Download Root genes for water response

Identifying genes for changes in root
architecture under water stress
Georgia Davis
University of Missouri
www.rootgenomics.org
Overview
 Root architecture QTLs
 vp mutants
 Root transcriptome map
Qualitative
•One gene
•Discrete distribution
Quantitative
•Several - many genes
•Continuous distribution
Quantitative Trait Mapping
 Population segregating for the trait
 Molecular markers to create a linkage map
 Trait measurements
 Enough replication to get a good idea of
genotype vs. environmental differences
Playing the Numbers
 A QTL of 15 cM contains 450 - 900 loci in
maize.
 QTL size is reduced by increasing
recombination (ex. random intermating,
larger sample of individuals) and to some
degree by mapping additional genetic
markers.
Mp313E
Molecular mapping
Gene 1
Lo
Va35
DNA fingerprint
Hi
1
2
3
Int. Hi Lo
4
5
Int. Lo
6
Int.
Gene 2
Lo Hi
Int. Hi
Lo Int. Lo
Int.
 Compare the DNA
fingerprint with trait
value.
 Look for bands on
fingerprint associated
with high value and
those associated with
low value.
QTL Mapping
 Using Intermated B73 x Mo17 (IBM) population to map
root architecture under well-watered and water-stress
conditions.
• Studying the IBM 94 reduced the number of candidate genes
per cM to 14.3.
• The IBM genetic map is linked to the physical map and
anchored sequence information allowing us to identify genes
not found on the genetic map.
Mike Gerau, undergraduate
Root Architecture QTL
 Measured under well-watered and waterstressed conditions:
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primary root length
root branching
root mass
seminal root number
shoot mass
leaf relative water content
Analysis
 Mean values for ww, ws and the response
(ww-ws)/ww were used for QTL analysis
against 643 markers spaced <10 cm apart on
the genetic map.
1
2
3
4
5
ww
Primary root length
Branching
Root mass
Shoot mass
6
ws
7
8
9
ww
resp
10
ws
resp
Seminal root #
Leaf #
Leaf RWC
58 Root Architecture QTL
Candidate Genes
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vp5
pds1
rt1
d10
d12
la1
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hsf1
knox
sod3
gst
rab15
rab28
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Endogenous ABA accumulation is
required for root growth
maintenance under water deficits
(Saab et al., 1990; 1992; Sharp et al., 1994)
phytoene
zeaxanthin
vp5 (maize)
fluridone (FLU)
antheraxanthin
phytofluene
all-trans-neoxanthin
9-cis-violaxanthin
neurosporene
9’-cis-neoxanthin
*
Xanthoxin
d-,g-carotene
a-,b-carotene
Modified from Taylor et al.
(2000) J Exp Bot 51: 1563-74
cleavage steps in
planta; reactions
catalyzed by NCED
(9-cis-epoxycarotenoid
dioxygenase)
all-transviolaxanthin
z-carotene
lycopene
*possible oxidative
ABAaldehyde
ABA
*vp14 (maize)
ROOT TIP ABA CONTENT (ng g-1 H2O)
118 ± 18
21 ± 5
96 ± 29
Sharp et al.
(1994) J Exp Bot
45: 1743-51
vp mutants
 viviparous (vp) mutants have defects in
carotenoid and/or ABA biosynthesis.
 Six vp mutants: vp5, vp5-DR3076, vp8, vp9,
vp10 and vp12
 WW and WS
 Same measurments as QTL.
Ryan Dierking, undergraduate
phytoene
zeaxanthin
vp5 (maize)
fluridone (FLU)
antheraxanthin
phytofluene
z-carotene
vp9
vp10
all-transviolaxanthin
all-trans-neoxanthin
9-cis-violaxanthin
neurosporene
9’-cis-neoxanthin
vp14 (maize)
lycopene
xanthoxin
d-,g-carotene
a-,b-carotene
ABAaldehyde
Modified from Taylor et al.
(2000) J Exp Bot 51: 1563-74
ABA
vp8
vp5-DR mutant
Mean difference between well-watered and waterstressed treatments.
Genotype
Root
length
(cm)
Branching
Seminal
Roots
5.973
-0.5*
0.1
0.143
0.273
0.0
wt vp5-DR
0.4
0.5
1.6
0.406
0.370
0.1
vp5
0.9
0.1
0.7
0.314
0.031
0.6
wt vp5
0.5
0.2
0.2
0.683
0.023
0.1
vp5-DR
* = significant at a = 0.5.
Root
Mass
(g)
Shoot
Mass
(g)
Leaf No.
vp8 mutant
Mean difference between well-watered and waterstressed treatments.
Genotype
Root
length
(cm)
Branching
Seminal
Roots
Root
Mass (g)
Shoot
Mass
(g)
Leaf
No.
vp8
-1.0
0.8*
0.9
1.460*
2.359*
-0.5
wt vp8
0.2
0.6*
0.9
0.960*
0.125
0.0
* = significant at a = 0.5.
phytoene
zeaxanthin
vp5 (maize)
fluridone (FLU)
antheraxanthin
phytofluene
z-carotene
vp9
vp10
all-transviolaxanthin
all-trans-neoxanthin
9-cis-violaxanthin
neurosporene
9’-cis-neoxanthin
vp14 (maize)
lycopene
xanthoxin
d-,g-carotene
a-,b-carotene
ABAaldehyde
Modified from Taylor et al.
(2000) J Exp Bot 51: 1563-74
ABA
vp8
Root transcriptome map
 8000 root unigenes based on EST
sequencing of clones from ww and ws root
segments.
 Goal: Use laboratory and computational
methods to identify map locations.
 Future: Align the map information with
relevant mutant and QTL information.
Root transcriptome map
 Three strategies:
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Wet-lab genetic mapping or physical mapping by
BAC pools. (300)
E-mapping by identity with previously mapped
probe. (~1700 genes)
E-mapping by sequence alignment to complete
BAC or BAC end sequence. (in progress)
Root transcriptome map
1L
 Built on IBM
neighbors framework
 Red are core markers
 Blue are newly mapped
 Black are prior mapped
 Can add kinematic
information
Acknowledgements
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Mike Gerau
Doug Davis
Theresa Musket
Hector Sanchez
Steve Schroeder
Bill Spollen
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Ryan Dierking
Nicole Grweizowzciak
Matt Meyer
Dustin Partney
Kristen Leach
Dana Woodruff