Project: Innovation in vegetable plant breeding by large scale deep phenotyping

The overall objective of this program is to develop new applications for the LemnaTec Scanalyzer for deep phenotyping on vegetable crops. To generate a set of parameters that will provide precise phenotyping results that can be correlated directly to the genotypic variations in crops plants, leading to new molecular markers or gene clones that positively contribute to complex commercial traits in vegetable plants._x000D_Consistent and quantitative measurements of phenotypic features in plants are essential to be able to grasp the complex interactions between phenotypic and genotypic variation. Now that the depth of genotyping the different haplotypes present between plant varieties is getting to the required level for high density mapping, LD mapping and association mapping, complex traits can be targeted as long as phenotypic measurements are precise. The challenge related to the overall objective of this project is to properly develop new applications for the newest phenotyping technologies to assist the plant breeder and apply the new technology on selected traits in order to identify molecular markers that are predictive for the complex traits that were selected. Besides getting the hardware adjusted to the specific requirements for vegetable phenotyping, a large proportion of the work will lie in the development of proper algorithms to extract useful data from the plant images produced by the LemnaTec Scanalyzer. _x000D_The traits that will be addressed in this program involve root development and plant growth development, both in relation to crop yield. Examining the first trait, root development, has been difficult for breeders up to now, since the root development process is normally not visible for the breeders. The LemnaTec Scanalyzer system and especially the near IR imaging station will make it possible to follow the root development just like we can follow the development of the green parts of the plant. In the second experiment we will try to make a correlation between the early seedling growth characteristics and the later maturation of the plant in order to predict yield parameters in an early stage of development. _x000D__x000D_Objective 1: Development of LemnaTec Scanalyzer for phenomics on vegetable crops_x000D_The results of this phase of the project is to prove the added value of the Scanalyzer for vegetable research programs, as well as demonstrate the feasibility of the use of the LemnaTec Scanalyzer system for phenomics data production in several crops for internal research and contract research for third parties._x000D_Milestone 1.1: Hardware and photograph analysis software systems work reproducibly at KeyGene analyzing vegetable plants_x000D_Milestone 1.2: Basic applications for both the aerial parts of the plant have been successfully completed._x000D_Milestone 1.3: Prerequisites for the “development and validation of vegetable plant phenomics” are accomplished and dataset production can be started. _x000D__x000D_Objective 2: Develop algorithms that will be capable of analyzing the complex phenomics datasets – the phenopipe_x000D_An important second objective is the development of optimal ways to analyze the complex phenotypic data included in the images. This starts with the transformation of the image data to a set of image derived quantitative phenotyping raw data (sizes, colors, shapes, orientations, skeletons) for each image. These datasets need to be recalculated into biological relevant data like stage dependent growth rates, germination time points, node identification and qualitative traits (flowers etc). In a subsequent step these data will be analyzed statistically within the tests and in relation to external (e. g. genetic) factors. _x000D_Milestone 2: A modular phenopipe data analysis tool has been developed _x000D__x000D_Objective 3: global plant phenotyping related to crop yield _x000D_In this phase we will test whether phenomics can be predictive for a complex trait like yield in vegetable crops. We will test the hypothesis if we can predict the performance of tomato inbred lines and its crosses based on early phenotypic information (e.g. stem thickness, internode length, growth rates, architectural parameters etc.). The CO goal is to predict hybrid performance in an early phase of development (seedling level) and early prediction of economically relevant traits. _x000D_Milestone 3: Predictive phenotypes in early plant development have been established and validated. _x000D__x000D_Objective 4: root development phenotyping related to crop yield_x000D_The objective is the identification of the genes responsible for root development in tomato IL lines combined with in depth FLX sequencing of the root transcriptome. So far, measuring of root characteristics has been a tedious task and therefore not an attractive characteristic for large scale phenotyping. Computer assisted image analysis will make root measurement non-destructive, faster, less subjective, and more accurate. _x000D_Milestone 4: Predictive phenotypes in (early) root development have been established and validated._x000D__x000D_

Acronym PhenoCrop (Reference Number: 4300)
Duration 01/01/2009 - 01/12/2010
Project Topic The overall objective is to develop new deep phenotyping applications for the LemnaTec Scanalyzer for vegetable crops. Correlation of genotypic data and phenotyping results will lead to new molecular markers or gene clones that positively contribute to complex commercial traits in vegetable plants.
Project Results
(after finalisation)
The extended provision of data sets on individual phenotype parameters vary from plant to plant and over time (eg leaf number), but at the same time every leaf has it's own set of properties. This made the dynamic extension of the database structure necessary and it was successfully implemented._x000D_Due to the extensions, LemnaTec completed the technical basis, allowing them to view the statistical correlation between genetic data and profit by breeders and molecular biologists._x000D_The data importation into the LemnaTec System was increased and made more flexible to create easy to use interfaces._x000D_For the data output the LemnaMiner was expanded, so that irrelevant of size, all data sets can easily be exported in the same form with an only once to create a Format- und Verrechnungsprotokoll._x000D__x000D__x000D_
Network Eurostars
Call Eurostars Cut-Off 1

Project partner

Number Name Role Country
2 LemnaTec GmbH Partner Germany
2 Keygene N.V. Coordinator Netherlands