Mobilizing genetic resources and optimizing breeding programs

J.-F. Rami – UMR AGAPDO NOT C

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Outline

• Genetic Diversity– characterization of ex situ Genetic Diversity– dynamics of in situ diversity– diversity and society

• Mobilizing diversity: pre-breeding• Optimizing breeding schemes• Final thoughts

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GENETIC DIVERSITY

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A continuous and collaborative effort of characterization of ex situ Genetic Diversity

Link with geographical information Lasky et al. 2015

2001

2001

2006

2013

2013

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Worldwide GWAS panel: biomass composition

Ingrid Vilmus

David Pot

Pectines

Fibre insolubles

hemicelluloses

cellulose

lignines

«Ce

llwa

ll»

Cellulose brute

WeendeNDF

ADF

ADL

ADF –ADL = « Cellulose Van

Soon »

• Genotyping : GBS : 200 000 imputed SNP withBeagle (Browning and Browning 2013)

• Analysis : Linear Mixed model taking into accountrelatedness using GEMMA (Zhou and Stephens, 2012) on each trial and 2-years blups in France and Mali

ClassTrait Abbreviate Description

Fibercomponents

NDF Neutral Detergent Fiber (% DM)

ADL Stem Acid Detergent Lignin (% DM)

ADF Stem Acid Detergent Fiber (% DM)

ADL/NDF Stem Lignin Content (% NDF)

CBW Stem Raw Cellulose (Weende, %DM)

CBW/NDF Stem Raw Cellulose Content (% NDF)

CVS Stem Cellulose Van Soon (% DM)

CVS/NDF Stem Cellulose Content (% NDF)

HEMI Stem Hemicellulose (% DM)

HEMI/NDF Stem Hemicellulose Content (% NDF)

Digestibility

CP Crude Protein (% DM)

MM Ash (% DM)

SMO Stem In Vitro organic matter degradation

IVNDFD Stem In Vitro NDF digestibility (% NDF)

Sugar and JuiceBRIX Brix (%)

BRIX30 Adjusted Brix to 30% DM in stems (%)

JUICE Stem Juice weight (g)DO N

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Worldwide GWAS panel: biomass composition

=> 78 genomic regions associated with BLUP for cell wall composition and digestibility

Ingrid Vilmus

David Pot

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From global to local:dynamics of in situ diversity

• Temporal dynamics (country scale)• Wild/cultivated gene flow

(country>village>field scale)• Impact of introduction of improved

variety in traditional system (village scale)

• Specific association panels (environments, uses)

Sagnard et al., 2011DO N

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Diversity and society

Social Process of Adaptation to Environmental Changes: How Eastern African Societies Intervene between Crops and Climate

Caroline Mwongera Montpellier SupAgro, UMR AGAP, Montpellier, France Joseph Boyard-Micheau CRC, Biogéosciences, UMR 6282 CNRS/ Université de Bourgogne, Dijon, France

Christian Baron CIRAD, UMR TETIS, Montpellier, France Christian Leclerc*CIRAD, UMR AGAP, Montpellier, France

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MOBILIZING DIVERSITY: PRE-BREEDING

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Integrating pre-breeding and genetic analysis: BCNAM

Grain yield (kg/ha)

GBS SNP density in 47 populations

47 populations4717 BC1F4 families

Direct variety development through PPB

Photo: ©E. Weltzien

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Biomass quality in BCNAM populations

GR KK KK

NDF (%MS) SMO (%OM)

Longueur d'ondes (nm)

Abso

rban

ce (l

og 1

/R)

Pectines

Fibre insolubles

hémicelluloses

cellulose

lignines

«Pa

rois

cel

lula

ire»

0,4 –0,6

< 0,2< 0,2

15/09/2016

KorotimiThera

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OPTIMIZING BREEDING SCHEMES

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A typical pedigree breeding schemeCross

Population

Evaluation

Fixation

Evaluation

Selection

Evaluation

Fixation

Selection…

Limiting

Limiting

Limiting

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A typical pedigree breeding schemeCross

Population

Evaluation

Cycle

Cycle

Cycle

Model

Fixation

Evaluation

QTLGS

Fixation

Cross

Population

Evaluation

Fixation

Evaluation

Selection

Evaluation

Fixation

Selection…

Limiting

Limiting

Limiting

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Integrating breeding and genetic analysis: MARS

Keninkeni Lata3Population 114 Population 118

x x

F4 seed increase (F5 Bulk)

Phenotyping3 sites x 2 sowing dates1 site for grain quality

F1

F2

F3

S2

S3

S4

Dec. 2008

March 2009

June 2009

Feb. 2010

QTL analysis Ideotype definition

Phenotyping3 sites x 2 sowing dates1 site for grain quality

F3 genotypingQTL analysis

Ideotype definition

Genotyping

C1 cycle (F4 families)C1 genotyping

C1 crosses

June 2010

Jan. 2011

June 2011

Jan. 2012C1 seed increase

(F2)

June 2012C1

evaluation (F3)

Tiandougou

C2 seed increase (F2)

C1 + C2 evaluation (F2)

Jan. 2013

June 2013C1 cycle (F4 families)

C1 genotypingC1 crosses

C2 cycle (C1 families)C2 genotyping

C2 crosses

C3 cycle(C2 + C1 families)

C3 genotypingC3 crosses

F4 seed increase (F5 Bulk)

June 2008

F1

F2

F3

S2

S3

S4

Jan. 2013

June 2014

C1 + C2 + C3 evaluation (F2)

C3 seed increase (F2)

Oct 2014

C2 cycle (C1 families)C2 genotyping

C2 crosses

C3 cycle(C2 + C1 families)

C3 genotypingC3 crosses

On Farm variety testing

C1 + C2 + C3 evaluation

SotubaSD1

SotubaSD2

CinzanaSD1

CinzanaSD2

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At the whole breeding program level

Cross

Population

Evaluation

Cycle

Cycle

Cycle

Model

Fixation Evaluation

Cross

Population

Evaluation

Cycle

Cycle

Cycle

Model

Fixation Evaluation

Cross

Population

Evaluation

Cycle

Cycle

Cycle

Model

Fixation Evaluation

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Historical dataPedigree

Crop models

Environmental data

QTLs database

Pectines

Fibre insolubles

hemicelluloses

cellulose

lignines

«Ce

llwa

ll»

Cellulose brute

WeendeNDF

ADF

ADL

ADF –ADL = « Cellulose Van

Soon »

Pre-

bree

ding

GWAS

GWAS results

At the whole breeding program level

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FINAL THOUGHTS

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New challenges for plant breeding

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New challenges for plant breeding

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