Plant photosynthesis in light fluctuation

This project aims to determine the physiological, biophysical and developmental consequences of plant exposure to fluctuating light conditions in order to design the most efficient phenotyping techniques to use for screening of plant germplasm, especially for crop plants, and to identify genetic variation controlling favourable phenotypes, under the most informative conditions for future marker-assisted breeding approaches to increase plant productivity or robustness under agronomic growth conditions through improved photosynthesis.


Plant photosynthesis is the main biological route to capture the energy of the sun and convert it into biomass. Crop yields largely rely on the efficiency of photosynthesis. While plant breeding has steadily increased crop yields over the past decades, this was obtained through improvements of the harvest index and the solar radiation interception efficiency of a crop canopy. Both traits were relatively easy to breed for as the associated phenotypes are obvious and easily observed by eye and there is ample relevant genetic variation to be found in the crop germplasm. Breeding for these traits gave rise to the Green Revolution, initiated by Nobel Peace prize winner Norman Borlaugh. Genetic diversity for both harvest index and radiation interception have been so successfully mined in the past that they are approaching their theoretical maximum. Another important factor contributing to yield is the conversion efficiency of solar radiation into biomass, which is dominated by photosynthetic efficiency. The maximum calculated efficiency is 4.6% for C3 plants and 6.4% for C4 plants, for the full solar spectrum, but the averages observed in the field are often lower by a factor of 5-10. In contrast to the other major yield-related traits mentioned above, photosynthesis has so far not been successfully improved by conventional plant breeding. There are several reasons for this. The first is the complexity of photosynthesis. Photosynthetic efficiency depends on several sub-processes, each with their own dynamics. By nature, the trait is also very responsive to the environment and shows large short-term phenotypic variation, often associated with changes in the limiting sub-process. Second, techniques to rapidly phenotype photosynthesis were lacking, a problem that was also connected with the complexity of the process. Finally the physiological complexity of photosynthesis is coupled to genetic complexity. Complexity and the inability to properly phenotype the trait meant that photosynthesis was bypassed in the Green Revolution. 

Given the need to further improve crop yields within the existing agricultural land area, photosynthesis is increasingly seen as an important target for improvement since it conspicuously under-achieves, while being the engine of crop productivity. At the moment this is the most important factor to focus plant breeding efforts on in order to improve crop yields, given that the gains to be expected from further improvement of the already close to optimal harvest index or the radiation interception efficiency are low. A clear route on how to improve photosynthesis, and which of its sub-processes to focus on, has been outlined. That there is scope and opportunity to improve crop yield through improvement of photosynthesis efficiency has already been shown, though not through conventional plant breeding, but by genetic modification. Fortunately there is also genetic variation for photosynthesis efficiency, and it is now possible to phenotype for photosynthesis using high-throughput techniques. Combining phenotypic with genotypic data allows the identification of quantitative trait loci (QTLs), and even the allelic variation underlying these QTLs, which will facilitate development of molecular genetic markers to allow breeding for improved photosynthesis. 

Project description

The objectives of this project are to: 

  • Obtain a comprehensive overview of the short term and long term physiological and developmental responses of tomato and Arabidopsis to fluctuating light conditions.
  • Determine the heritability for photosynthetic performance and related parameters affecting growth of Arabidopsis in response to fluctuating light conditions.
  • Identify alleles of genes underlying natural genetic variation for Arabidopsis responses to fluctuating light conditions.
  • Characterize the function of Arabidopsis and tomato genes with i) allelic variation conferring variation in the phenotypic response to fluctuating light or ii) impact on responses to fluctuating light known from literature or inferred from transcriptome analyses.
  • Determine the possibilities and limitations for high-throughput phenotyping of a range of crops for their response to fluctuating light conditions to facilitate future breeding for improved photosynthesis.

Our proposed plan is two-pronged; high-throughput (and deep) phenotyping and gene identification will use Arabidopsis thaliana (Arabidopsis), while trait exploration will use tomato as a crop model. As responses to fluctuating light are an ancient trait we believe the underlying genes will be generic. These two research routes will work closely together and will be mutually interconnected. 

We will need to initiate the research into genetic variation with Arabidopsis; this is a species for which we know, and have shown, we can make rapid progress in phenotyping, gene localisation and the subsequent genetic analysis required to confirm the identity of candidate genes. We realize, however, that in order for this program to be a success, a clear opening should be made to genetic variation in crops. This will also be important for the next step, the improvement of photosynthesis in crops. In view of the diversity of private partners involved, working with a range of crops, we propose to work on tomato as a crop model for the following reasons: 1) tomato has a strong 3D-architecture, making a vertical rather than a horizontal canopy, certainly different from the 2D-architecture of Arabidopsis; 2) it is a fast growing species; 3) it is an important commercial crop for several private partners, and is closely related to potato, another important crop for several other private partners; 4) suitable genetic material to use in this research is in the public domain and thus readily available. We expect that research on Arabidopsis and tomato is currently the most feasible approach to translate fundamental knowledge on response to fluctuating light to application. Orthologues of genes identified in Arabidopsis could be identified in the genomes of crop plants, providing a short-cut to working further with natural variation for kinetic responses to fluctuating light in crops. In addition, the phenotyping procedures we will develop will provide methods to quantify traits connected to fluctuating light and determine whether these are generic. They could be used immediately to screen crop plants, either in our existing phenotyping systems or in the new Netherlands Plant Eco-Phenotyping Centre (NPEC) facility. The traits for which we will phenotype, and thus identify the underlying genes, are extensive and will include, for example, a response to a photosynthetic irradiance increase and decrease (such as electron transport, stomatal opening, non-photochemical quenching (NPQ)), how exposure to fluctuating light affects short-term and long-term leaf acclimation to irradiance and how leaf and shoot architecture respond to and determine light quality and quantity fluctuations. 

There are 5 WPs

  1. Trait exploration for short-term responses to fluctuating light
  2. Analysis of Arabidopsis natural genetic variation
  3. Effects of fluctuating light on plant development
  4. Gene function analysis
  5. Crop variation for response to fluctuating light

Here, at the Laboratory of Genetics, we lead WP2 and WP5 and are involved in WP1 and WP4.

WP2 Genetic analysis 

A high throughput phenotyping system in Wageningen University (the Phenovator II) has been set up and utilised to measure photosynthetic traits of Arabidopsis natural population. The population is a collection of 169 Dutch accessions, for which we gathered more than one million SNP markers. There were two experiments performed to study the photosynthesis acclimation to steady light after fluctuation treatments, and its genetic regulation. These experiments complemented each other in order to dissect the developmental and light treatment effect on photosynthetic responses and the reliability of identified genetic loci. 

For the first experiment, the photosynthetic traits have been analyzed as well as the genetic mapping for these traits have been performed. As a result, there were abundant genetic loci identified. Two of the major QTLs are being further characterized to find the causal genes. The characterization involves haplotype analysis, candidate genes expression and sequence analysis, and T-DNA mutants. Once the most promising candidate gene(s) the verification will be done by complementation approach, either by quantitative crossing or transformation. 

The second experiment was carried out, acquired photosynthetic traits will be analyzed in the same approach and will be compared with the first experiment.