Transcript Plant Development - University of Missouri

Genetics and Plant Development
MUPGRET Workshop
March 27, 2004
Developmental stages
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Germination
Juvenile
Adult
Reproductive
Germination
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Seed takes up ~30% of its weight in
water.
Enzymes drive cell division and
expansion.
Radicle root emerges first.
Next the coleoptile emerges followed by
lateral seminal roots.
Germination
From: How a Corn Plant Develops.
http://maize.agron.iastate.edu/corngrows.html#how
Factors that affect development
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Environmental
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Temperature
Moisture
Disease/Pests
Nutrients
Genetic
Vegetative Stage
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Growth of the plant.
Divided into juvenile and adult.
Plants must become adult before can
become reproductive.
Juvenile tissues have distinct properties.
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Lack leaf hairs.
Different epicuticular wax.
Seedling Structure
From: How a Corn Plant Develops.
http://maize.agron.iastate.edu/corngrows.html#how
Adult
V3
VE
V8
V12
V15
V6
V18
VT
Adult
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By V6 the tassel is already preformed.
By V12 the number of rows in the
kernel are determined.
Reproductive
R1-silking
R4-Dough
R2-Blister
R3-Milk
R5-Dent
R6-Phys. Maturity
Leaf development
Corn leaf cross section
Epidermis
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Interfaces with the environment.
Epidermis contains guard cells that
open and close the stomates to regulate
water loss.
Epidermal surfaces are often covered
with cuticular wax, also to prevent
water loss.
Epidermal development
Root Development
Mutants help to understand
development
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The letters in DNA spell out instructions
for the gene product and the phenotype
we observe.
Mis-spellings can often cause changes
in the phenotype.
A copy of the gene containing a spelling
error is called a mutant.
Mutants II
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Mutants can be silent, missense or
nonsense.
By disrupting the normal function of a
gene they tell us what the genes
normal function was.
Examples
orp1
Kn1
D8
vp5
Functional Genomics of Root Growth
and Root Signaling Under Drought
http://rootgenomics.missouri.edu
Henry Nguyen
Robert Sharp
Hans
Bohnert
Daniel
Schachtman
Collaborators:
Yajun Wu, Utah
State Univ.
Georgia Davis
Dong Xu, Univ.
Missouri-Columbia
Gordon Springer
Roberto Tuberosa,
Univ. Bologna, Italy
University of
Missouri at Columbia
University of
Illinois at UrbanaChampaign
Donald Danforth
Plant Science
Center, St Louis
Steve Quarrie, John
Innes Ctr., UK and
Univ. Belgrade,
Yugoslavia
John-Marcel Ribaut,
CIMMYT, Mexico
Root growth objectives
• Genetic diversity in growth responses to water
stress
• Gene expression profiles in the root growth
zone (ESTs and microarrays)
• Cell wall protein profiles in the root growth zone
• Role of ABA in root growth maintenance
Primary Root
Shoot
-1
ELONGATION RATE (mm h )
Maize seedlings
WELL
WATERED
3
2
WATER
STRESSED
1
0
0.0
After germination,
transplanted to
vermiculite at various
water potentials, and
grown under nontranspiring conditions
(darkness and nearsaturation humidity)
to achieve precise,
constant and
reproducible water
deficits.
Roots continue to
grow under water
stress.
-0.4
-0.8
-1.2
-1.6
VERMICULITE WATER POTENTIAL (MPa)
Shoots do not.
Taking advantage of a kinematic approach
“A knowledge of the spatial and temporal variation
in growth rates within tissues can be a powerful
tool in physiological studies.
Little of the existing literature on the physiology of
growing tissue contains this kind of information.”
Erickson RO, Silk WK (1980) The kinematics of plant growth.
Scientific American 242: 134-151
1 cm
WELL WATERED
WATER STRESSED
(-1.6 MPa)
Growth rate is slower for
water stressed roots than
for well-watered roots.
Sharp RE et al. (1988)
Plant Physiol 87: 50-57
-1
RELATIVE ELONGATION RATE (h )
MO17 x FR27
0.4
WELL
WATERED
(WW)
0.2
WATER
STRESSED
(WS)
0.0
0
2
4
6
8
10
12
DISTANCE FROM ROOT APEX (mm)
Root
apex
End of growth
zone, WS
End of growth
zone, WW
16 20
2
3
4
-1
RELATIVE ELONGATION RATE (h )
1
0.4
WELL
WATERED
(WW)
0.2
WATER
STRESSED
(WS)
0.0
0
2
4
6
8
10
DISTANCE FROM ROOT APEX (mm)
Region 1, elongation
completely
maintained in WS
12
16 20
2
3
4
-1
RELATIVE ELONGATION RATE (h )
1
0.4
WELL
WATERED
(WW)
0.2
WATER
STRESSED
(WS)
0.0
0
2
4
6
8
10
DISTANCE FROM ROOT APEX (mm)
Region 1, elongation
completely
maintained in WS
Region 2, maximum
elongation in WW,
inhibition in WS
12
16 20
2
3
4
-1
RELATIVE ELONGATION RATE (h )
1
0.4
WELL
WATERED
(WW)
0.2
WATER
STRESSED
(WS)
0.0
0
2
4
6
8
10
DISTANCE FROM ROOT APEX (mm)
Region 1, elongation
completely
maintained in WS
Region 2, maximum
elongation in WW,
inhibition in WS
Region 3,
deceleration in WW,
cessation in WS
12
16 20
2
3
4
-1
RELATIVE ELONGATION RATE (h )
1
0.4
WELL
WATERED
(WW)
0.2
WATER
STRESSED
(WS)
0.0
0
2
4
6
8
10
12
16 20
DISTANCE FROM ROOT APEX (mm)
Region 1, elongation
completely
maintained in WS
Region 2, maximum
elongation in WW,
inhibition in WS
Region 3,
deceleration in WW,
cessation in WS
Region 4, nonelongating in
WW and WS
Root growth objectives
• Genetic diversity in growth responses to water
stress
• Transcript profiles in the root growth zone
(ESTs and microarrays)
• Cell wall protein profiles in the root growth zone
• Role of ABA in root growth maintenance
cDNA libraries and expressed
sequence tag (EST) analysis
(Hans Bohnert et al., unpublished)
•
Line FR697 (stress tolerant), root tip regions 1-4
•
Well-watered, 5 h and 48 h after transplanting,
combined for one library
•
Water-stressed (-1.6 MPa), 5 h and 48 h after
transplanting, two libraries
•
~6,000 ESTs sequenced per library (normalized)
7
3
S1
S2
12
S3
In each library, the region of origin of
sequences was tracked by adding one of
four segment-identifying tags to the 3’ end
of each mRNA source
well watered
5h water stress
20 mm
S4
Segment 1
Segment 2
Segment 3
Segment 4
S1
S2
S3
S4
ACGCA18(T)
ACCGA18(T)
TCGCA18(T)
TCCGA18(T)
48h water stress
7000
6000
5000
20,000+ sequences
have been submitted
to GenBank, with
more to follow
4000
3000
2000
1000
0
ESTs Sequenced
(3’-end)
Segment Tag
Found
Accepted
Sequences
~7,000 unigenes
Unigenes summary
• 3,446 specific to libraries and
segments
WW, well watered
WS 5h, water stress 5h
WS 48h, water stress 48h
• 2,331 in more than one library
and/or segment
• 3,184 ESTs with no known
protein alignment
With additional sequencing from
subtracted library (in progress),
9-10,000 unigenes expected
Estimated that most of the
root transcript complement
has been sampled (<10,000
genes [Goldberg, 1980s])
Most of the top 10
abundant transcripts are
functionally unknown
WW
WS 5h
WS 48h
S1
262
275
123
S1 specific
S2
214
49
61
S2 specific
S3
125
293
578
S3 specific
S4
181
282
251
S4 specific
no tag
164
313
275
No segment
identity but
unique in each
library
Total in
library
946
1,212
1,288
libraryspecific
libraryspecific
libraryspecific
WS 5h, S3
WW, S3
Segment similarities assessed by
composition and redundancy of
all ESTs (using “virtualSAGE”,
Bohnert et al.)
WW, S4
WS 48h, S2
WS 48h, S3
WS 5h, S2
WS 5h, S4
S2
S3
S4
-1
RELATIVE ELONGATION RATE (h )
WS 48h, S4
S1
0.4
WW
0.2
WS
0.0
WS 5h, S1
WW, S1
WS 48h, S1
WW, S2
0
2
4
6
8
10
12
16 20
DISTANCE FROM ROOT APEX (mm)
Most distinct profile, region of
maximum elongation in WW and
inhibition of elongation in WS
Highlights the strength of the
kinematic approach to transcript
profiling
Postdocs
Eric Ober
Imad Saab
Bill Spollen
Jinming Zhu
Graduate Students
In-Jeong Cho
Eleanor Thorne
Yajun Wu
Research Associate
Mary LeNoble
Collaborators
Dan Cosgrove, Penn State Univ.
Steve Fry, Univ. Edinburgh, UK
Jennifer MacAdam, Utah State Univ.
Don McCarty, Univ. Florida-Gainesville
Mayandi Sivaguru, Molecular Cytology
Core, Univ. Missouri-Columbia
Yajun Wu, Utah State Univ.
Ted Hsiao, Univ. California-Davis
Wendy Silk, Univ. California-Davis
Research Specialist
Lindsey Sharp
Undergraduate
Rachel Maltman
DBI 0211842