Population structure of European oat germplasm using the 6K oat SNP array and association analysis of frost tolerance

Birmingham, 25 Nov 2015

Giorgio Tumino

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

Plant material: the AVEQ collection

Diverse collection of 138 European oat accessions

Cultivars and landraces

DNA extracted from 10 plants

AVEQ project

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

Population structure

Continental Europe

Medit / Atlantic Europe

FT HD

Phenotyping

Heading date

Hullessness

Lemma colour

Frost Tolerance

Year2008

Year2009

64 5111

126 accessions

Dataset AVEQ0875 accessions

Dataset AVEQ0962 accessions

Growth chamber

Field trials

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.

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

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

GWAS – Lemma colour

Whole dataset

Marker order relative to Chaffin et al. (submitted)

Mrg20Mrg13Mrg17

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

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

Acknowledgements

René SmuldersRoeland VoorripsJoao PauloLuud Gilissen

CREA-GPG:

Valeria TerziCaterina MorciaRoberta GhizzoniFranz BadeckFulvia Rizza

JKI:

Christoph Germeier

AVEQ project

Nick TinkerJessica Schlueter

PCA and Ward’s clustering

Continental Europe

Medit / Atlantic Europe

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