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

Friday, November 12, 2010

New paper in PLoS Genetics!

Our paper "A Coastal Cline in Sodium Accumulation in Arabidopsis thaliana Is Driven by Natural Variation of the Sodium Transporter AtHKT1;1" has just been published in PLoS Genetics. There is an accompanying perspective, "Beyond QTL Cloning", by Jill Anderson and Thomas Mitchell-Olds which says (among other nice things):
In this issue of PLoS Genetics, Baxter et al. [9] present an elegant study of the geographic variation in salinity tolerance, and allelic variation at the sodium transport gene AtHKT1;1 in European populations of A. thaliana.

As always, it was great team effort and many thanks go out to our collaborators at Purdue, UChicago, and USC. Here is the non-technical summary of the paper:
The unusual geographical distribution of certain animal and plant species has provided puzzling questions to the scientific community regarding the interrelationship of evolutionary and geographic histories for generations. With DNA sequencing, such puzzles have now extended to the geographical distribution of genetic variation within a species. Here, we explain one such puzzle in the European population of Arabidopsis thaliana, where we find that a version of a gene encoding for a sodium-transporter with reduced function is almost uniquely found in populations of this plant growing close to the coast or on known saline soils. This version of the gene has previously been linked with elevated salinity tolerance, and its unusual distribution in populations of plants growing in coastal regions and on saline soils suggests that it is playing a role in adapting these plants to the elevated salinity of their local environment.

and here is the technical abstract:

The genetic model plant Arabidopsis thaliana, like many plant species, experiences a range of edaphic conditions across its natural habitat. Such heterogeneity may drive local adaptation, though the molecular genetic basis remains elusive. Here, we describe a study in which we used genome-wide association mapping, genetic complementation, and gene expression studies to identify cis-regulatory expression level polymorphisms at the AtHKT1;1 locus, encoding a known sodium (Na+) transporter, as being a major factor controlling natural variation in leaf Na+ accumulation capacity across the global A. thaliana population. A weak allele of AtHKT1;1 that drives elevated leaf Na+ in this population has been previously linked to elevated salinity tolerance. Inspection of the geographical distribution of this allele revealed its significant enrichment in populations associated with the coast and saline soils in Europe. The fixation of this weak AtHKT1;1 allele in these populations is genetic evidence supporting local adaptation to these potentially saline impacted environments.

Thursday, October 21, 2010

Prof Salt accepts new position at University of Aberdeen

Professor David Salt accepts new position as 6th Century Chair in the School of Biological Sciences at the University of Aberdeen starting May 2011. Professor Salt will continue his ionomic's projects and development of the ionomicsHUB (iHUB)

Thursday, June 17, 2010

Arabidopsis RILs paper is published

Our paper on "Natural Genetic Variation in Selected Populations of Arabidopsis thaliana Is Associated with Ionomic Differences" has just been published in PLoS ONE. I'm really happy that this paper is out because it demonstrates something that we have been talking about for several years now: that the ionome is dynamic and interconnected, and the relationships between elements are dependent on both genetics and the environment. The first three figures in this paper describe experiments which were the basis for three other papers that we have already published. Here is the abstract and none technical summary:

Controlling elemental composition is critical for plant growth and development as well as the nutrition of humans who utilize plants for food. Uncovering the genetic architecture underlying mineral ion homeostasis in plants is a critical first step towards understanding the biochemical networks that regulate a plant's elemental composition (ionome). Natural accessions of Arabidopsis thaliana provide a rich source of genetic diversity that leads to phenotypic differences. We analyzed the concentrations of 17 different elements in 12 A. thaliana accessions and three recombinant inbred line (RIL) populations grown in several different environments using high-throughput inductively coupled plasma- mass spectroscopy (ICP-MS). Significant differences were detected between the accessions for most elements and we identified over a hundred QTLs for elemental accumulation in the RIL populations. Altering the environment the plants were grown in had a strong effect on the correlations between different elements and the QTLs controlling elemental accumulation. All ionomic data presented is publicly available at

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, and mapping populations derived from those collections. We find that when the soil environment changes, the identity of the genes important for elemental accumulation changes as well. We also find that elements will have different relationships between them depending on the environment and the lines under study. This suggests that crop varieties developed for improved elemental uptake and accumulation will be highly environment specific.

Sunday, April 25, 2010

Arabidopsis Association Paper published in Nature

The big Nature paper, to which we contributed phenotype data, is now out. Its a great example of the power of plant genetics, many different phenotypes evaluated on a common population resulting in a wealth of really interesting associations. Its way cool, but the bigger populations that we have analyzed are even better and soon we will be submitting some really cool new results for publication.

Friday, March 5, 2010

David Salt Wins McCoy Award

Congratulations to David for this well deserved honor!!!

"David Salt, professor of horticulture and landscape architecture in the College of Agriculture, is the winner of the 2010 Herbert Newby McCoy Award, the most prestigious research award given by Purdue. The award is in recognition of Salt’s pioneering and innovative efforts in the use of genome-scale biological approaches and information technologies to define and drive the field of ionomics. He is an international leader in the field of plant nutrition and has made significant impacts on environmental sustainability, agriculture and human health."