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Translation of digital phenotypic traits: from<br />
promise to commercial relevance<br />
Dr. Shital Dixit
Presentation outline<br />
• Challenges in plant phenotyping<br />
• Novelty of PhenoFab ® projects<br />
• Journey of PhenoFab ® (2011-2012)<br />
• Phenodays 2011 offer projects<br />
• Game changing role of data analysis<br />
• Conclusions<br />
Shital Dixit 11-10-2012 2
Challenges in plant phenotyping<br />
Cold<br />
Salt<br />
Drought<br />
Abiotic agents<br />
• Objective phenotyping<br />
• Digital Phenotyping<br />
• High-throughput<br />
Biotic agents<br />
Subjective/bias scoring<br />
Shital Dixit 11-10-2012 3
Digital Phenotyping<br />
Objective data collection from digital images to<br />
measure morphological and physiological<br />
characteristics through image analysis is known<br />
as digital phenotyping<br />
Shital Dixit 11-10-2012 4
Novelty of PhenoFab facility<br />
Automation of scientific images<br />
Value creation<br />
for<br />
Customer<br />
Agri Food Biotech company<br />
Software/hardware development Traits/genes/genomics/bioinformatic<br />
Shital Dixit 11-10-2012 Slide 5
PhenoFab ® – the facility<br />
3D Conveyor Scanalyzer<br />
•Greenhouse setup with climate control<br />
•Moving pots/trays: capacity: 1200 pots<br />
•GMO authorized<br />
Shital Dixit 11-10-2012<br />
Slide 6
3D Image stations<br />
Capacity: Plant Height 2.6 mts.<br />
Visible light NIR Fluorescence<br />
-Shape - internal structure -Chlorophyll analysis<br />
- Color - Water content<br />
Shital Dixit 11-10-2012<br />
Slide 7
Drought, WUE<br />
NUE<br />
Flowering time<br />
Crop architechture<br />
Height, width<br />
Canopy structure<br />
Heavy metal toxicity<br />
Effect of growth substrate<br />
Crop growth rate<br />
Fruit shape, color and shelf life<br />
Cotton Tobacco Sorghum Miscanthus Sugarbeet Grass<br />
Lettuce Taraxacum Canola Rice Wheat Tomato<br />
Grass Pepper Maize Ficus Cabbage Cucumber<br />
8
Idea<br />
to workplan<br />
PhenoFab ® project workflow<br />
PhenoFab ®<br />
5 weeks<br />
From image<br />
to digital<br />
phenotyping<br />
4 months<br />
Statistical<br />
correlation<br />
study<br />
Conclusions<br />
Shital Dixit 11-10-2012<br />
Slide 9
The PhenoDay 2011 offers<br />
Evaluate the power of digital phenotyping<br />
• Growth curve evaluation between genotypes<br />
– Sorghum<br />
– Sugarbeet<br />
– Tobacco<br />
– Grasses<br />
– Miscanthus<br />
Shital Dixit 11-10-2012<br />
10
Project 1: Phenoday 2011 offer project<br />
GOAL: Phenotype biomass development in sugarbeet hybrids<br />
Experimental set-up<br />
5 sugarbeet hybrid seeds<br />
GAA, GBA, GCA, GDA & GEA<br />
8 repetitions<br />
Phenotyped for 5 weeks<br />
4 side + 1 top camera images<br />
Shital Dixit 11-10-2012<br />
Slide 12
GEA<br />
Growth model analysis<br />
Initial size per genotype<br />
GAA<br />
GEA is the smallest,<br />
fastest in the initial growth and<br />
• Initial size of genotype<br />
slowest<br />
• Initial<br />
in<br />
growth<br />
the secondary<br />
rate of<br />
growth<br />
genotype<br />
GCA is the biggest,<br />
• Secondary growth rate of genotype<br />
Slowest in the initial growth and<br />
Fastest in the secondary growth<br />
GBA<br />
GDA<br />
GCA<br />
GCA<br />
Initial growth per genotype<br />
GBA<br />
GDA<br />
GAA<br />
GEA<br />
Secondary growth per genotype<br />
GEA<br />
GAA<br />
Shital Dixit 11-10-2012<br />
13<br />
GCA<br />
GBA<br />
GDA
Growth curve analysis for 5 week period<br />
No significant difference between genotypes<br />
Shital Dixit 11-10-2012<br />
14
Discussion of the results with the client<br />
Genotypes were treated with seed priming treatment<br />
GEA and GCA with treatment-A<br />
GAA with treatment-B<br />
GBA and GDA control treatment-C<br />
Effect on growth expected in 2-3 weeks after germination<br />
Seedling delivered to PhenoFab 2 weeks after germination<br />
Zoom into the first 11 days of the experiment<br />
Shital Dixit 11-10-2012<br />
Slide 15
Growth curve analysis for first 11 days<br />
No significant difference between genotypes<br />
Shital Dixit 11-10-2012<br />
16
Growth curve analysis for first 11 days<br />
Treatment A shows 5% boost in the growth of<br />
the plant compared to its non-treated control<br />
Shital Dixit 11-10-2012<br />
17<br />
GCA<br />
GEA<br />
GAA<br />
GDA<br />
GBA
Conclusions for project 1<br />
Research question must be clearly addressed to design<br />
the right experiment<br />
Parameters measured some times might not be<br />
correlated to the desired trait/effect but can be<br />
additional effects measured on the plants<br />
Digital phenotypic data analysis is very dynamic and<br />
can be very trait specific<br />
Shital Dixit 11-10-2012<br />
Slide 18
Project 1: Commercial relevance<br />
Seed priming treatment A showed 5% higher growth<br />
compared to its control and counter standard treatment.<br />
(1-1.5% in root yield in field is of commercial relevance)<br />
Image analysis of the first 2-3 weeks after germination in<br />
sugarbeet might even show higher differences between<br />
treatments.<br />
Uniform and faster germination (>30%) is of commercial<br />
relevance<br />
Shital Dixit 11-10-2012<br />
Slide 19
Project 2: PRS company project<br />
GOAL: PRS (gel-based growth medium) enhances plant growth<br />
PRS gel at the bottom of the pot<br />
Shital Dixit 11-10-2012<br />
20
PRS system tested on Pepper and Ficus<br />
Shital Dixit 11-10-2012<br />
21
PRS system tested on Pepper and Ficus<br />
Plant type<br />
1. Fast growing= Pepper<br />
2. Slow growing = Ficus<br />
Watering regimes<br />
1. W1= sub-optimum<br />
2. W2= Optimum<br />
Design<br />
1. Pepper grown with gel = PG<br />
2. Pepper grown without gel = PN<br />
3. Ficus grown with gel =FG<br />
4. Ficus grown without gel =FN<br />
22
Growth curve analysis in pepper<br />
Sub-optimum water<br />
Optimum water<br />
Sub-optimum water<br />
Optimum water<br />
Missing data<br />
Shital Dixit 11-10-2012<br />
23
Growth curve analysis in Ficus<br />
Sub-optimum water<br />
Optimum water<br />
Sub-optimum water<br />
Optimum water<br />
Shital Dixit 11-10-2012<br />
24
Growth rate analysis in pepper<br />
Shital Dixit 11-10-2012<br />
25
Growth rate analysis in Ficus<br />
Shital Dixit 11-10-2012<br />
26
Biomass development in ficus and pepper<br />
Does PRS system enhances plant growth?<br />
Biomass comparison of plants<br />
Shoot Shoot Root Root<br />
Average (g) Stdev Average (g) Stdev<br />
FGW1 9.0 2.4 7.4 4.6<br />
FGW2 11.0 2.0 9.9 1.5<br />
FNW1 10.3 2.9 6.7 1.3<br />
FNW2 13.4 2.4 10.9 2.3<br />
PGW1 220.6 32.8 42.5 8.6<br />
PGW2 262.3 33.6 52.1 13.8<br />
PNW1 242.5 23.7 70.5 15.4<br />
PNW2 267.9 38.5 66.1 17.3<br />
Shital Dixit 11-10-2012<br />
27
Water and Nutrition use efficiency<br />
Water (ml)<br />
FGW1 375<br />
FGW2 604<br />
FNW1 574<br />
FNW2 925<br />
PGW1 3978<br />
PGW2 4560<br />
PNW1 4320<br />
PNW2 4936<br />
Water (ml) and Nutrition average per plant/treatment (ml * EC)<br />
35%<br />
35%<br />
8%<br />
Ficus grown on gel-based<br />
medium needs 35%<br />
less water to produce<br />
similar amount of biomass<br />
produced by plant grown<br />
On a non-gel medium<br />
Shital Dixit 11-10-2012<br />
28
Conclusions for project 2<br />
• PRS gel based system does not enhances plant<br />
growth<br />
• Plant growth speed variation: Observed only in<br />
pepper but only in combination with water regime<br />
• PRS system allows plants to use both water and<br />
nutrients more efficiently (35% less water in ficus)<br />
• Digital phenotyping data allows to study the problem<br />
in dynamic manner.<br />
Shital Dixit 11-10-2012<br />
29
Commercial relevance of PRS system<br />
PRS system can claim that plants grown on their<br />
medium are more water and nutrient efficient (35% in<br />
ficus and 8% in pepper)<br />
System can be used to grow plants where water is a<br />
scarce resource e.g<br />
in dry and arid regions<br />
Water quality is poor to grow plants<br />
Maintaining plants longer without watering, thereby<br />
reducing manual costs for watering<br />
Shital Dixit 11-10-2012<br />
Slide 30
PhenoFab ® summary<br />
PhenoFab ® has:<br />
1. gained experience in different crops and relevant<br />
traits<br />
2. overcomed image analysis and data analysis<br />
challenges to greater extent, hence speed up the<br />
project duration.<br />
3. generated output towards creating commercial<br />
value in crops<br />
Shital Dixit 11-10-2012<br />
Slide 31
<strong>PhenoDays</strong> 2012<br />
Wanna try PhenoFab in 2012 ?<br />
Just let us know<br />
shital.dixit@keygene.com<br />
Shital Dixit 32
Acknowledgements<br />
Gert-Jan Speckmann<br />
Jose Guerra<br />
Koen Huvenaars<br />
Marco van Schriek<br />
Anker Sørensen<br />
Arjen van Tunen<br />
Dirk Vandenhirtz<br />
Joerg Vandenhirtz<br />
Kevin Nagel<br />
Ralph Schunk<br />
Shital Dixit Slide 33
PhenoFab: The plant phenotyping<br />
facility in Europe<br />
Shital Dixit Slide 34
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