A genome-wide SNP scan for QTL associated with adult plant rust resistance in East African bread wheat G. Macharia 1 , S. Chao 2 and J. Anderson 1 ty of Minnesota, Department of Agronomy and Plant Genetics, S 2 USDA-ARS Biosciences Research Laboratory, FARGO ND BGRI Workshop_2012
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A genome-wide SNP scan for QTL associated with adult plant rust resistance in East African bread wheat
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A genome-wide SNP scan for QTL associated with adult plant rust resistance
in East African bread wheat
G. Macharia1 , S. Chao2 and J. Anderson1
1University of Minnesota, Department of Agronomy and Plant Genetics, ST PAUL MN
2USDA-ARS Biosciences Research Laboratory, FARGO ND
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Outline
• Section 1: General overview, definitions
• Section 2: Materials, Methods, Pre-analyses
• Section 3: Association mapping results
• Section 4: Research highlights
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Section 1
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Source: Tester and Langridge, 2007
Cereal Production targets
• 37% increase required to meet 2050 demand
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yield gap
Wheat: projecting ahead
• Wheat needs to contribute 25% by 2025
1966-79 1984-94 1995-050
1
2
3
4 3.6
2.8
1.1
Global wheat yield growth
Period
Rate
(%)
• At 1.1% growth, wheat can only contribute 17%Data source: CIMMYT
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Confronting the yield gap
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Source: CIMMYT, 2011
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Breeding for Durable resistance
• Key to circumvent rust-associated losses
• An opportunity to tap cutting edge techniques Marker assisted recurrent selection Genomic selection Association mapping
• Gene/QTL discovery a pre-requisite
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Association Mapping
• Identification of significant statistical association between a phenotypic trait and molecular marker based on LD
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Linkage Disequilibrium
Source: Hamblin et al, 2011
• Non-random co-inheritance of alleles at different Loci
…higher marker density
…greater resolutionBGRI Workshop_2012
Population Structure
P3
P1 P2
• Subpopulations at differing allele frequencies
Mapping panel
• Could arise from adaptation, domestication
• Creates LD between unlinked loci (false positives)
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Section 2
Materials, Methods & pre-analyses
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Bread wheat mapping panel
• 160 Kenyan lines• 70 Ethiopian
Historicals to recent releases
• 37 Founders
• Additionally, 35 Minnesota lines
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Phenotyping Trait Location Year
Stem rust APR St Paul, MN 2010 St Paul, MN 2011 St Paul, MN 2012 Njoro, Ken 2011 Njoro, Ken 2012
Leaf rust APR St Paul,MN 2010 St Paul, MN 2011 St Paul, MN 2012 El Batan, MX 2011 Crookston, MN 2012
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Modified Cobb Scale Severity (%) × Infection type = Coefficient of infection0 - 100 R (0.0) MR (0.4) e.g. 60MS MS (0.8) (60 x 0.8) = 48 S (1.0)
Disease scoring• 2 to 3 scores taken for each line
• Last score converted to Coefficient of infection
Stem rust
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Leaf rust
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Genotyping
• 9000 SNP Illumina’s infinium assay
• GenomeStudio® for ‘Allele calling’
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Polymorphic Ambiguous
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• Low quality SNPs, MAF < 0.05 eliminated
• 5987 polymorphic SNPs used
Genotyping
Population Structure (Q)
• Estimated using 235 SNPs >4 cM apart
• Software: ‘STRUCTURE v.2.3.4’ (Pritchard et al., 2000)