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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