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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