Melissa Garcia

13th International Wheat Genetics Symposium

Exploring genetic diversity in bread wheat using

nested association mapping

2

• Spring wheat grown in winter season

• Average yield ≈ 1.8 t/ha

• Total area ≈ 12 mill ha

• A bad drought year can lead to a loss of 20% (AUD 350 million)

Wheat belt in Australia

Delphine Fleury

3

QTL mapping in bi-parental populations

X• 3 mapping populations

• RAC875 x Kukri

• Excalibur x Kukri

• Drysdale x Gladius

• >50 field trials

• Yield

• Yield components

• Maturity, heading date

• Plant height

• Early vigour

• Floret sterility

• Grain and flour quality

• Leaf chlorophyll

• GlaucousnessDelphine Fleury

4

Delphine Fleury

A Triticeae diversity panel of 1018 accessions~560 bread wheat accessions

T. aestivum varieties

T. aestivum landraces

Synthetic T. aestivum

T. turgidum durum

T. urartu

T. monococcum

T. boeticum

T. turgidum dicoccum

T. turgidum dicoccoides

Triticale

• Australian elite lines

• CIMMYT drought and heat

stress collection

• Parents of populations

developed for evaluating

drought and heat stress

tolerance

• Key germplasm from

breeding programs around

the world

5

Genotyping using the Illumina 90k SNP Array

Ute Baumann, Andy Timmins, Matt Hayden ,Takashi Okada

• 432 varieties, 96 landraces, 37 synthetic hexaploid

• ~ 35,000 polymorphic markers

• GWAS for heat and drought tolerance in field and controlled conditions

6

Yu et al. 2008Photos Takashi Okada

NAM populations

7

Selection of Parents

Diverse donor parents

• Mostly based on origin

• Areas affected by heat and drought

• Heat tolerance panel

• Nitrogen use efficiency panel

Ken ChalmersNick CollinsMamoru Okamoto

Reference Parents

• Australian elite varieties

8

Origin of the NAM parents

9

Diversity Panel

Beata SznajderDiane Mather

Genetic diversity of the NAM parents

NAM parents

10

Genotype

75 Diverse Donors x 2 Recurrent Parents (Gladius and Scout)

Recurrent x F1

BC1F2

150 BC1F4 families

Culling

BC1 BC1 BC1 BC1 BC1 BC1 BC1 BC1 (75)

Ken ChalmersPeter Langridge

Wheat NAM Population

BC1F3

11

Genotyping of the NAM families

Matthew HaydenKerrie Forrest

• Good coverage

• Low cost per line

• Targeted genotyping-by-sequencing (GBS) approach

• Used information from the Illumina 90K SNP genotyping of the

parents to select target SNPs

12

Genotyping of the NAM families

Matthew HaydenKerrie Forrest

• Mapped polymorphic SNPs against IWGSC WGA v0.4

• Selected SNPs well distributed across the genome

• 1 SNP per Mb

• ~ 7,000 SNPs

• Higher number at ends of the chromosomes

• 1 SNP per 250Kb

• ~ 5,000 SNPs

1A#

SNP

pe

r M

B

MA

F

# SN

P p

er

MB

# SN

P p

er

MB

MA

FM

AF

Matthew HaydenKerrie Forrest

14

Targeted GBS Assay (tGBS)

A B D

1 700 921 339 1,960

2 723 1,095 579 2,397

3 624 715 272 1,611

4 598 446 116 1,160

5 766 1,009 287 2,062

6 626 636 220 1,482

7 787 676 337 1,800

4,824 5,498 2,150 12,472

Distribution of SNP loci contained in tGBS assay

Matthew HaydenKerrie Forrest

Genotyping test run

15

• 413 lines from 28 populations

• 20 Exotic x Gladius

• 8 Exotic x Scout

• ~ 16,000 markers

• Presence of awns segregating in 3 populations

• GWAS to validate genotyping and population

design

16

Exotic x Scout

Exotic x Gladius

GWAS for presence of awns

17

awn suppressor B1

11/09/2017 18

2017

• Single location yield trials

2018 - 2019

• Selected populations in multi-location yield trials

Plan

19

Simulation Studies

• Aim to optimise detection power of the NAM population by altering the

design

• More families, fewer lines each or vice versa?

• One or two reference parents?

• Do certain designs perform better for different QTL architectures?

• Is there a good all-rounder?

20

www.wheathub.com.au

Acknowledgments

09/03/17 21

Delphine Fleury Priyanka Kalambettu Sayuri Watanabe

Pooja VashistMihiranga Gunesekara

Nick CollinsMamoru OkamotoStephan Haefele

Ute BaumannElena Kalashyan

Ken ChalmersPeter LangridgeDiane MatherBeata SznajderAndy Timmins

Matthew HaydenKerrie Forrest

Robert Pontre

Dan Mullan

ARC Wheat Hub Director Technical Support