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David E. Salt
Professor of Horticulture and Landscape Architecture
Professor David E. Salt’s long-term research interest is to understand the function of the genes and gene networks that regulate the plant ionome (elemental composition), along with the evolutionary forces that shape this regulation. To achieve this, his laboratory couples high throughput elemental profiling with bioinformatics, genomics and genetics, biochemistry, and physiology in both genetic model species (yeast, Arabidopsis thaliana, and rice) and “wild” plants that hyperaccumulate various metals (Cd, Ni, and Zn), metalloids (As), and non-metals (Se) in their native habitat, including various Thlaspi, Pteris, and Astragalus species. Professor Salt has been involved in related work since his PhD (Liverpool University, UK, 1985–1988), working on the mechanisms of evolved copper tolerance in Mimulus gutattus (yellow monkey flower). He also has a BSc in Biochemistry (University of North Wales, Bangor, UK, 1981–1984) and an MSc in Computer Science (Hallam University, UK, 1984–1985), and has held faculty positions at Rutgers University (1993–1997), Northern Arizona University (1998–2001), and is currently a professor at Purdue University, where he has been since 2001. Professor Salt has published over 85 peer-reviewed papers with currently over 5,100 citations. Professor Salt has obtained over $15 million in competitive research awards, trained 17 postdoctoral researchers, and graduated four PhD students. Professor Salt has also been on the editorial board of five international science journals and was nominated by Nature Biotechnology as one of the “thought leaders and technology pioneers” in biotechnology in the past 10 years. Dr. Salt is also interested in informal science education, and the science-based interactive game he helped develop, the Genomics Digital Lab (GDL), recently won first prize (2008) in the Interactive Media Award sponsored by NSF and AAAS.
Understanding how plants control their ionome, or mineral nutrient and trace element composition, will have an impact on agricultural resilience and productivity and on human health through improved nutrition. Ionomics uses systems biology approaches to couple high-throughput, multi-element quantification with genomics, genetics, biochemistry, and physiology to identify and characterize significant connections between a plant’s genome and its ionome. Using such an approach, we have uncovered specific genes, and networks of genes, that regulate and integrate a plant’s ionome during normal growth and development and in response to the environment. Further, associating changes in these genetic networks with the distribution on the natural landscape of individual plants is telling us how these plants adapt genetically to harsh environments, such as elevated soil salinity.
The idea that mineral elements function as nutrients for plants is now taken for granted. However, this idea was still a matter of great scientific controversy 150 years ago and not codified until the late 1930s. Surprisingly, as recently as 1987 nickel was identified as an essential plant nutrient. The release of the DNA sequence of the first plant genome (Arabidopsis thaliana) in 2000 led to an explosion of discoveries by facilitating the application of genetic tools for the dissection of the mechanisms of fundamental biological processes. It was against this backdrop that David E. Salt and his coworkers had the original insight and vision to conceptualize that such genomic-scale biology could be used to study the mechanistic processes involved in plant mineral nutrition. The description of the mineral nutrient and trace element composition of an organism as the ionome arose from this work, and led to the new research paradigm that the ionome needs to be studied as an integrated whole. With funding from the National Science Foundation, the National Institutes of Health, and the state of Indiana, Salt implemented a system to study the ionome using high-throughput elemental analysis technologies integrated with both bioinformatic and genetic tools. With the solid conceptual framework of the ionome as a foundation and the implementation of a powerful experimental approach in place, Salt has gone on to publish a series of high-impact papers over the last five years that not only provide new biological insight into the mechanisms regulating the plant ionome, but also strongly validate the approach and original insight. Three of these papers involve the cloning and characterization of genes that underlie natural variation in the accumulation of cobalt, molybdenum, and sodium in A. thaliana, and a fourth paper for the first time dissects the molecular basis of how suberin in roots controls shoot accumulation of various elements including, calcium, zinc, and manganese.
This ionomics approach has also identified multiple other novel genes in A. thaliana involved in regulating accumulation of various elements, including potassium, sodium, calcium, iron, and molybdenum, which are currently being prepared for publication. To achieve this level of productivity, it was also critical that Salt was a pioneer in the use of DNA microarray technology to help map the physical location of mutations, allowing the rapid identification of ionomic loci in A. thaliana accessions with no existing genetic markers. In keeping with this early adoption of new genomic technologies, Salt has successfully applied genome-wide association analysis (GWA) for the identification of loci involved
in regulating the ionome. Using this information, Salt is now uncovering associations of natural variation in genes controlling life history traits such as sodium accumulation with the landscape distribution of plants, revealing the genetic architecture underlying specific adaptations to the environment. Salt has also gone on to also extend the ionomics concepts into yeast as a model cellular system and rice as an important crop, and through collaborations in C. elegans and mouse. Interwoven with the development of the biological and technological sides of ionomics, Salt has also displayed innovation in areas of storage and dissemination of the large datasets generated by the projects. By developing and deploying the ionomicsHUB (www.ionomicshub.org), Salt has now provided a mechanism to “open source” ionomic data and discovery. The ionomicsHUB is now delivering ionomics data (18–21 trace elements and mineral nutrients) on approximately 140,000 A. thaliana samples, 15,000 rice samples, and 52,000 yeast samples to over 4,107 unique users using 43 different languages in 932 cities in 78 countries and is being updated with new data regularly. In parallel with his efforts in the science of ionomics, Salt has also made major contributions in the dissemination of these ideas to the public. He has led the development of a 2,000-square-foot informal science exhibit on genomics called Genomics Explorer (www.genomicsexplorer.com ). This exhibit was recently on display at the Owensboro Museum of Science and History. Salt has also led a team in the development of the award-winning, sciencebased interactive game called the Genomics Digital Lab (GDL). This game won first prize in 2008 in the Interactive Media Award, Science and Engineering Visualization Challenge, sponsored by the NSF and the American Association for the Advancement of Science (AAAS), and in the World Summit Awards
e-Science & Technology, 2009. The game is currently distributed free of charge by the American Society of Plant Biologists (http://www.aspb.org/education/GDLProject.CFM).