Friday, September 1, 2017 at 11:15am
Associate Professor, Plant Molecular and Cellular Biology Laboratory
Salk Institute, San Diego
Abstract: Hidden from view, roots play a crucial role for plant survival and productivity. They forage the soil for nutrients and water, thereby providing the shoots with molecules that are essential for photosynthesis, growth and defense. This foraging is enabled by growth regulation that determines direction and growth rates of individual root tips in the root system. Nutrient and water distribution in the soil fluctuates spatially and temporally, as does the presence of potential pathogens and toxic minerals. To function efficiently, roots therefore need to determine the biotic and abiotic properties of local soil environments and whether the optimal response in given environments is to sustain growth or instead to initialize defense programs. Importantly, these priorities might change in different habitats.
To understand the fundamental principles of environmentally determined root growth regulation and its adaptive value, we use the root of Arabidopsis thaliana, a plant species that has successfully colonized large parts of Eurasia; a range displaying stark variations of climates and soils. Using a systems genetics approach that integrates high throughput phenotyping, genome wide association mapping and functional genomic approaches, we identify the genes and their variants that make roots respond differently to the same cues and study their relations to environmental variables. Among the most notable mechanisms that we found, is a signaling module of Leucine-Rich-Receptor-Like-Kinases in which natural genetic variation determines root growth responses to low iron levels. Interestingly, these genes are also involved in defense responses and our data suggest a model in which iron availability and the presence of microbes are integrated by this receptor kinase module. A similar pattern can be observed for growth responses to low zinc levels. There, allelic variation of a gene involved in systemic immunity (AZI1) determines growth responses and we observe a tight interplay of zinc levels and defense signals to determine growth and immune responses. Overall, our work demonstrates that extrinsic signals are interpreted in a context dependent manner by roots and that natural genetic variation can determine how this context is interpreted and lead to sustained root growth or the onset of defense responses.
While flowers and shoots are the more visible features of plants, what lies beneath the surface is just as important: plants’ roots are critical for obtaining water and nutrients from the soil. But how plants process environmental information and which genes and molecular mechanisms determine how a plant root decides to grow in a certain direction in the soil, are still open questions. A better understanding of plant roots could help scientists grow more resilient food sources—an increasingly urgent problem in the face of the planet’s shifting climate and more extreme environments, such as drought.
The flowering plant Arabidopsis thaliana is an easy-to-grow weed, popular for plant biology research. Different strains, all with very similar genomes, grow all over the world, making the plant especially useful for studying which genes and genetic variants make plants respond to different environments and help them to thrive and survive. Wolfgang Busch uses a systems genetics approach—which combines techniques from genetics, genomics and other science fields—to understand how root growth in given environments is determined by a plant’s genes.
Genome-wide association studies (GWAS) correlate genetic variation with physical characteristics, such as having long or short roots. But to be meaningful, studies have to measure the physical characteristic of interest in significant quantities. Because it is difficult to measure roots accurately and in large numbers, Busch has employed a number of cutting-edge technologies and computational methods for evaluating roots.
The Innovations and Discoveries
Busch developed novel methods to evaluate hundreds of thousands of roots using imaging and machine vision algorithms to automatically extract root length and shape data.
He deployed statistical and computational methods to identify the genomic variants that determine whether an individual plant has a short or long root.
Combining GWAS, automated confocal microscopy, and expression analyses in a pioneering way, Busch identified a novel regulator of root development in Arabidopsis, a member of a family of proteins with a characteristic region called an F-box.