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At the root of development Anker Sørensen Marco van Schriek


At the root of development Outline • Introduction – Digital phenotyping – KeyTrackTM system

• Root phenotyping • Conclusions / next steps


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


From phenotyping system to a digital phenotyping project

Idea to workplan

KeyTrack run

From image to digital phenotyping

Statistic correlation study

Conclusions


Root phenotyping


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 Core questions to be answered

1. Can we use the KeyTrack for root imaging

2. Can we measure variation in root phenotypes


Root phenotyping Technical aspects

? Light reflection in pictures

Pot type

? Zoom level of camera Optimized

? Pot condensation Watering/imaging scheme optimized

? Pot covering Automated


Root phenotyping


Root phenotyping Core questions to be answered

1. Can we use the KeyTrack for root imaging

2. Can we measure variation in root phenotypes


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

M82

S. pennellii

IL 1

IL 2

IL 3


Root phenotyping From image to digital phenotype

Digital based root phenotype


Root phenotyping

Direct root mass measurement

Digital root 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


Candidate genes Approach

WGS Gene Prediction Annotation

Root ESTs and Unigenes

Candidate gene list (per IL line)


Next steps

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


Acknowledgements     

Gert-Jan Speckmann Jose Guerra Koen Huvenaars Marco van Schriek Anker Sørensen

   

Dirk Vandenhirtz Joerg Vandenhirtz Kevin Nagel Ralph Schunk


THANK YOU

KeyTrack Root Phenotyping - At the Root of Development  

At the root of development Anker Sørensen Marco van Schriek • Conclusions / next steps – Digital phenotyping – KeyTrack TM system • Introduc...