One of the most important challenges in biology is to understand how the genotype of an organism gives rise to its phenotype. Major progress towards this goal would enable rational and efficient breeding, biological engineering, and, eventually, synthetic organisms. Growth and development of organisms are of particular interest in regard to the genotype to phenotype problem since they generate the physiology of organisms. In plants growth and development occur throughout the entire lifetime and are coordinated with the environment, Consequently, these processes determine both form and function, dictating biomass, light-harvesting, root foraging ability, and resistance to biotic and abiotic stresses. An excellent model to relate genotypes to growth related phenotypes is the root of the model plant Arabidopsis thaliana (Figure 1A). Here, phenotypic variation in growth and development exists. Growth rate, cell division, and cell elongation are quantitatively modulated at different stages of root development, in different Arabidopsis accessions (strains) (Figure 1B), or upon stimuli and stress. Moreover, large systems-type data sets such as cell-type specific transcriptome, proteome, and metabolome data sets are available. These data sets depict molecular states and represent important intermediates linking genotypes to growth and developmental phenotypes. Using the root, we want to obtain a systems level understanding of the dynamics of growth and development, as well as understand and predict genotype to phenotype relations. For this we use a systems genetics approach which integrates genetics, genomics, systems biology and phenomics. Our long-term goal is to understand how and by which molecular mechanisms root growth is quantitatively determined by the genotype and, using this knowledge, to develop mathematical models with predictive power that accurately capture how the genotype determines root growth in given environments.
The Genetic and Molecular Basis of Root Growth Control
Using powerful tools for phenotyping (Movie 1) and integrative genome-scale data analysis that we have developed, we were able to identify major genes and their alleles involved in the quantitative regulation of root growth and development. Most notably, using high-throughput confocal microcopy, GWAS, and expression analysis, we discovered the novel F-box gene KUK and its alleles. KUK quantitatively regulates proliferation and differentiation in the root tip, thereby determining root length (Figure 2). Large-scale organ-level phenotyping led to an atlas of root growth phenotypes and the identification of a calcium sensing receptor gene that quantitatively determines root growth rate. We are currently moving beyond the single gene level and are applying network approaches to identify complete regulatory networks and pathways that regulate root growth and the resulting root system architecture.
Meijón M, Satbhai SB, Tsuchimatsu T, et al. (2013) Genome-wide association study using cellular traits identifies a new regulator of root development in Arabidopsis. Nature Genetics 46(1):77-81.
Slovak R, Göschl C, Su X, et al. (2014) Scalable Open-Source Pipeline for Large-Scale Root Phenotyping of Arabidopsis. Plant Cell 26(6): 2390-403.
Tuning Root Growth to Environmental Conditions
Plant growth is exquisitely coordinated with environmental conditions. In particular, root architecture is highly dependent on soil conditions and local mineral contents. We are investigating which genes and gene networks are involved in the root growth response to changes in growth conditions (Movie 2). We measured large variations in root development under multiple environmental conditions. We found multiple highly associated genomic regions close to high-confidence candidate genes and are currently conducting gene network-based approaches to identify central regulatory units that are responsible for the modulation of root growth responses to specific growth conditions.
Root Growth Regulation Beyond Arabidopsis
The root is an organ of fundamental importance for vascular plants. In the vast majority of land plant species, the root fulfills the same functions and needs to respond to similar cues. However, it is not clear whether the genes and regulatory networks that control root growth are the same in different species or whether they are different. We are currently adjusting our phenotyping and analytical approaches to work with other species to answer such questions. In particular, we are conducting phenomic approaches in species with large numbers of sequenced accessions that allow us to conduct GWAS.
Joining the Busch Lab
We are always looking for talented new members with biological and/or quantitative backgrounds (e.g. bioinformatics, computer science, math, physics etc.).
Prospective postdocs are expected to have at least one first-author publication in a peer-reviewed journal. If you are interested in working with us, please send an e-mail to Wolfgang Busch explaining which aspect of our research you are interested in, and why. Please attach a CV and the names of three referees.
We are happy to provide opportunities for Bachelor/Master/Diploma theses (biology and/or computer science related) as well as summer internships. Interested students should contact Wolfgang Busch directly. The earlier, the better as we may be able to apply for funding. Please include a CV, describe your background and which aspect of our research you’re most interested in.