Mobilizing genetic resources and optimizing breeding programs DO NOT COPY. J.-F. Rami UMR AGAP

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1 Mobilizing genetic resources and optimizing breeding programs J.-F. Rami UMR AGAP

2 Genetic Diversity Outline characterization of ex situ Genetic Diversity dynamics of in situ diversity diversity and society Mobilizing diversity: pre-breeding Optimizing breeding schemes Final thoughts

3 GENETIC DIVERSITY

4 A continuous and collaborative effort of characterization of ex situ Genetic Diversity Link with geographical information Lasky et al

5 Worldwide GWAS panel: biomass composition «Cell wall» Pectines Fibre insolubles hemicelluloses cellulose lignines Cellulose brute Weende Genotyping : GBS : imputed SNP with Beagle (Browning and Browning 2013) Analysis : Linear Mixed model taking into account relatedness using GEMMA (Zhou and Stephens, 2012) on each trial and 2-years blups in France and Mali NDF ADF ADL ADF ADL = «Cellulose Van Soon» David Pot Class Trait Abbreviate Description NDF Neutral Detergent Fiber (% DM) ADL Stem Acid Detergent Lignin (% DM) ADF Stem Acid Detergent Fiber (% DM) ADL/NDF Stem Lignin Content (% NDF) Fiber CBW Stem Raw Cellulose (Weende, %DM) components 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) CP Crude Protein (% DM) Digestibility MM Ash (% DM) SMO Stem In Vitro organic matter degradation IVNDFD Stem In Vitro NDF digestibility (% NDF) BRIX Brix (%) Sugar and Juice BRIX30 Adjusted Brix to 30% DM in stems (%) JUICE Stem Juice weight (g) Ingrid Vilmus

6 Worldwide GWAS panel: biomass composition => 78 genomic regions associated with BLUP for cell wall composition and digestibility David Pot Ingrid Vilmus

7 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., 2011

8 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

9 MOBILIZING DIVERSITY: PRE-BREEDING

10 Photo: E. Weltzien Integrating pre-breeding and genetic analysis: BCNAM Direct variety development through PPB 47 populations 4717 BC 1 F 4 families Grain yield (kg/ha) GBS SNP density in 47 populations

11 Biomass quality in BCNAM populations NDF (%MS) SMO (%OM) GR KK KK Pectines Fibre insolubles hémicelluloses «Parois cellulaire» 15/09/2016 cellulose lignines 0,4 0,6 Absorbance (log 1/R) < 0,2 < 0,2 Korotimi Thera Longueur d'ondes (nm)

12 OPTIMIZING BREEDING SCHEMES

13 A typical pedigree breeding scheme Cross Population Fixation Selection Fixation Selection Limiting Limiting Limiting

14 A typical pedigree breeding scheme Cross Population Fixation Selection Fixation Selection Cross Limiting Population Fixation Limiting Limiting Fixation Model QTL GS

15 Integrating breeding and genetic analysis: MARS June 2008 Dec March 2009 June 2009 Feb June 2010 Jan June 2011 Jan June 2012 Jan June 2013 Jan June 2014 Oct 2014 Population 114 Population 118 Keninkeni x Tiandougou x Lata3 Genotyping C1 seed increase (F2) C1 evaluation (F3) F4 seed increase (F5 Bulk) Phenotyping 3 sites x 2 sowing dates 1 site for grain quality QTL analysis Ideotype definition C1 cycle (F4 families) C1 genotyping C1 crosses C2 seed increase (F2) F1 F2 F3 C1 + C2 evaluation (F2) On Farm variety testing S2 S3 S4 C2 cycle (C1 families) C2 genotyping C2 crosses C3 cycle (C2 + C1 families) C3 genotyping C3 crosses C3 seed increase (F2) C1 + C2 + C3 evaluation (F2) F1 F2 F3 S2 S3 S4 F4 seed increase (F5 Bulk) Phenotyping 3 sites x 2 sowing dates 1 site for grain quality F3 genotyping QTL analysis Ideotype definition C1 cycle (F4 families) C1 genotyping C1 crosses C2 cycle (C1 families) C2 genotyping C2 crosses C3 cycle (C2 + C1 families) C3 genotyping C3 crosses Sotuba Sotuba Cinzana Cinzana SD1 SD2 SD1 SD2

16 At the whole breeding program level Cross Population Fixation Model Cross Population Fixation Model Cross Population Fixation Model

17 Pre-breeding GWAS At the whole breeding program level «Cell wall» Pectines Fibre insolubles hemicelluloses cellulose lignines Cellulose brute Weende NDF ADF ADL ADF ADL = «Cellulose Van Soon» GWAS results QTLs database Environmental data Crop models Historical data Pedigree

18 FINAL THOUGHTS

19 New challenges for plant breeding

20 New challenges for plant breeding