At the root of development

Anker Sørensen

Marco van Schriek

• Introduction

– Digital phenotyping

– KeyTrackTM system

• Root phenotyping

• Conclusions / next steps

At the root of development Outline

The importance of phenotyping

• For plant breeders the phenotype is the final goal…

• Detection of QTLs requires:

– high quality molecular markers

– high quality phenotypes!

• But .. Phenotyping is not (always) straightforward

– Genetic and environmental factors are intertwined

– Subjective / biased observations

– Phenotype may depend on complex interactions of plant and

(a)biotic agent (resistance, tolerance)

High quality phenotypes

Left centre circle smaller than right one? Two shades of red in this picture?

What is the KeyTrackTM system

From phenotyping system to a

digital phenotyping project

KeyTrack

run Idea

to workplan

From image

to digital

phenotyping

Statistic

correlation

study

Conclusions

From phenotyping system to a

digital phenotyping project

Root phenotyping

Rootstock breeding constitute ~50% of the tomato market revenue

Not in line with the investments made in research

Root phenotyping / breeding

Tedious

Difficult

Root phenotyping

1. Can we use the KeyTrack for root imaging

2. Can we measure variation in root phenotypes

Core questions to be answered

Root phenotyping

?Light reflection in pictures

?Zoom level of camera

?Pot condensation

?Pot covering

Pot type

Optimized

Watering/imaging

scheme optimized

Automated

Technical aspects

Root phenotyping

Root phenotyping

1. Can we use the KeyTrack for root imaging

2. Can we measure variation in root phenotypes

Core questions to be answered

Root phenotyping

Zamir Tomato ILL

Parents : M82 and S. pennellii

10 replicates

35 ILL lines

5 replicates

4 side imaging for 18 day’s

Root phenotyping

S. pennellii M82

IL 2 IL 1 IL 3

Root phenotyping

From image to digital phenotype

Digital based root

phenotype

Root phenotyping

Digital root

measurement

Direct root mass

measurement

93 % Correlation !

Root phenotyping

Root phenotyping

1. Can we use the KeyTrack for root imaging?

2. Can we measure variation in root phenotypes?

Digital based root

phenotype

Exploitation in breeding

Root phenotyping

Gene

Prediction

Annotation

Approach

WGS

Root ESTs and

Unigenes

Candidate gene list (per IL line)

Candidate genes

1) Scale up to the PhenoFab system Join our workshops !

2) Screen breeding germplasm for root phenotype variation

3) Create populations for marker development on root phenotypes

4) Validate on more crops

Next steps

2) Screen germplasm for root phenotype variation

48 tomato varieties tested

Early stage root development is correlated with plant yield

88% accuracy when predicting varieties with having below avg. yield performance

Next steps

4) Validate on more crops like maize & wheat

Next steps

Gert-Jan Speckmann

Jose Guerra

Koen Huvenaars

Marco van Schriek

Anker Sørensen

Dirk Vandenhirtz

Joerg Vandenhirtz

Kevin Nagel

Ralph Schunk

Acknowledgements

THANK YOU