Crop Development Centre Durum Wheat Breeding and Genetics Program

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The 10 Wheat Genome Project: Towards a Pan-genome of wheat

Curtis Pozniak

A Post-Genome Sequence Era

2017

Need for a Pan Genome• Single reference is not

representative of the genetic diversity available in wheat

• Growing evidence of the roll of CNV and PAV diversity in phenotypic expression of traits

• A need to develop a complete atlas of the gene content of wheat to support biology and breeding

The Ten Genomes Project(Associate Program of the Wheat Initiative)

Goal: Begin characterization of PAV, CNV, Structural Variation in wheat

“NRGene RefSeq” Assemblies

N

200X PE/MP30X Chromium (10X Genomics)

Assembly

Scaffolding/Anchoring

Annotation

RNASeq- Standardized

tissues/treatments

HI-C MappingHigh Density Mapping

Sequencing

Parameter

Wild emmer

vs. Zavitan(AABB)

Durumvs. Svevo(AABB)

AK58 Bread Wheat

(China)(AABBDD)

CDC Landmark

Bread Wheat(Canada)(AABBDD)

CDC Stanley Bread Wheat

(Canada)(AABBDD)

JaggerBread Wheat

(USA)(AABBDD)

JuliusBread Wheat

(Germany)(AABBDD)

Fold coverage

x180 x210 X200* X200 X200 X200 X210

Scaffold L50 (N50)

7.0 Mbp(414)

6.0 Mbp(493)

28.9 Mbp(147)

5.75 Mbp(721)

5.1 Mbp(796)

7.1 Mbp(573)

5.3 Mbp(768)

Scaffold L90 (N90)

1.15 Mbp(1,827)

1 Mbp(2,013)

5.9 Mbp(564)

1.1 Mbp(2,879)

1 Mbp(3,194)

1.2 Mbp(2,457)

1 Mbp(3089)

Total assembly size

10.50 Gbp 10.45 Gbp 14.6 Gbp 14.44 Gbp 14.46 Gbp 14.55 Gbp 14.47

Unfilled gaps(=n)

1.63% 1.42% 1.48% 1.92% 1.64% 1.72% 1.77%

*- Including 30X coverage of Chromium data - Increases L50 by approx. 5X.

Current Status of Wheat Genomes

--Tetraploid-- ---------------- Hexaploid------------------

Next Steps

Complete assemblies with the addition of 30X coverage Chromium data – April, 2017 (C. Pozniak, A. Sharpe, N. Stein, NRGene)

Begin automated annotation of NRGENE RefSeq assemblies (K. Mayer)

RNASeq supported annotation (Earlham Institute)

Characterize structural variation (M. Mascher)

Comparative genomics (T. Wicker, B. Keller, H. Budak)

Cloning of priority genes (J. Poland/G. Muehlbauer , C. Pozniak, B. Keller, S. Krattinger)

Low coverage sequencing of wheat cultivars (JIC, Earlham Institute)

Richard Cuthbert Yuefeng RuanRon Knox Brain BeresColin Hiebert Curt McCartneyHarpinder Randhawa Rob Graf

Pierre Hucl Krysta WiebeKirby Nilsen Sean Walkowiak

Acknowledgments

Raju Datla Sateesh Kagale

Nils Stein Jesse Poland Martin Mascher

Andrew Sharpe*Kevin Koh

Gil Ronen

Assaf Distelfeld Gary Muehlbauer

Alvaro Hernandez*

Hikmet Budak Beat Keller

Klaus Mayer

Matt ClarkeMike Bevan

Thanks to our Funders

Pan-genome Feb 17 (Edwards lab, Australia)

Montenegro et al 2017. Plant Journal

Re-assembly of CSS and 18 additional varieties

Cultivar Total bases (Gbp) Sequencing depth

ABC-1 166 9.8

Alsen 190 11.2

BX-1 197 11.6

CH7 252 14.8

Drysdale 173 10.2

Excalibur 161 9.5

Gladius 184 10.9

H45 172 10.1

Kukri 247 14.5

OpataM85 196 11.5

Pastor 214 12.6

RAC 167 9.8

Volcani 169 9.9

W7984 341 20.0

Westonia 142 8.4

Wyalkatchem 339 19.9

Xi-1 244 14.3

Yp-1 222 13.1

Pan-genome Feb 17 (Edwards lab, Australia)

Genes

Average of 128,656 genes per cultivar (49 unique genes)

(89k shared by all 19 cultivars; 49k variable)

Pangenome of 140,500 genes

Core genome of 81,070 genes

SNP

36.4 M SNPs (99% are intergenic)

Gbrowse: http://appliedbioinformatics.com.au/cgi-bin/gb2/gbrowse/WheatPan/Download: http://wheatgenome.info/wheat_genome_databases.php