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16th - 17th November 2015

Clermont-Ferrand, FranceInternational

Wheat

Innovation

Workshop

Genomic selection in a real

wheat breeding programmes

Gilles Charmet INRA UMR GDEC

Jrme Auzanneau, Ari-Obtentions

International Wheat Innovation Workshop - 16th & 17th November 2015 - Clermont-Ferrand, France

Wheat in France: a strategic crop

Breeding goals-high yield

-Lodging tolerance

-Disease resistance

-Protein content

-High test weight

-High bread making grade

40000 hectares organic

farming

Average yield: ~7.5 t/ha

9 t/ha Pas de Calais

5 t/ha Gers

~5 millions hectares

conventionnal

farming

On average 6.3 pesticide

Tilling (55%), No-till

(45%)

# 165 kg/ha mineral N

DURUM

Worldwide ranking 5th (1st in EU)2015 highest harvest: 40.8 Mt on 5.1 Mha

average yield 7.9 t/ha)

International Wheat Innovation Workshop - 16th & 17th November 2015 - Clermont-Ferrand, France

Typical wheat breeding scheme: long cycles

F1

F2

F3

F4

F5

F6

F7

F8

F9

lines

10

years

Crosses: 10

105

104

103

102

101

100

F2 bulks

F3 bulks

REGISTRATION

International Wheat Innovation Workshop - 16th & 17th November 2015 - Clermont-Ferrand, France

Typical wheat breeding scheme:

Crosses: 10

105

104

103

102

101

100

F2 bulks

F3 bulks

Experiment /traits

Loc No remarks

Single plantsVisual trait

One Low h# random selection

1-3 rowsVisual+diseases

1-2 Negative selection of worse rows/plants

Yield plots%protein

2-3, 1 rep

Low h

Yield plot % protIndirect Q test

5-82-4 rep

Accurate yield evaluation+ GxL

Yield plot % protBread making

8-104 reps

Accurate yield + BM tests + G x Y

Official registration trials

12-15 4 repsT NT,LI

2 year official trialsBM test on year 1 harvest

(Relatively) inefficient for complextraits in early generations

International Wheat Innovation Workshop - 16th & 17th November 2015 - Clermont-Ferrand, France

Genomic selection: how does it work

BWGS pipeline V2.0: General structure

Dimentional

reduction

Dimentional

reduction

Imputation of

genotypes

Imputation

Comparison

of models

(cross-

validation)

Optimal

models GEBV

Training

genotypic

data

Training

phenotypic

data

Target

phenotypic

data

Cor (y, GEBV)

MSEP, SD

(yhat)Cor (y, GEBV)

bwgs.selgen.cv()

bwgs.predict()

quality indicators

International Wheat Innovation Workshop - 16th & 17th November 2015 - Clermont-Ferrand, France

Advantages of GS over phenotypic selection

DG = i h sG / L

Selection intensity: Can be increased if Genotyping cost < phenotyping

Cycle length: can beShortenned by juvenilSelection and intermating

h or prediction accuracyGenetic variability: can bemonitored by markers

International Wheat Innovation Workshop - 16th & 17th November 2015 - Clermont-Ferrand, France

Where to insert GS in a wheat breeding scheme ?

Where to insert GS in a wheat

breeding scheme ?

Crosses: 10

105

104

103

102

101

100

F2 bulks

F3 bulks

REGISTRATION

DG = i h sG / L

International Wheat Innovation Workshop - 16th & 17th November 2015 - Clermont-Ferrand, France

Propose new schemes

Crosses: 10

105

104

103

102

101

100

F2 bulks

F3 bulks

REGISTRATION

DG = i h sG / L

Select parents

crosses

F2 or DH

Apply GS

2-3 yearsCycles

GS

Adapted from J HickeyEUCARPIA Biometrics in Plant Breeding 2015

Use historicaldata for training

Select parents on GEBV per se of expected

progeny BV

Re-invent short cycle Recurrent selection

An application to INRA-AO real winterwheat breeding programme:

Preliminary results

Jrme AUZANNEAU

AGRI OBTENTIONS

International Wheat Innovation Workshop - 16th & 17th November 2015 - Clermont-Ferrand, France

Genotyping: The BW420K SNP Axiom chip

International Wheat Innovation Workshop - 16th & 17th November 2015 - Clermont-Ferrand, France

Use of historical dataCrossa et al 2010, Dawson et al 2013, Rutkoski et al 2015)

Yield, protein: 35 298 records/ 1589 lines (760 Genotyped) Fusarium HB: 27 135 records, 1705 lines (672 G) Bread-making traits: 5887records / 526 lines (357 G)

F7 issued in 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014

year of trial

2002 F7: 184

2003 F8: 64 F7: 186

2004 F9: 4 F8: 72 F7: 221

2005 F9: 6 F8: 93 168

2006 F9: 11 72 161

2007 8 65 183

2008 5 77 176

2009 7 66 172

2010 8 54 176

2011 4 56 178

2012 6 66 147

2013 8 73 177

2014 9 88 176

2015 ? ?

BLUE lmer(Y~geno+(1|year:site:trial:bloc)+(1|year:site:geno),data=)

BLUP lmer(Y~(1|year:site:trial:bloc)+(1|geno)+(1|year:site:geno),data=Y)

Cor (YieldBLUP, YieldBLUE)=0.97

International Wheat Innovation Workshop - 16th & 17th November 2015 - Clermont-Ferrand, France

Heritability and prediction accuracy

(GBLUP 10 000 random markers)

TRAIT h = s2G/(s2G+s2

GE+s2

e) r = cor(GEBV, y) r/sqrt(h)

Yield and protein %:

Yield 0,307 0,558 1,007

Protein 0,513 0,557 0,778

Alveograph:

dough strength W 0,705 0,536 0,638

tenacity P 0,757 0,622 0,715

extensibility L 0,564 0,574 0,764

P / L 0,062 0,301 1,209

Bread making

dough score 0,392 0,404 0,645

crumb score 0,371 0,448 0,736

bread score 0,275 0,405 0,772

total score 0,433 0,452 0,687

loaf volume 0,44 0,427 0,644

Other:

heading date 0,787 0,38 0,428

plant height 0,296 0,353 0,649

hagberg FN 0,505 0,427 0,601

dietary fibre (visco) 0,908 0,68 0,714

Fusarium HB score 0,563 0,63 0,84

GS accuracy is good enough for most traits to enable genetic progress

International Wheat Innovation Workshop - 16th & 17th November 2015 - Clermont-Ferrand, France

Comparing accuracy among methods

Yield, N=760, 10 000 markersMETHOD r = cor(GEBV, y)

MKRKHS 0.5698 a

RKHS 0.5688 a

Bayesian LASSO 0.5646 a

RF regression 0.5628 a

Bayes B 0.5618 a

EGBLUP 0.5606 a

Bayes A 0.5560 a b

Bayes C(p) 0.5514 a b

Bayesian RR 0.5508 a b

GBLUP 0.5452 b

LASSO 0.5316 b

Elastic net 0.5282 b

SVM 0.2882 c

NK homogeneous groups

Various prediction methods giveconsistent results: GS is robust

International Wheat Innovation Workshop - 16th & 17th November 2015 - Clermont-Ferrand, France

Application to real breeding linesDoubled haplode production from 14 crosses (1000 DH)Year 1

CTPS1

Genotyping (WP1)

2nd generation crosses

Genomic

Selection

DH production

Phenotypic

Selection

Genotyping WP1

Genomic

Selection

2

3

4

5

6

7

8

Yie

ld:

Tre

ate

d v

s

Un

tre

ate

d

Yield + quality test

(7 to 9 locations)

CTPS2

registration

?

CTPS1

Yie

ld:

Tre

ate

d v

s

Un

tre

ate

d

Yiled + quality test

(7 to 9 locations)

CTPS2

regisration

?Phenotypic

Selection

(Classic selection)

1st cylcle of GSY

iled

:

Tre

ate

d v

s

Un

tre

ate

d

Yield + quality test

(7 to 9 locations)

2nd cycles of

GS

International Wheat Innovation Workshop - 16th & 17th November 2015 - Clermont-Ferrand, France

Phenotypic selection

DH

1600 haploid plantlets from 14 crosses

Seed X: 990 DH with > 30 seeds

Nursery

990 rows, inoculation Yellow rust

140 lines selected

Yield

Nursery + unreplicated plots x 3 loc

35 best lines selected for comparison

International Wheat Innovation Workshop - 16th & 17th November 2015 - Clermont-Ferrand, France

Genomic selection

DNA

990 DH lines genotyped with BW420K

188 000 polymorphic SNP

training

Training set = 760 historical lines

GEBV with GBLUP

GEBV

Selection on GEBV for yield in H/L input

30/990 or 10 /140 for comparison

International Wheat Innovation Workshop - 16th & 17th November 2015 - Clermont-Ferrand, France

2014 2015 Comparison on trials

Qx / ha % Tem Qx / ha % Tem Qx / ha % Tem

Min 72,8 75,8 36,8 45,1 57,7 63,4

Max 98,6 103,6 85,5 104,7 92 103,6

Mean 86,3 89,7 70,1 85,9 78,2 87,8

Genomic selection

Treated Untreated Treated + Untreated

Qx / ha % Tem Qx / ha % Tem Qx / ha % Tem

Min 87,3 89,7 65,6 80,5 79 87,7

Max 106,6 109,5 89,2 109,5 97,9 109,5

Mean 94,4 97,3 75,9 93,1 85,2 95,2

Treated + Untreated

Phenotypic selection

Treated Untreated

International Wheat Innovation Workshop - 16th & 17th November 2015 - Clermont-Ferrand, France

PS vs GS comparison: top lines