Software supporting: Analysis of natural variation in photosynthesis in a panel of Brassicaceae species

doi: 10.4121/13f4d7fa-63d2-4892-ab7e-36ff08cb410e.v1
The doi above is for this specific version of this dataset, which is currently the latest. Newer versions may be published in the future. For a link that will always point to the latest version, please use
doi: 10.4121/13f4d7fa-63d2-4892-ab7e-36ff08cb410e
Datacite citation style:
Garassino, Francesco (2023): Software supporting: Analysis of natural variation in photosynthesis in a panel of Brassicaceae species. Version 1. 4TU.ResearchData. software.
Other citation styles (APA, Harvard, MLA, Vancouver, Chicago, IEEE) available at Datacite

This software package contains all scripts employed to analyze data from an high- and low-throughput investigation of natural variation in photosynthetic light-use efficiency (LUE), and a number of traits potentially correlated to it, in a panel of ten Brassicaceae species. In this study, I performed an analysis of photosynthetic efficiency at high irradiance in ten species that reflect key evolutionary events within the Brassicaceae family: Arabidopsis thaliana, Brassica oleracea, Brassica nigra, Brassica rapa, Brassica tournefortii, Erucastrum littoreum, Hirschfeldia incana, Sinapis alba, Sisymbrium irio, and Zahora ait-atta. I made use of high-throughput phenotyping techniques to measure photosynthetic efficiency, and integrated these measurements with other image-based parameters, such as the Excess Green Index (ExGI) and the Normalized Difference Vegetation Index (NDVI), as well as a range of anatomical and biochemical characteristics that potentially influence photosynthetic efficiency. I then explored the resulting multivariate dataset using various statistical methods to identify trends across species and investigated if more species within the Brassicaceae family show high-photosynthetic LUE at high irradiance. Furthermore, I assessed the alignment of these trends with the evolutionary history of the Brassicaceae family. This study delivers a detailed description of inter-specific variation in photosynthetic parameters for the Brassicaceae family, completed by a selection of anatomical and biochemical characteristics that may play a role in supporting high photosynthetic LUE under high irradiance. The gained insights will be important in developing strategies to enhance the photosynthetic LUE at high irradiance of crop species.

  • 2023-08-25 first online, published, posted
.Rmd and .py scripts
Laboratory of Genetics, Wageningen University & Research


To access the source code, use the following command:

git clone
files (1)