Genetic and developmental basis for natural variation in plant stem architecture

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The height and shape of plants depends to a large extent on the way the stem grows. Although stem height and shape varies widely in nature and in cultivated plants, the genes and mechanisms behind this variation are still poorly understood. Changes in stem height have been very important to increase crop yields in the last decades, but the mutations responsible for these changes can have undesirable side effects (for example, by reducing seed size). Therefore, knowledge about how the stem forms and novel genetic changes that can be used to modify stem growth have both fundamental and practical interest. One way to identify genes that affect stem formation is to look for genetic changes responsible for differences seen between plant lines of the same species that have originated from different locations and environments. This has two advantages: naturally selected genetic changes are less likely to cause negative side effects and can be more varied and complex than those induced and selected in the lab. This project aims to identify novel genes responsible for natural variation in stem development, and their mechanisms of action. To achieve this, we will combine two recent technical developments. First, resources and methods of unprecedented power have been developed to analyse natural genetic variation in the model species, Arabidopsis. Second, novel imaging and image analysis methods allow a much more detailed and quantitative analysis of how plant tissues grow and how growth relates to changes in gene activity. In collaboration with a lab at the Gregor Mendel Institute (Vienna), where many of the resources to analyse natural variation in Arabidopsis have been established, we have recently identified small regions of the Arabidopsis genome associated with natural variation in stem width and length. These regions contain only a few genes, for which the available information suggests how they could affect stem growth. For example, in the case of stem width, one of the three candidate genes is similar to genes that affect the orientation of cell growth, so we hypothesize that changes in this gene may affect radial growth at early stages of stem formation. For stem length, one of the two candidate genes has been proposed to control formation of the stem vasculature, which when fully developed is expected to restrict further elongation of the stem, so we hypothesize that this gene may determine terminal stem length through the timing of vascular development. We now propose to prove which candidate genes are responsible for changes in stem growth. For this, we will swap each of the candidate genes between Arabidopsis lines with different stem shapes. After the causative genes are identified, we will determine the exact changes in DNA sequence that modified gene function. To fully understand the functions of these genes, we will then study where and when they are expressed, and test the effect of turning these genes on and off in specific tissues and developmental stages during stem formation. To understand in detail how these genes modify the growth of stem tissues, we will measure in three dimensions the differences in cell behavior (cell division, oriented cell elongation) between natural accessions and after artificially manipulating when and where these genes function. Finally, we will extend our analysis from simple, static measurements of stem shape (such as width and length) to more complex but also more informative measurements of the speed and timing of changes in stem shape. Revealing the genetic changes and mechanisms behind changes in stem shape in Arabidopsis will be an essential first step before equivalent genetic changes and mechanisms can be tested in crop species such as rapeseed or wheat. Ultimately our work will provide knowledge and genetic tools understand how stem architecture can be modified not only in crops, but also during plant evolution.