Polyploidy and Plasticity in the Crop Brassicas

University Of Missouri-Columbia, Columbia MO

Investigators

Abstract

Rapid global changes are placing unprecedented pressure on plants in agricultural and natural landscapes. This project explores a poorly understood area of plant biology: how genome and biological complexity are related and how that relationship can be manipulated to design responses such as increased tolerance to abiotic and biotic stresses for agricultural applications. The future promises rich synthetic biology applications, if the next generation of scientists is appropriately trained. To address this gap, this project will provide research training in systems biology and predictive modeling for postdoctoral fellows, and graduate and undergraduate students. This team will partner with computer scientists, modeling experts, and journalism students to provide a vision of integrated systems biology for the new century. All research and outreach activities proposed are integrated with recruiting and mentoring students from underrepresented groups. This project will expose trainees and other students through daily dialogues, joint seminars, team-taught courses, and other venues. In addition, this project will develop novel computational and genomic methods that will start to integrate genotype with phenotype, thus transforming comparative biology. Access to all data, computational tools and resources generated in this project will be provided to the broader research community through long-term repositories and through CABBAGE: Community Assets for Brassica Biology And Genome Evolution, a web portal that will be integrated with the cyberinfrastructure developed by the NSF-supported iPlant Collaborative. Brassica crops have tremendous morphological and chemical diversity and are ideal for studying domestication and other economically important plant processes. The goal of this project is to explore the relationship between polyploidy (the merger and doubling of two genomes) and plasticity using the crop Brassicas. By integrating comparative genomics, networks, and genetic models, this project confronts the key question "Did a whole genome triplication in the crop Brassicas facilitate their domestication and adaptability?". This project leverages the systems biology and -omics resources of Arabidopsis to focus on two hypotheses regarding how whole genome triplication (WGT) affected the Brassicas. The first is whether polyploidy in the crop Brassicas are associated with global alterations to the metabolic and gene expression networks, possibly allowing faster growth through duplication of core, high-flux, enzymes. The second is whether polyploidy and subsequent domestication by human farmers altered the networks related to biotic stress in the crop Brassicas. The specific objectives are to: (1) map post-polyploid duplicated genes using comparative genomics (across species of Brassica and Arabidopsis) and identify post-polyploid changes in gene co-expression and metabolism; (2) search for signatures of selection and recent adaptations to biotic stress during the parallel domestications of Brassica oleracea (broccoli, cabbage, cauliflower, Brussels sprouts, and kohlrabi) and B. rapa (turnips, Chinese cabbage, Pak Choi, and oilseeds); and (3) survey gene expression and glucosinolate levels in F1 hybrids of B. oleracea morphotypes to identify functional elements in genetic response to stress. Analyses of genome organization and gene expression will improve the current understanding of the genetic basis of metabolic innovation. Analyses of transcriptome and metabolic data will identify the types of variation selected during domestication and describe the resulting changes to metabolism, growth, and biotic stress response. Further, this project will describe the evolution of gene expression patterns in Brassica and test genome-scale models of metabolic networks in Brassica, which will be refined with glucosinolate measurements.