Page 1

Imagine Phenomenal Breeding

Arjen J. van Tunen CEO


Introduction

• the AgFood Biotechnology World: Vision of KeyGene • Identity KeyGene • Imagine Phenotyping Applications for genetic improvements of crops


World Crop Production

Need for doing more with less: 2x increased crop production with less resources (land, water & nutrients) and with lower impact on environment Genetic improvement of 6F Crops necessary to meet future demands - Traditional breeding - Biotechnology KeyGene actively participates in meeting (part of) these challenges


Global seed market

43.5%

23.4% 16.4%

2.1% 14.6%

• • • • • • • • •

Maize 40.3% Soybean 18.4% Vegetables 15.8 % Cereals 7.4% Rice 5.7% Rapeseed 4.4% Cotton 4.2% Sugarbeet 1.9% Sunflower 1.9%


Global seed market

Growth 2011: 11.9% to $34,5b* GM seed growth 21.9% to $15.7b few major traits: targets for KeyGene via our non GM approach

Conventional seeds growth 4.8% to $18.8b many trait targets for KeyGene *Phillips McDougall September 2011


Why the value/price of tomato seeds are so high? Like an iPhone many apps included: • High yield: 50 kg/m2 (~5 kg/m2 in Others) • Multiple resistances • Others (taste, shape, color, …) TyTmC5VF2N Nematode Fusarium race 1 & 2 Verticilium wilt Cladosporium 5 Tomato mosiac virus TYLCV

How to breed such cultivars in future? Molecular Breeding & Molecular Mutagenesis Combined with HT Phenotyping


KeyGene 2012: active world-wide

Rockville Washington DC

Wageningen

Shanghai

22 years experience, 140 scientists Largest Ag Food Biotech Company in EU


Passion KeyGene’s passion is a Green Gene Revolution approach to explore and exploit existing and induced natural genetic variation in vegetable and other 6F crops

Food

Feed

Fiber

Fuel

Flowers

Fun


Long-term partnerships With leading industry players

Vegetables


KeyGene’s Proprietary Technology & Trait platforms Lead Discovery Molecular Mutagenesis Molecular Breeding

Traits Phenotyping

Improved Varieties to sustainably feed the world


Breeding practices for crop improvement Phenotyping

Field

Greenhouse

Past

Phenotyping

B r e e d i n g

DNA Genotyping

Field Molecular & GM & Conventional Breeding Greenhouse

Current

G e n o m i c s


Breeding for crop improvement: Future Phenotyping

Sequence Based Genotyping

* Molecular breeding

Field

PhenoFab * Molecular Pheno mutagenesis typing * GM breeding Greenhouse

Genomics

Data handling and data integration

<Crop>Pedia Growth regulators, treated seeds, substrates


Molecular Breeding & Molecular Mutagenesis Complex trait QTL GWAS GS

Precision Phenotyping Plant Phenotypes

Data integration <Crop>Pedia

Metabolomics Proteomics Transcriptomics

HTP sequencing

Genes

Genome

Omics based trait discovery (KeySeeQ速)

Trait Validation KeyPoint速- MB

Trait Application


Sequence based genome assemblees in <CROP>pedia Species Finished

Genome size(Mb)

Combination with WGS

Arabidopsis

120

+

Tomato*

950

+

Pepper

2500

+

B. oleraceae

700

+

B. rapa

450

+

B. napus

1200

+

Cucumber**

370

+

Melon

450

+

Potato*

1800

+

Lettuce***

2600

+

Wheat chr 3b

230

+

Strawberry

170

+

Tobacco

4200

+/-

Sunflower

3600

Cotton

1700

*with WUR; ** with TTI GG, ***with BGI UC Davis


<CROP>-Pedia

Genome browser Variomics viewer Sequence annotation Phenotype Databases GO2Traits


KeyGene’s Mutation Breeding Trait Pipeline Major traits and new pre-breeding material in 9 months Discovery

all genes

Trait Application Patents

Validation

Pre breeding material

KeySeeQ®

50 genes

KeyPoint®MB

Phenotyping

1-3 genes


KeyPoint速MB for large scale screening of (EMS) mutagenized plant populations

1. 2. 3. 4. 5.

Isolate DNA from individual EMS M1 plants Pool in smart way PCR Amplify fragments of genes of interest HT Sequence & Analyze Select mutants, throw away rest of population


de novo mutants in a few months mutation detection

mutagenized seed

A

C

0.004 0.003 0.002 0.001 0 -0.001 1

young M1 plants

B

X, Y, Z

14

4

9

IX

verified M1 carrier

D

X

XV

d

i

n


Mutagenized corn and canola populations covering almost all amino acids, genome-wide

0.008

0.008 0.007 0.006

0.007 0.006 0.005

0.002

0.005 0.004 0.003 0.002

0.001

0.001

0

0 -0.001

0.004 0.003

-0.001 1

12 15

3

6

9

III

V VIII b

e

h

k

1 12 15 3

6

9

III

V VIII b

e

h

k


KeyPoint速MB: proven trait development method

2011

crop tomato

popul. size 9.400

# mutations 99

pepper melon dandelion oil seed rape

2.000 2.000 3.000 12.000

69 7 19 91

maize

2.000

60


Trait 1. Drought tolerant mutant in tomato Next: maize & rice Case


Trait 2: Yield improvement in tomato unique allele for enhanced growth in a hormone response gene

Case BC

HOM

old

new

WT

frequency

14 12 10 8 6 4 2 0 20

22

24

26

28

30

32

34

36

38

40

42

44

46

plant height at leaf 6 (cm)

enhanced growth w.o. pleiotropy


Trait 3: preventing lodging without yield penalty in Brassica napus Allelic series: 91 mutations in 700bp of gene sequence

Case

WT M1

WT M2

WT M3

WT M4

WT M5

WT M6

WT M7

reduced height w.o. pleiotropy


Trait 3: preventing lodging without yield penalty in Brassica napus WT

semi dwarf 1

Case

semi dwarf 2


WT

semi dwarf 1

KeyPoint速MB in B. napus

orange lines indicate plant height until shoot tips

WT semi dwarf 2

Case


Trait 3: preventing lodging without yield penalty in Brassica napus WT

semi dwarf 2

semi dwarf 1

Case


KeyPoint速MB: scaling up From mutagenesis on individual genes to multiple genes and pathways

2011

2012

crop tomato

popul. size 9.400

# mutations 99

pepper melon dandelion oil seed rape

2.000 2.000 3.000 12.000

69 7 19 91

maize

2.000

60

pepper

4.000

>900

oil seed rape

6.000

>1200


KeyGene’s non GM Trait Pipeline An allele factory

Discovery

all genes

Trait Application Patents

Validation

Pre breeding material

KeySeeQ®

50 genes

PARTNER LEADS

x100 KeyPoint®MB

Phenotyping by PhenoFab®

alleles

genes

x10


Intermezzo • Output of genomics is enormous and overwhelming • Number of mutants and type of breeding material exceeds current manual phenotyping potential • Additional phenotyping expertise is needed: e.g. to measure growth differences / improvements and to handle large numbers Strong need for automated and robotized phenotyping:

e.g. PhenoFab®


Hi-tech plant phenotyping community Featuring some examples:

CropDesign Traitmillâ&#x201E;˘


PhenoFab速: The plant phenotyping facility in Europe

+ Shital Dixit

20.02.12

Slide 31


PhenoFab®– the facility

• Greenhouse setup with climate control • Moving pots/trays: capacity: 1200 pots, plants up to 2.6 m Shital Dixit

20.02.12

Slide 32


3D Imaging stations 3 different camera systems

Visible light -Shape - Color

NIR

Fluor.

- internal structure - Water content

-Chlorophyll analysis

Shital Dixit

20.02.12


PhenoFab Facility


PhenoFab project workflow See also Shital Dixit presentation tomorrow

Idea to workplan

PhenoFab

From image to digital phenotyping

Statistical correlation study

Shital Dixit

Conclusions

20.02.12

Slide 35


PhenoFab ® experiment portfolio • Biomass development under different growth conditions – – – –

• • • • • •

Drought stress, WUE NUE Heavy metal toxicity Different growth substrate

Crops growth rate Germination efficiency Fruit shape and shelf life, color Flowering time Growth phase effects on treatments Crop architechture, height, width and canopy structure


Why does PhenoFab® make a difference? • Deep understanding of the commercial trait needs of seed industry • It combines the strengths of LemnaTec (automatization & software) and KeyGene (crop genomics & algorithms) • Newest greenhouse & conveyor belts & imaging stations • More than 5 yrs experience in various crops and multiple traits • More than 5 yrs experience of phenotyping data handling and data analysis with proprietary enabling software

+


The PhenoDays offers Early access for digital phenotyping evaluation • Evaluate the power of digital phenotyping – Corn – Rapeseed – Cotton – Rice – Vegetables Phenodays – Grasses 2011 – Miscanthus – Tobacco – Sugarbeet – Sorghum Phenodays – Let us know .. 2012 – Shital.dixit@keygene.com


It’s a Green Gene Revolution

THANK YOU

The KeyPoint®MB technology is covered by patents and patent applications owned by Keygene N.V. KeyGene, KeyPoint, KeySeeQ and PhenoFab are registered trademarks of Keygene N.V. in one or more territories in the world.

Imaging Phenomial Breeding  

PDF of the talk at the PhenoDays 2012 in Wageningen, NL

Read more
Read more
Similar to
Popular now
Just for you