Mapping connections between the genome,
ionome and the physical landscape
Photo by Bruce Bohm
David E Salt
Purdue University, USA
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
“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
Landscape
distribution
Environmental
Network
Photo by Bruce Bohm
Ionomics – Unraveling the networks that link
the genome and the ionome
Arabidopsis thaliana
yeast
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ICP-MS Sample
Analysis
Element
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Sample
Preparation
Arabidopsis ionome
Shoot
Seed
average
%RSD
average
%RSD
Li
12
25
0.9
59
B
44
22
7.0
31
Na
860
25
65
23
Mg
12900
22
3283
19
P
9700
9
9937
16
K
46100
10
10690
22
Ca
45000
6
5645
10
Mn
64
20
32
17
Fe
101
8
42
44
Co
1.9
8
0.3
56
Ni
1.4
19
0.4
39
Cu
1.8
40
1.6
68
Zn
61
23
59
25
As
1
195
1.3
36
Se
9.3
97
12
49
Mo
5.5
15
1.0
41
Cd
2.0
13
0.4
31
Li
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Bioinformatics
B
Na Mg
P
Mn Fe Co Ni Cu Zn
K Ca
Mo
As Se
Cd
Pb
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Web Portal
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Plant Growth
Salt et al Ann Rev Plant Biol 2008
High-throughput ionomic analysis of
Saccharomyces cerevisiae
Danku et al., JAAS 2008
www.IonomicsHUB.org
Community HUB to share data
e-Laboratory
controlling workflow and data acquisition
Baxter et al., Plant Physiol 2007
Search
Data visualization and download
Baxter et al., Plant Physiol 2007
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
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 2
4
2
0
-2
BY4741
-4
YPR065w
YDL227c
-5
0
5
10
Principle component 1
15
Danku et al., JAAS 2008
Networks connecting genes the ionome
and the landscape
80
Frequency
70
60
50
Shoot Na in 360 different
populations
40
30
20
10
0
0
1250
2500
3750
Shoot Na (mg/kg)
Genome-wide genetic association analysis
for genes controlling Na accumulation
High Na locus maps to HKT1 a known Natransporter
HKT1 gene variant also controls Na tolerance
0 mM NaCl
100 mM NaCl
Col-0
Col-0
Ts-1
Ts-1
Ts-1
Col-0
Segregation of NaCl tolerance
F2 progeny (Ts-1 x Col-0)
Rus et al., PLoS Genetics 2006
HKT1 variant broad geographic distribution
Bur-0
Ws-0
Bor-4
C-24
Ts-1 Ll-0
Tsu-1
Networks connecting genes (HKT1), the
ionome (Na) and the landscape
Collect ~60 Arabidopsis thaliana
populations on Spanish Riviera
Shoot
Na levels
Tossa del Mar
Association of HKT1 gene with
soil Na and geographic location
Does HKT1 determine the landscape
distribution of Arabidopsis on the
Spanish Riviera ?
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)