The latest news about the ionomics project and thoughts from team members.

Thursday, June 28, 2012

New Perspective in Science

Brian Dilkes and I have a perspective in the new issue of Science titled "Elemental Profiles Reflect Plant Adaptations to the Environment". The abstract is below. Science puts a very (and I mean VERY) tight word limit on the manuscript and so one of the things that we needed to cut was the acknowledgements. So we would like to take the time here to give huge thanks to all the great people who took the time to read drafts and give us (lots of) feedback. 

Jim Fleet,David Salt, Kirsten Bomblies, Elizabeth Haswell, Elizabeth Buescher, Nancy Emery, Clint Chapple, Jody Banks, Joanna Dinsmore, Luca Comai, Aimee Terauchi, Greg Ziegler and five anonymous reviewers for comments on the perspective. 

Pamela Hines, our editor at Science, contributed lots of wisdom, insight and most of all patience, for which we are ever grateful. 



Most mineral elements found in plant tissues come exclusively from the soil, necessitating that plants adapt to highly variable soil compositions to survive and thrive. Profiling element concentrations in genetically diverse plant populations is providing insights into the plant-environment interactions that control elemental accumulation, as well as identifying the underlying genes. The resulting molecular understanding of plant adaptation to the environment both demonstrates how soils can shape genetic diversity and provides solutions to important agricultural challenges.                      


Monday, June 18, 2012

New Paper in PLoS ONE

Our most recent paper was just published in PLoS ONE. "Biodiversity of Mineral Nutrient and Trace Element Accumulation in Arabidopsis thaliana" is our first installment of all the association panel data that we have generated.  It looks at the corrections between elements within and between tissues in the initial 96 accession 'Nordborg' panel.  It includes some very nice data on hydroponics grown plants from samples generated by Christian Hermans and Nathalie Verbruggen from Universit√© Libre de Bruxelles in Belgium.  Special thanks are due to Jennie Hard for all the help with figure preparation. There will be several more papers analyzing this and similar data submitted in the (hopefully) near future.  


Here is the abstract:

In order to grow on soils that vary widely in chemical composition, plants have evolved mechanisms for regulating the elemental composition of their tissues to balance the mineral nutrient and trace element bioavailability in the soil with the requirements of the plant for growth and development. The biodiversity that exists within a species can be utilized to investigate how regulatory mechanisms of individual elements interact and to identify genes important for these processes. We analyzed the elemental composition (ionome) of a set of 96 wild accessions of the genetic model plant Arabidopsis thaliana grown in hydroponic culture and soil using inductively coupled plasma mass spectrometry (ICP-MS). The concentrations of 17–19 elements were analyzed in roots and leaves from plants grown hydroponically, and leaves and seeds from plants grown in artificial soil. Significant genetic effects were detected for almost every element analyzed. We observed very few correlations between the elemental composition of the leaves and either the roots or seeds. There were many pairs of elements that were significantly correlated with each other within a tissue, but almost none of these pairs were consistently correlated across tissues and growth conditions, a phenomenon observed in several previous studies. These results suggest that the ionome of a plant tissue is variable, yet tightly controlled by genes and gene×environment interactions. The dataset provides a valuable resource for mapping studies to identify genes regulating elemental accumulation. All of the ionomic data is available at


and here is the non-technical summary:

Understanding how plants regulate element composition of tissues is critical for agriculture, the environment, and human health. Sustainably meeting the increasing food and biofuel demands of the planet will require growing crops with fewer inputs such as the primary macronutrients phosphorus (P) and potassium (K). Ionomics is the study of elemental accumulation in living systems using high-throughput elemental profiling. With this technique, we can rapidly generate large quantities of data on thousands of samples, allowing for the profiling of large genetic mapping populations and the discovery of hundreds of loci important for elemental accumulation. We have used this approach to sample the natural diversity present in collections of a model plant, the wild mustard Arabidopsis. We find that the elemental composition of a plant is tightly controlled by its genes. We also find that elements will have different relationships between them depending on the environment and the tissues (root, seed or leaf) under study. This suggests that crop varieties developed for improved elemental uptake and accumulation will be highly environment specific.

Friday, April 27, 2012

First iHUB workshop

The first NSF sponsored iHUB workshop held 26 & 27 April, 2012 in St Louis, US was a success. New tools and features discussed at the workshop should be appearing on the iHUB soon.

Aberdeen Ionomics Facility running

The ICP-MS instruments in David Salt's Ionomics Facility at the University of Aberdeen are now up and running.