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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