identifying genes for changes in root architecture under water stress georgia davis university of...
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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 Quantitative
•One gene•Discrete distribution
•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.
Molecular mapping
Compare the DNA fingerprint with trait value.
Look for bands on fingerprint associated with high value and those associated with low value.
DNA fingerprintGene 1
Mp3
13E
Va3
5
1 2 3 4 5 6
Lo Hi Int. Lo LoHi Int. Int.
Lo Hi Int. Lo LoHi Int. Int.
Gene 2
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 water-stressed conditions: 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.
Primary root lengthww ws resp
BranchingRoot massShoot mass
Seminal root #ww ws resp
Leaf #Leaf RWC
1 2 3 4 5 6 7 8 9 10
58 Root Architecture QTL
Candidate Genes
vp5 pds1 rt1 d10 d12 la1
hsf1 knox sod3 gst rab15 rab28
Endogenous ABA accumulation is required for root growth maintenance under water deficits
(Saab et al., 1990; 1992; Sharp et al., 1994)
vp5 (maize)
fluridone (FLU)
vp14 (maize)
phytoene
phytofluene
-carotene
neurosporene
lycopene
-,-carotene
-,-carotene
zeaxanthin
antheraxanthin
all-trans-violaxanthin
all-trans-neoxanthin
9’-cis-neoxanthin
9-cis-violaxanthin
Xanthoxin
ABA-aldehyde
ABA
*possible oxidative cleavage steps in planta; reactions catalyzed by NCED (9-cis-epoxycarotenoid dioxygenase)
Modified from Taylor et al.
(2000) J Exp Bot 51: 1563-74
*
*
ROOT TIP ABA CONTENT (ng g-1 H2O)
21 ± 5 96 ± 29118 ± 18Sharp et al. (1994) J Exp Bot 45: 1743-51
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.
vp mutants
Ryan Dierking, undergraduate
9-cis-violaxanthin
vp14 (maize)
vp5 (maize)
fluridone (FLU)
phytoene
phytofluene
-carotene
neurosporene
lycopene
-,-carotene
-,-carotene
zeaxanthin
antheraxanthin
all-trans-violaxanthin
all-trans-neoxanthin
9’-cis-neoxanthin
xanthoxin
ABA-aldehyde
ABAModified from Taylor et al.
(2000) J Exp Bot 51: 1563-74
vp9
vp10
vp8
vp5-DR mutant
Genotype Root length (cm)
Branching Seminal Roots
Root Mass (g)
Shoot Mass (g)
Leaf No.
vp5-DR 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
Mean difference between well-watered and water-stressed treatments.
* = significant at = 0.5.
vp8 mutant
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
Mean difference between well-watered and water-stressed treatments.
* = significant at = 0.5.
9-cis-violaxanthin
vp14 (maize)
vp5 (maize)
fluridone (FLU)
phytoene
phytofluene
-carotene
neurosporene
lycopene
-,-carotene
-,-carotene
zeaxanthin
antheraxanthin
all-trans-violaxanthin
all-trans-neoxanthin
9’-cis-neoxanthin
xanthoxin
ABA-aldehyde
ABAModified from Taylor et al.
(2000) J Exp Bot 51: 1563-74
vp9
vp10
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: 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
Built on IBM neighbors framework
Red are core markers Blue are newly mapped Black are prior mapped Can add kinematic
information
1L
Acknowledgements
Mike Gerau Doug Davis Theresa Musket Hector Sanchez Steve Schroeder Bill Spollen
Ryan Dierking Nicole Grweizowzciak Matt Meyer Dustin Partney Kristen Leach Dana Woodruff
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