1. Bioinformatics and Biostatistics in Limagrain / Biogemma
JOBIM Conference, July 2015

2. An international agricultural cooperative group
4th largest seed company
worldwide
Nearly
2,000 farmer members
Sales of nearly 2 billion Euros
Nearly
9,000 employees
Subsidiaries in 42 countries
13.5% of turnover
re-invested in research
A portfolio of strong brands

3. A group that specializes in seeds and cereal products
Field Seeds
Field
Seeds
Limagrain Coop
Vegetable
Seeds
Vegetable
Seeds
Cereal Products
Bakery
Products
Garden
Products
Cereal
Ingredients

4. A European group open to the world
64% of sales
64% of workforce
Nearly ,000 employees
66 nationalities
69% of sales achieved outside France
Subsidiaries in countries
23% of sales
16% of workforce
7% of sales
12% of workforce
Americas
Asia & Pacific
6% of sales
8% of workforce
Africa & Middle East

5. An innovative group 13.5% of turnover invested in research 200 M€
with collabora-
tions)
13.5%
10.2%*
5.4%*
2.25%*
Average
industry
Automobile industry
Pharmaceutical industry
Limagrain
* Source : Leem - April 2013

6. BIOGEMMA, a research partnership
Biotechnologies
9.5%
16%
55 %
10%
Field Seeds

7. Biogemma Identification of genes associated with agronomic traits
Development of GM varieties in cereals
Development of tools and knowledge
BIOINFORMATICS |

8. Bioinformatics for breeding
Molecular Breeding
Biostatistics
Discover Associations
Bioanalysis
Explain Associations
Tools
Bioinformatics db
Analyze NGS-based data
Develop databases and tools to store and analyse biological data

9. HPLC Crystallo-graphy
Omics analysis
Phenotype
Environment
Chromatin
Silencing
Regulation of transcription
miRNA, siRNA
Protein modification, interaction, turnover
Regulation of translation
RNA stability
What we
measure
Markers
mRNA
Transcription levels, DGE
Protein
Quantity, Activity levels
Trait
Phenome
Regulation
of expression
How we
Genotyping
Sequencing
RNA-Seq
microarrays
HPLC Crystallo-graphy
IA, NIR, HPLC, eyeball
DNA
Genes, Genomes
Biological
material
RNA
mRNA, rRNA
Transcriptome
Enzyme
Proteome
Metabolome
Transcription
Translation
Expression
LD mapping, GWAS, GS

10. A great deal of complex information to correlate
Environment
Genotype
Phenotype
Data processing tools getting more and more sophisticated

11. Data analysis & processing
Data Life Cycle
Data production & acquisition
Results interpretation & decision support
field trials
predicting cross value
genotyping sequencing
genomics
LIMS, databases
evaluation of individuals
data retrieval
quality control
building predictive model
statistical analyses
Data analysis & processing

12. Data production & acquisition
Sequencing
NGS based: whole genome, targeted sequencing, transcriptome
Deliverables: SNP, structural variations, gene expression level, genomes
Genotyping
High density chips
103 – 105 SNP
105 samples
Automate calling / quality control
Steem_Z30_rep1
Steem_Z30_rep2
Steem_Z32_rep1
Steem_Z32_rep2
Steem_Z65_rep1
Steem_Z65_rep2

13. Data production & acquisition
Phenotypic data
Automate data collection
Sensors, images, NIR spectrometry…
Adjustments/corrections by geostatistical methods
Extraction of relevant information

14. Data production & acquisition
Environmental data
Local / internal:
Sensors, airborne imagery, …
Global / external:
Databases, internet, satellite images, …
Precise description of the growing conditions
Air temperature
Relative humidity
Dew point

15. Modelling Molecular data Cost  Availability 
Predict: genotype  phenotype
QTL/GWAS – identify genomic regions involved
genomic selection – "black box" approach

16. Modelling Statistical methods Linear mixed models Bayesian approaches
More and more complex models
GxE
Epistasis
 computationally intensive methods
(from Van Eeuwijk et al., 2010)

17. Data management Integrative viewer for genomic data Databases
BIG DATA: large volume of structured and unstructured data

18. Infrastructure Local on-the-premises computing
"data-centric computing"
Central
enterprise resources
Security
NGS data analysis on BIOGEMMA HPC (912 cores)
Elastic (cloud)
flexibility
low cost / hour CPU

19. Take Home Messages
Bioinformatics: a major activity supporting a large range of applications in Limagrain
Genomics
Phenomics
Enviromics
Biostatistics, Modelling and Prediction
Big Data (HPC, data management)
Both R&D and Applied
In a highly competitive and challenging research area
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20. More information…
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21. Thank you