Genetic and developmental basis for natural variation in plant stem architecture

Lead Research Organisation: John Innes Centre
Department Name: Contracts Office


Plant architecture depends in large part on the size and shape of the stem, which vary widely in nature and in crops. The genetic and developmental basis for this variation, however, is mostly unknown. Knowledge about stem ontogenesis and novel genetic variation that modifies stem development is not only of fundamental interest in plant development and evolution, but also has great strategic potential for crop improvement.
An effective approach to reveal the genetic basis of natural variation is genome-wide association (GWA) analysis, and in recent years Arabidopsis has emerged as a powerful model for GWA studies. Also in the last years, novel imaging and quantitative, 3D image analysis methods have created unprecedented opportunities to study the cellular basis of plant growth. Here, we propose to combine both approaches to reveal the genetic basis for natural variation in stem development and the mechanism of action of the underlying genes.
We initiated GWA studies in collaboration with Wolfgang Busch (Gregor Mendel Institute, Vienna) and found two significant association peaks, one for terminal stem length and one for stem width. Neither coincided with peaks for flowering time and both were independently supported by QTL analysis. Each peak spanned 2-3 genes, whose predicted functions suggest hypotheses for how they could control stem growth, for example through the timing of vascular differentiation or through polarized cell growth. We now aim to identify causative loci and alleles, to functionally characterize the genes using localized loss and gain of function, and to use quantitative 3D image analysis to reveal their cellular and developmental mechanisms of action. We also propose to extend our GWA analysis from static measurements to dynamic aspects of stem development, with a view to predictive modeling of stem growth, and to allow comparison with GWA studies carried out by our collaborator on the dynamics of root growth.


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