Melissa Garcia 13 th International Wheat Genetics Symposium Exploring genetic diversity in bread wheat using nested association mapping
Melissa Garcia
13th International Wheat Genetics Symposium
Exploring genetic diversity in bread wheat using
nested association mapping
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• 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
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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
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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
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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
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Yu et al. 2008Photos Takashi Okada
NAM populations
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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
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Origin of the NAM parents
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Diversity Panel
Beata SznajderDiane Mather
Genetic diversity of the NAM parents
NAM parents
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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
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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
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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
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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
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• 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
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Exotic x Scout
Exotic x Gladius
GWAS for presence of awns
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awn suppressor B1
11/09/2017 18
2017
• Single location yield trials
2018 - 2019
• Selected populations in multi-location yield trials
Plan
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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?
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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