Genetics and Plant Development

MUPGRET WorkshopMarch 27, 2004

Developmental stages Germination Juvenile Adult Reproductive

Germination 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

Environmental Temperature Moisture Disease/Pests Nutrients

Genetic

Vegetative Stage Growth of the plant. Divided into juvenile and adult. Plants must become adult before

can become reproductive. Juvenile tissues have distinct

properties. Lack leaf hairs. Different epicuticular wax.

Seedling Structure

From: How a Corn Plant Develops. http://maize.agron.iastate.edu/corngrows.html#how

Adult

VE V3 V6

V8 V12 V15 V18 VT

Adult By V6 the tassel is already

preformed. By V12 the number of rows in the

kernel are determined.

Reproductive

R1-silking R2-Blister R3-Milk

R4-DoughR5-Dent

R6-Phys. Maturity

Leaf development

Corn leaf cross section

Epidermis 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

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 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

D8

orp1

Kn1

vp5

Background

The roots of plants play a vital role in water and mineral acquisition which are essential for plant growth and development. Under conditions of drought, roots can adapt to continue growth while at the same time producing and sending “early warning” signals to shoots which inhibit the plant growth above ground.

The broad aim of the project is:•to develop an understanding of the molecular mechanisms used by plant roots to acquire water and minerals from the soil;•to elucidate the role roots play in adaptation to drought conditions; •and to transfer this knowledge to crop improvement through biotechnology.

Background

The roots of plants play a vital role in water and mineral acquisition which are essential for plant growth and development. Under conditions of drought, roots can adapt to continue growth while at the same time producing and sending “early warning” signals to shoots which inhibit the plant growth above ground.

The broad aim of the project is:•to develop an understanding of the molecular mechanisms used by plant roots to acquire water and minerals from the soil;•to elucidate the role roots play in adaptation to drought conditions; •and to transfer this knowledge to crop improvement through biotechnology.

Background

The roots of plants play a vital role in water and mineral acquisition which are essential for plant growth and development. Under conditions of drought, roots can adapt to continue growth while at the same time producing and sending “early warning” signals to shoots which inhibit the plant growth above ground.

The broad aim of the project is:•to develop an understanding of the molecular mechanisms used by plant roots to acquire water and minerals from the soil;•to elucidate the role roots play in adaptation to drought conditions; •and to transfer this knowledge to crop improvement through biotechnology.

http://rootgenomics.missouri.edu

University of Missouri at Columbia

University of Illinois at Urbana-

Champaign

Donald Danforth Plant Science

Center, St Louis

Henry Nguyen

Robert Sharp

Georgia Davis

Gordon Springer

Hans Bohnert

Daniel Schachtman

Collaborators:

Yajun Wu, Utah State Univ.

Dong Xu, Univ. Missouri-Columbia

Roberto Tuberosa, Univ. Bologna, Italy

Steve Quarrie, John Innes Ctr., UK and Univ. Belgrade, Yugoslavia

John-Marcel Ribaut, CIMMYT, Mexico

Functional Genomics of Root Growth and Root Signaling Under Drought

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

0.0 -0.4 -0.8 -1.2 -1.60

1

2

3

ELO

NG

AT

ION

RA

TE

(m

m h

-1)

VERMICULITE WATER POTENTIAL (MPa)

Primary Root Shoot

After germination, transplanted to vermiculite at various water potentials, and grown under non-transpiring conditions (darkness and near-saturation humidity) to achieve precise, constant and reproducible water deficits.

Roots continue to grow under water stress.

Shoots do not.

Maize seedlings

WATER STRESSED

WELL WATERED

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

WELL WATERED WATER STRESSED

(-1.6 MPa)

1 cm

Sharp RE et al. (1988) Plant Physiol 87: 50-57

Growth rate is slower for water stressed roots than for well-watered roots.

Root apex

End of growth zone, WS

End of growth zone, WW

WATER STRESSED(WS)

WELL WATERED (WW)

MO17 x FR27

WATER STRESSED(WS)

WELL WATERED (WW)

1 2 3 4

Region 1, elongation completely maintained in WS

WATER STRESSED(WS)

WELL WATERED (WW)

1 2 3 4

Region 1, elongation completely maintained in WS

Region 2, maximum elongation in WW, inhibition in WS

WATER STRESSED(WS)

WELL WATERED (WW)

1 2 3 4

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 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, non-elongating in WW and WS

WATER STRESSED(WS)

WELL WATERED (WW)

1 2 3 4

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)

S1 S2 S3 S4

3 7 12 20 mm

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

Segment 1 S1 ACGCA18(T)Segment 2 S2 ACCGA18(T)Segment 3 S3 TCGCA18(T)Segment 4 S4 TCCGA18(T)

20,000+ sequences have been submitted to GenBank, with more to follow

0

1000

2000

3000

4000

5000

6000

7000

ESTs Sequenced Segment TagFound

AcceptedSequences

well watered 5h water stress 48h water stress

(3’-end)

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

library-specific

library-specific

library-specific

Unigenes summary

WW, well wateredWS 5h, water stress 5hWS 48h, water stress 48h

~7,000 unigenes

• 3,446 specific to libraries and segments

• 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

Most of the top 10 abundant transcripts are functionally unknown

Estimated that most of the root transcript complement has been sampled (<10,000 genes [Goldberg, 1980s])

Segment similarities assessed by composition and redundancy of

all ESTs (using “virtualSAGE”, Bohnert et al.)

WW, S2

WS 5h, S1

WW, S1

WS 48h, S1

WS 5h, S4

WS 5h, S2

WS 48h, S2

WS 48h, S3

WS 48h, S4

WW, S4

WW, S3

WS 5h, S3

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

S1 S2 S3 S4

WW

WS

PostdocsEric OberImad SaabBill SpollenJinming Zhu

Graduate StudentsIn-Jeong ChoEleanor ThorneYajun Wu

Research AssociateMary LeNoble

Research SpecialistLindsey Sharp

UndergraduateRachel Maltman

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

DBI 0211842