Digital plant phenotyping - ELIXIR · The crop innovation company ‐from leads to seeds • For...
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Digital plant phenotyping March 2015 / Timo Doeswijk The crop innovation company – from leads to seeds High throughput phenotyping and data‐analysis Timo Doeswijk
Transcript of Digital plant phenotyping - ELIXIR · The crop innovation company ‐from leads to seeds • For...
Digital plant phenotyping
March 2015 / Timo DoeswijkThe crop innovation company – from leads to seeds
High throughput phenotyping and data‐analysis
Timo Doeswijk
The crop innovation company ‐ from leads to seeds 2
Sustainable molecular genetic innovations for crop improvements
Founded in 1989 by Royal Sluis, Cebeco Trade Council, RZ Research, De Ruiter Seeds, Enza Seeds (Netherlands)
Staff
Wageningen NL
Rockville USA Shanghai China
About KeyGene
Curren
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lders
The crop innovation company ‐ from leads to seeds 3
Technology platforms
WGP™Assemble your genome sequence to the highest quality
Digital PhenotypingNew targeted traits in your germplasm
Breeding StrategiesFast stacking of traits in your germplasm
Sequence Based GenotypingSimultaneous SNP discovery and genotyping in your crops
KeyGene®SNPSelectThe ultimate flexibility in genotyping
KeyBase®New targeted traits in your germplasm
KeyPoint® Mutation BreedingNew variable traits in your germplasm
KeySeeQ®Candidate gene discovery for trait improvement
<Crop>PediaThe best platform for fast and effective marker development and gene research
The crop innovation company ‐ from leads to seeds
• For plant breeders the phenotype is the final goal…
• Detection of QTL/GWAS requires:• high quality markers• high quality phenotypes• precision• resolution
The importance of phenotyping
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The crop innovation company ‐ from leads to seeds
• PhenoFab® system• 3 RGB Camera’s:
• Topview Shoot• Sideview Shoot (4 angles)• Sideview Roots (4 angles)
• Lemnatec (~1000 pots)• WPS (~400 pots)
Digital Phenotyping Systems
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The crop innovation company ‐ from leads to seeds
Digital Phenotyping Systems
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The crop innovation company ‐ from leads to seeds
• PhenoFab® system• 3 RGB Camera’s:
• Topview Shoot• Sideview Shoot (4 angles)• Sideview Roots (4 angles)
• Lemnatec (~1000 pots)• WPS (~400 pots)
Digital Phenotyping Systems
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• KeyBox• Portable phenotyping• Image analysis algorithms
standard/custom made
The crop innovation company ‐ from leads to seeds
Digital phenotypingprocedure
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PhenoFab® run
Idea
to workplan
From image to digital
phenotyping
Statistic correlation
study
Conclusions
The crop innovation company ‐ from leads to seeds
• 1400 plants• Daily imaging• Roots/Shoots/Top• ~12,600 images/day• ~500,000 images/project• <5 TB images
High throughput
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The crop innovation company ‐ from leads to seeds
• Flexible environment• Matlab
• Segmentation• Trait derivation• Quality control image
Image analysis
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The crop innovation company ‐ from leads to seeds
• Total area• Shape related traits
• Height• Width• Perimeter• Eccentricity• …
• Color traits• >100 digital traits
Digital Traits
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The crop innovation company ‐ from leads to seeds
• Quality control images• Movies
• Original images• Quality control images
• Growth curves• Example:
• Top Images• 250 plants, 40 Days = 10,000 images
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Image analysisquality control
The crop innovation company ‐ from leads to seeds 13
Image analysisquality control
The crop innovation company ‐ from leads to seeds 14
Image analysisquality control
The crop innovation company ‐ from leads to seeds
• 500,000 images x 100 traits => 50M data points• Daily comparisons (40 days, >100 dig. traits)
• Between genotypes• Treatments• Genotype treatment combinations
• Growth curve analysis• Smoothing• Growth rate
Data analysis
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The crop innovation company ‐ from leads to seeds 16
Experimental results (1)
The crop innovation company ‐ from leads to seeds
Experimental results (2)
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Average growth curves Corn
A: optimal treatment special soil mixture
B: drought special soil mixtureC: low nutrition special soil mixtureD: optimal watering standard
potting soil mixture
The crop innovation company ‐ from leads to seeds
Case study
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Can digital phenotypes be used as predictive markers for late season traits ?
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Dig. phenotype to field B. napus15 genotypes
1 dig. phenotype: 0.51 average R‐square
Dig. phenotype to tomato greenhouse30 genotypes1 dig. phenotype: 0.4 R‐square2 dig. phenotype model: 0.57 adj. R‐square
The crop innovation company ‐ from leads to seeds
• Complete control over the pipeline• Hardware configuration (pot selection to imaging)• Flexible image analysis platform• Solid statistical analysis of traits (daily and growth
related)• High quality results• Digital traits are predictive for late season field traits
Summary
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PhenoFab run®Idea
to workplan
From image to digital phenotyping
Statistic correlation study
Conclusions
The crop innovation company ‐ from leads to seeds
• Digital trait development (e.g. root angle)• Detect plant parts
• Incl. time series analysis of plant parts• 3d‐image analysis
• 3d related traits (architecture)• Resolution
New developments
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The crop innovation company ‐ from leads to seeds
Thank you!
The KeyBase®, KeyPoint® Mutation Breeding, WGP™, Sequenced Based Genotyping and KeyGene® SNPSelect technologies are protected by patents and/or patent applications owned by Keygene N.V. KeyGene, KeyBase, KeyPoint, Phenofab and KeySeeQ are registered trademarks of Keygene N.V. in one or more territories in the world. All other products names, brand names or company names are used for identification purposes only, and may be (registered) trademarks of their respective owners.
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