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:
Abstract:
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 www.ionomicshub.org.
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.
Thursday, June 17, 2010
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."
"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."
Tuesday, November 3, 2009
Ferroportin Paper published in Plant Cell
Our paper describing the function of the two Ferroportin genes in Arabidopsis has just been published in the early access feed of Plant Cell!
The pdf is here (also available from our publications page)
here is the abstract......
Relatively little is known about how metals such as iron are effluxed from cells, a necessary step for transport from the root to the shoot. Ferroportin (FPN) is the sole iron efflux transporter identified to date in animals, and there are two closely related orthologs in Arabidopsis thaliana, IRON REGULATED1 (IREG1/FPN1) and IREG2/FPN2. FPN1 localizes to the plasma membrane and is expressed in the stele, suggesting a role in vascular loading; FPN2 localizes to the vacuole and is expressed in the two outermost layers of the root in response to iron deficiency, suggesting a role in buffering metal influx. Consistent with these roles, fpn2 has a diminished iron deficiency response, whereas fpn1 fpn2 has an elevated iron deficiency response. Ferroportins also play a role in cobalt homeostasis; a survey of Arabidopsis accessions for ionomic phenotypes showed that truncation of FPN2 results in elevated shoot cobalt levels and leads to increased sensitivity to the metal. Conversely, loss of FPN1 abolishes shoot cobalt accumulation, even in the cobalt accumulating mutant frd3. Consequently, in the fpn1 fpn2 double mutant, cobalt cannot move to the shoot via FPN1 and is not sequestered in the root vacuoles via FPN2; instead, cobalt likely accumulates in the root cytoplasm causing fpn1 fpn2 to be even more sensitive to cobalt than fpn2 mutants.
The pdf is here (also available from our publications page)
here is the abstract......
Relatively little is known about how metals such as iron are effluxed from cells, a necessary step for transport from the root to the shoot. Ferroportin (FPN) is the sole iron efflux transporter identified to date in animals, and there are two closely related orthologs in Arabidopsis thaliana, IRON REGULATED1 (IREG1/FPN1) and IREG2/FPN2. FPN1 localizes to the plasma membrane and is expressed in the stele, suggesting a role in vascular loading; FPN2 localizes to the vacuole and is expressed in the two outermost layers of the root in response to iron deficiency, suggesting a role in buffering metal influx. Consistent with these roles, fpn2 has a diminished iron deficiency response, whereas fpn1 fpn2 has an elevated iron deficiency response. Ferroportins also play a role in cobalt homeostasis; a survey of Arabidopsis accessions for ionomic phenotypes showed that truncation of FPN2 results in elevated shoot cobalt levels and leads to increased sensitivity to the metal. Conversely, loss of FPN1 abolishes shoot cobalt accumulation, even in the cobalt accumulating mutant frd3. Consequently, in the fpn1 fpn2 double mutant, cobalt cannot move to the shoot via FPN1 and is not sequestered in the root vacuoles via FPN2; instead, cobalt likely accumulates in the root cytoplasm causing fpn1 fpn2 to be even more sensitive to cobalt than fpn2 mutants.
Thursday, October 8, 2009
Review publications
We have added a new publications page to hold review papers produced by the ionomics team. You can find it here or follow the link from the top of the main publications page.
Thursday, September 24, 2009
Database repairs Oct 9
The ionomicshub will be down for a few essential security patches on Friday, October 9th. These updates will start at 11:00am and be complete by 1:00pm (ET) (may be before).
Yeast database goes live
The Beta version of our yeast database is now live. This database holds over 50,000 samples worth of ionomic data on all viable yeast strains from both the full genome knockout and over expression collections. A description of how the data was collected has been published in Danku et al., J Anal. At. Spectrom. 2009, 24, 103-107. The database supports searches for specific genes, data display and download. We have also included features that allow the re-upload of downloaded data sets after user-defined manipulations have been performed. These new up-loaded user-defined data sets then become searchable by the community. We are currently working on a paper in which we describe the statistical analysis of the data and its biological implications. Please report bugs or suggestions to dsalt@purdue.edu or IBaxter@danforthcenter.org.
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