Mapping connections between the genome, ionome and the physical landscape. Photo by Bruce Bohm. David E Salt Purdue University, USA

Transcription

1 Mapping connections between the genome, ionome and the physical landscape Photo by Bruce Bohm David E Salt Purdue University, USA

2 What is the Ionome Environment Transcriptome Proteome Ionome The elemental composition of an organism, tissue or cell Metabolome Genome Lahner et al., Nat Biotech 2003

3 plant adaptation to different soil types is evidence of the strong natural selection imposed by ecological discontinuities ALFRED RUSSEL WALLACE (1858) Genome Cellular Network Ionome Environmental Network Landscape distribution Photo by Bruce Bohm

4 Ionomics Unraveling the networks that link the genome and the ionome yeast The image cannot be displayed. Your computer may not have enough memory to open the image, or the image may have been corrupted. Restart your computer, and then open the file again. If the red x ICP-MS still appears, you may have to delete the Sample image and then insert it again. Analysis Arabidopsis thaliana The image cannot be displayed. Your computer may not have enough memory to open the image, or the image may have been corrupted. Restart your Sample computer, and then open the file again. If the red x still appears, you may have to delete the image an Preparation Element Li B Na Mg P K Ca Mn Fe Co Ni Cu Zn As Se Mo Cd Arabidopsis ionome Shoot Seed average %RSD average %RSD The image cannot be displayed. Your computer may not have enough memory to open the image, or the image may have been corrupted. Bioinformatics Li Na Mg K Ca Mn Fe Co Ni Cu Zn Mo Cd B P As Se Pb The image cannot be displayed. Your computer may not have enough memory to open the image, or the image may have been corrupted. Restart your computer, and then op Web Portal The image cannot be displayed. Your computer may not have enough memory to open the image, or the image may have been corrupted Restart your computer a Plant Growth Salt et al Ann Rev Plant Biol 2008

5 High-throughput ionomic analysis of Saccharomyces cerevisiae Danku et al., JAAS 2008

6 Community HUB to share data

7 e-laboratory controlling workflow and data acquisition Baxter et al., Plant Physiol 2007

8 Search Data visualization and download Baxter et al., Plant Physiol 2007

9 Cellular Networks: Genes to ionome in yeast Ionomic analysis of the complete S. cerevisiae deletion collection Discrimination of 4 positive control strains of yeast used throughout the complete screen (~260 plates) based on their ionomic profiles 6 4 YLR396c Na, Mg, P, S, K, Ca, Mn, Fe, Co, Ni, Cu, Zn, Mo, Cd analyzed 20 lines per plate (n = 4) 240 lines per week (12 plates) Full collection of 5153 deletion strains completed in 6 months. Principle component BY4741 YDL227c YPR065w Principle component 1 Danku et al., JAAS 2008

10 Networks connecting genes the ionome and the landscape Frequency Shoot Na in 360 different populations Shoot Na (mg/kg)

11 Genome-wide genetic association analysis for genes controlling Na accumulation High Na locus maps to HKT1 a known Natransporter

12 HKT1 gene variant also controls Na tolerance 0 mm NaCl 100 mm NaCl Col-0 Ts-1 Col-0 Ts-1 Segregation of NaCl tolerance Col-0 Ts-1 F2 progeny (Ts-1 x Col-0) Rus et al., PLoS Genetics 2006

13 HKT1 variant broad geographic distribution Bur-0 Ws-0 Bor-4 C-24 Ts-1 Ll-0 Tsu-1

14 Networks connecting genes (HKT1), the ionome (Na) and the landscape Collect ~60 Arabidopsis thaliana populations on Spanish Riviera Shoot Na levels Tossa del Mar

15 Association of HKT1 gene with soil Na and geographic location Does HKT1 determine the landscape distribution of Arabidopsis on the Spanish Riviera?

16 Acknowledgments Salt Laboratory Dr Ivan Baxter Dr Ana Rus Dr Muthukumar Jessica Brazelton Elena Yakubov Marina Tikhonova Brett Lahner (Arabidopsis) John Danku (yeast) Analytical Chemists Dr Mourad Ouzzani (Purdue, Cyber Center) Brad Kennedy, Gemez Marshall Dr Olga Vitek (Purdue University) Danni Yu Dr Kirsten Bomblies (MacArthur Fellow, Harvard) Dr Magnus Nordborg (University Southern California)