The project involves exploration of how plants adapt naturally to harsh environments, in order to understand stress tolerance mechanisms and inform development of food and energy crops that can better tolerate changing environments. The outcomes have broad societal relevance, as crop production is frequently constrained by environmental stresses, such as salinity. This project will provide a learning platform for diverse teams to design new computational and molecular tools for studying naturally existing genetic variation. These teams will consist of biological and computer science graduate students, undergraduates, including underrepresented minorities, high school students and instructors, and international collaborators. The project also supports career development for two beginning investigators. Data generated from this project will be used to design an interactive visual data analysis interface with contributions from high school student programmers. Other activities include plant nutrient awareness events for the public and K-12 students, a summer workshop to train high school teachers and students in PCR and DNA fingerprinting, and discussions with local high school students on ethical issues related to genetic engineering. DNA sequence datasets and bioinformatics programs resulting from this project will be shared publicly, which will enable scientific activities ranging from basic research exploring mechanisms in genetics and evolution to generating markers and resources for crop improvement.
This project will investigate how a species achieves stress adaptation compared to a closely related stress sensitive species by analyzing genomic signatures that lead to transcriptomic responses to stress, followed by targeted transgenics and molecular phenotyping. The overall analysis will be tested in a conceptual framework that highlights stress adaptation achieved by modifications in existing core stress response systems, and/or recruitment of new genetic components. Extremophile plants represent emerging models for understanding genetic mechanisms governing plant survival under extreme abiotic stresses. Schrenkiella parvula and Eutrema salsugineum, the two most salt-tolerant species among known wild relatives of Brassica crops, will be used as model genomes, and multiple salt stresses will be applied to study adaptation compared to the stress sensitive model A. thaliana. Genomes of both S. parvula and E. salsugineum show extensive overall synteny with the A. thaliana genome, which enables comparative studies benefiting from the wealth of genetic information available on A. thaliana. Inter-species comparative RNAseq methods are planned to uncover the dynamics of abiotic stress responsive gene regulation caused by excessive Na+, K+, or Li+ salts. Transgenic plants in all test species will be created targeting representative genes in major stress responsive units identified. Molecular level phenotyping will be achieved via ionomic and metabolomic profiling of wild-type and transgenic lines collected from control and stress-treated samples. Finally, descriptive genetic modules will be developed with a core data set linking genomic restructuring that enables improved stress adaptation in known and novel stress responsive pathways, in both stress-adapted and stress-sensitive species. The work will provide a strategic case study that can be expanded to other organisms, to evaluate genomic organization via targeted genetic studies assisted by transgenic plants, transcriptomic regulation, and metabolomes used for molecular phenotyping.
This project is co-funded by the Genetic Mechanisms Cluster in the Division of Molecular and Cellular Biosciences in the Biological Sciences Directorate and by the NSF EPSCoR Program.
