Wheat Genome Sequencing Consortium (IWGSC) Wheat Diversity Project addresses the critical need to preserve, discover, and mobilize these genetic resources by sequencing 12 landrace genomes that are foundational to early regional growing centers and represent the worldwide diversity of bread wheat. Platinum-quality reference genomes produced by this project will also update the IWGSC Chinese Spring reference sequence (IWGSC CS RefSeq), which serves as a primary reference sequence for bread wheat research. Comprehensive annotation and representation of the wheat pangenome as a Practical Haplotype Graph will provide powerful tools to accelerate future genomics and breeding research. This project is funded by NSF Award #2322957, the European Research Council ERC (project 3Dwheat #101044399), INRAE Plant Biology and Breeding department, and the IWGSC.

<figure><img src="image_70.png" /><figcaption>### Aim 1: Generate platinum quality genome assemblies for 12 maximally diverse bread wheat landrace accessions and the community reference cv. Chinese Spring (CS)</figcaption></figure>

• 8 Phylogenetic haplotypes among 632 genotyped landraces = 8 subpopulations corresponding to early regional growing centers.
• Genome sequence & assembly using long-reads, optical mapping, and conformation capture sequence.

<figure><img src="image_71.png" /></figure>

## International Wheat Genome Sequencing Consortium (IWGSC)
### Wheat Diversity Project

Overnight, management & NCBI
Submissions, outreach & education
Services & Tools

Key: NSF Funded EU Funded

Gemplaspi Collection:
8 landraces + Chinese Spring
9 accessions: Sequence & assembly
Corteva Agriscience, Genomics
Technologies (Johnston, IA)
13 accessions: mRNA Iso-Seq
Benhamed
(U. Paris-Saclay)

4 accessions: Sequence & assembly
Benhamed
(U. Paris-Saclay)
Poncet
(INRAE)

13 accessions: mRNA Iso-Seq
Benhamed
(INRAE)

Practical Haplotype Graph: 13 accessions + other published genomes
Outreach & education
Buell (U. Georgia)

<caption>### Aim 2: Establish transcriptome data and gene annotations for these accessions and update the IWGSC CS RefSeq annotation in a manner that sustains its role as a community-cured resource</caption>

• Transposable element identification: ClentTE (Daron et al., 2014).

• Map loci from CS RefSeq v2.1 to new genomes: Liftoff (Shumate et al., 2020) & MAGATT (Rimbert, 2021).
• Gene annotation-driven transcriptome evidence.

Market-Identified Gene Annotation Transfer for Triticeae (MAGATT) pipeline

<figure><img src="image_72.png" /></figure>

PPanGolliin Egg-NOG Map

MAKER: Evidence- based gene build

Retain Gene Identifiers: e.g.

Tracs C53A3A3C6847489

• De novo gene-build: MAKER (Campbell et al., 2014).

• Annotation assessment and UTRs: InGenAnnot (Lapalu 2023).

• Functional annotation/Egg-NOG mapper (Huerta-Cepas et al. 2019).

• Pangenome analysis with PPanGolliin

Accession-derived Evidence

Iso-Seq long-read transcriptome

sequencing from 5 tissues x 3 stages

Wheat Growth Stages

Daron et al. 2014; Shumate et al. 2020; Campbell et al. 2014; Huerta-Cepas et al. 2019; Lapalu 2023; Rimbert 2021

### References:

Belfortel, F., Bouquet, S., Robert, S., De Oitres, R., Renard, H., Kriw, J., Choulet, V. International Wheat Genome Sequencing Consortium. BroadWheat Consortium, Pex, E., Wotkabla, Photography and History of Wheat Genomes (Dorsey, 2014) 2019, 111, 1005-1010.

Daron, J., Givner, N., Project L, Thiel, T., Jandlitz, E., Pex, E., Berthe, V., Margot, S., Albert, A., Winger, P., Quenardes, N., Feller, C., Choulet, F., Organization and Evolution of Transposable Elements along the Bread Wheat Chromosome 37.

Genome Biol 2014, 15(12), 1544 (DOI: 10.1186/s13041-014-0446-4)

Shumate, A., Alaux, F., 2009, 1.1RFF: Accurate Mapping of Gene Annotations (Borinmann, Darmstadt)

Braedum, P.J., Cavaillerie, T., Jena, SE., Johnson, LC., Miller, ZN., Morier, B., Runyon, MC., Song, B., Russell, ES. The Practical Haplotype Graph, 5. Platform for Storing and Using Pangenomes for Impulation (Borinmann, 2002).

Campbell, MS, Lee, M., Mol, C., Shen, JC, et al., 5'NADP+P: a tool for the rapid creation, management, and quality control of plant genome annotations. Plant Physiol. 2014, 164(2): 512-524.

Huerta-Cepas, D., Salinas, D., Haller, D., Hamandou-Pita, A., Fondund, S.K.

Cook, N., Mendonca, DR., 2019, 1.0GG: 5.0 A Hierarchical, Functional and Phylogenetic, Associated Orthology Resource, Based on 500 Organism and 2000 Genomes. Nature Genomics 10(2), 200-203.

Lepage, N., 2018, 1.0GG: 1.0 Tandem. GtLab.

https://www.fgenomics.org/101044399

The 101044399: Defining Microsatellite Density as a Functional Pangenome Graph. I

Bakos, P., 2018, 1.0GG: Defining Microsatellite Density as a Functional Pangenome Graph. I

https://www.fgenomics.org/101044399

The 101044399: Defining Microsatellite Density as a Functional Pangenome Graph. II

Bakos, P., 2018, 1.0GG: Defining Microsatellite Density as a Functional Pangenome Graph. II

https://www.fgenomics.org/101044399

The 101044399: Defining Microsatellite Density as a Functional Pangenome Graph. III

Bakos, P., 2018, 1.0GG: Defining Microsatellite Density as a Functional Pangenome Graph. III

https://www.fgenomics.org/101044399

### Funding Acknowledgements:

<figure><img src="image_73.png" /></figure>

### IWGSC Sponsors:

<figure><img src="image_74.png" /><figcaption>### Aim 3: Construct a Practical Haplotype Graph (PHG) to catalog all genetic diversity within bread wheat and enable community-driven discoveries across the species</figcaption></figure>

Graph-based representation of genic and intergenic regions representing diversity across taxa.

<figure><img src="image_75.png" /></figure>

<figure><img src="image_76.png" /></figure>

Bradley et al., 2023.

See you then!
Thanks!

<figure><img src="image_77.png" /></figure>