Genetic and developmental basis for natural variation in plant stem architecture

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.

Plant architecture depends in a 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 studies (GWAS), and in recent years Arabidopsis has emerged as a powerful model for GWAS. 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 GWAS 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 GWAS from static measurements to dynamic aspects of stem development, with a view to predictive modeling of stem growth, and to allow comparison with GWAS carried out by our collaborator on the dynamics of root growth.

This project will benefit four main non-academic beneficiaries in the following ways:

1. Breeders will benefit from knowledge and novel genetic variation that can be used to change plant architecture precisely and predictably, potentially with fewer undesirable pleiotropic effects. The expected time frame for this beneficial impact will be 5-10 years after the start of the project.

2. Agricultural businesses will benefit from our work indirectly, through future use of the resources and knowledge made available to academic peers and to breeders. The most obvious potential benefit will be crop varieties with increased yield through reduced lodging and more favorable allocation of resources. Changes in stem growth due to changes in vascular development and lignification also have potential use in the bioenergy industry. The channels to these beneficiaries will be breeders, as mentioned above, and licensing of patented knowledge through JIC's technology transfer office, Plant Bioscience Limited (PBL). The time frame for this type of impact is expected to be 10-20 years.

3. The general public will benefit from interacting with researchers working in areas of public concern, such as food security and genetic modification. The channels for interaction with the public include the Teacher-Scientist Network and the Year 10 Science Camp (3-4 years).

4. BBSRC will benefit because the project is relevant to two of the current research priorities: using quantitative methods to understand biological processes, and bridging the gap between model and crop species. The long-term impact of the project is also relevant to the BBSRC priority areas of food security and bioenergy (3-10 years).