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Population structure of European oat germplasm using the 6K oat SNP array and association analysis of frost tolerance
Birmingham, 25 Nov 2015
Giorgio Tumino
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Contents
Genotyping of a European oat collectionPopulation structure
Phenotyping
FROST TOLERANCEHeading date
Genome-wide Association Study (GWAS)
GWAS for simple traitsGWAS for frost tolerance
HullessnessLemma colour
Simple traits
Complex traits
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Plant material: the AVEQ collection
Diverse collection of 138 European oat accessions
Cultivars and landraces
DNA extracted from 10 plants
AVEQ project
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Genotyping and SNP signals analysis
6K Infinium SNP Array4975 beads
Hybridization ratio X/(X+Y)
Genotype calling
- Analysis of DNA from bulks of plants- Continuous vs discrete variables
SNP Filtering:- NA < 25%- Variance > 0.001
126 accessions3567 SNPs
ratios
Freq
uen
cy
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Population structure
Continental Europe
Medit / Atlantic Europe
FT HD
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Phenotyping
Heading date
Hullessness
Lemma colour
Frost Tolerance
Year2008
Year2009
64 5111
126 accessions
Dataset AVEQ0875 accessions
Dataset AVEQ0962 accessions
Growth chamber
Field trials
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Phenotyping
Treatment 1
3-1°C (day/night) 4 weeks
freezing –12°C
Frost tolerance-
Chlorophyll fluorescenceevaluation (Fv/Fm)
Growth chamber1 week-old plants Treatment 2
12-7°C (day/night) 3 weeks
freezing –7°C
The Fv/Fm ratios were measured after a recovery period of 24 h.
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GWAS – Statistical models
1. LM - Simple association2. MLM - Correction for kinship3. MLM - Structure compensation by principal components
3. MLM
1. LM
Frost tolerance
Hullessness
P-P plots
AVEQ08 AVEQ09
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GWAS - Hullessness
Hull percentagequantitative
Hullessnessqualitative
AVEQ08
Mrg21
N1 locusCdo482 (199 cM)De Koeyer et al. 2004
AVEQ09
Whole dataset
Marker position relative to Chaffin et al. (submitted)
Mrg21
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GWAS – Lemma colour
Whole dataset
Marker order relative to Chaffin et al. (submitted)
Mrg20Mrg13Mrg17
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GWAS – Frost toleranceA
VEQ
08
AV
EQ0
9
Mrg20 - Vrn1Nava et al. 2012
Marker order relative to Chaffin et al. (submitted)
Mrg01Mrg11Mrg21 – Wooten et al. 2008
Mrg33
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Conclusions
Population structure analysis detected two groups mainly based ongeography, but also related to growth habit
GWAS is a feasible option for QTL mapping of winterhardiness
The use of hybridization ratios may represent a successfull approach forpolyploids genomes in which SNPs are detected in more than onesubgenome, requiring manual curation for genotype calling
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Acknowledgements
René SmuldersRoeland VoorripsJoao PauloLuud Gilissen
CREA-GPG:
Valeria TerziCaterina MorciaRoberta GhizzoniFranz BadeckFulvia Rizza
JKI:
Christoph Germeier
AVEQ project
Nick TinkerJessica Schlueter
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PCA and Ward’s clustering
Continental Europe
Medit / Atlantic Europe
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Locus_Name AVEQ08 -12 AVEQ08 -7 AVEQ08 AVEQ09 -12 AVEQ09 -7 AVEQ09 Group Distance
GMI_ES01_c1416_473 3 Mrg01 101.5
GMI_ES02_c15652_109 3 Mrg01 115.4
GMI_ES14_c16380_214 6 6 6 Mrg01 117.4
GMI_DS_LB_6614 3 3 3 Mrg02 10.8
GMI_ES05_c119_150 3 3 Mrg02 67.4
GMI_ES03_c4470_197 3 Mrg03 46.3
GMI_ES15_c6000_411 3 Mrg03 46.3
GMI_DS_CC7686_215 4 Mrg03 58.6
GMI_DS_LB_9109 4 Mrg04 44.7
GMI_GBS_80856 3 Mrg05 111.3
GMI_ES05_lrc12441_760 4 Mrg08 149.2
GMI_ES01_c30278_396 4 Mrg11 8.8
GMI_ES05_c13603_259 6 6 Mrg11 9.8
GMI_ES15_c2773_491 3 3 Mrg11 9.8
GMI_ES17_c2917_533 5 5 Mrg11 9.8
GMI_ES_CC13854_225 5 Mrg11 42
GMI_ES01_c14408_309 4 Mrg12 71.9
GMI_ES_CC9053_245 3 Mrg13 114.6
GMI_ES02_c911_580 4 Mrg15 87.2
GMI_ES01_c26788_88 3 6 6 Mrg20 143.6
GMI_ES_LB_7159 3 Mrg21 27.3
GMI_GBS_111208 3 3 Mrg21 113.2
GMI_ES05_c8031_345 3 Mrg21 114.7
GMI_GBS_4508 3 Mrg21 142
GMI_DS_LB_10188 4 Mrg23 18.3
GMI_ES01_c10257_104 6 Mrg23 28.5
GMI_ES15_c6451_437 6 Mrg23 28.5
GMI_GBS_96887 3 Mrg24 95.3
GMI_GBS_17527 6 4 Mrg33 26.3
GMI_ES01_c10712_810 5 5 NA NA
GMI_ES01_c13250_258 3 4 NA NA
GMI_ES15_c265_213 3 3 6 NA NA
GMI_ES22_c10794_54 3 NA NA