Title:	  Realizing the Potential of Plant Genomics: From Model Systems
 	  To The Understanding Of Diversity
Date:     October 11, 2000


Realizing the Potential of Plant Genomics: From Model Systems
To The Understanding Of Diversity

                                APRIL, 1999



FOREWARD TO THE REPORT

Since  the discovery  of the  structure of  DNA, the  field of  biology has
experienced a series of revolutionary changes in the ways in which problems
are  approached.  The  recent  development  of high  capacity  methods  for
analyzing the  structure and  function of genes, which  may be collectively
termed "genomics",  represents a  new paradigm with  broad implications for
biologists. Instead  of characterizing genes one or a few  at a time, it is
now possible  to determine the  complete nucleotide sequence of  all of the
genes in an organism and to measure the amount of mRNA corresponding to all
of the genes. Although  comprehensive information of this kind is currently
available for only a  few organisms, it seems likely that comparable levels
of  information  will  rapidly become  available  for  most widely  studied
organisms, including several higher plants. Access to this information, and
new  tools  that  exploit  it, will  profoundly  alter  the  ways in  which
biologists  select and  approach  questions. This,  in turn,  will directly
impact the  application of  directed genetic methods to  the improvement of
economically important plants.

Although future  developments in a rapidly  emerging field can be difficult
to predict,  some projection of  trajectory can be helpful  in planning for
the  development  of community  resources  and other  initiatives that  may
facilitate progress. Indeed, the  success of the Arabidopsis genome project
stands  as an  example of productive  foresight. Now  that the sequence  of
Arabidopsis is  nearing completion, it was  deemed useful to reinitiate the
process that  led to the formulation of the  original vision of the project
(NSF document 90-80). Toward this end a group of plant biologists (Appendix
I) met to discuss  the subject at an NSF-sponsored workshop "New Directions
in  Plant  Biological Research"  held  on November  23  & 24,  1998 at  the
Carnegie Institution  of Washington, Department of  Plant Biology, Stanford
University.  This document  summarizes the  perspectives that  emerged from
these discussions and presents the views/vision of a diverse group of plant
scientists.  The  report  also  includes  input  from the  North  American
Arabidopsis Steering  Committee (NAASC)  as well as from  the plant biology
community at large.





MISSION STATEMENT:

To exploit  the revolution in plant  genomics by understanding the function
of  all  plant genes  within  their cellular,  organismal and  evolutionary
context and  to create  an information structure  to coordinate, integrate,
analyze and make accessible knowledge about plant biology.

Specific Recommendations:

 Development of and  ready access to comprehensive  data, materials sets,
tools  and   enabling  technologies  including  a   complete  inventory  of
full-length cDNAs, gene knockouts, and genome chips/arrays

 Promoting "systems"  approaches to biological processes using integrative
and functional genomic information

 Development of  a computerized knowledge base, "the electronic plant", to
capture all plant functional genomic and systems data

 Training of  graduate  students  and postdoctoral  fellows in  "systems
approaches" to understand plant biological processes

 Establishment of training courses in computational plant genomics/systems
biology  to prepare students  to integrate  information about a  variety of
plant systems to formulate testable hypotheses


I. INTRODUCTION

Plant Genomics: Early Lessons from the Arabidopsis Genome Sequence

Plant biologists have been  at the forefront of the shift to genomics. As a
result, one  of the  first eukaryotic organisms to  be completely sequenced
will  be the  small mustard  species  Arabidopsis thaliana (Meinke  et al.,
Science 1998, 282:662). Because  of certain technical advantages, including
a highly compact genome of about 130 Mb with little interspersed repetitive
DNA,   Arabidopsis is  one  of the  most  widely used  model organisms  for
studying the biology of  higher plants. It is also a close relative of many
food  plants  such  as  canola,  cabbage,  cauliflower,  broccoli,  turnip,
rutabaga,  kale, brussel  sprouts, kohlrabi  and radish. More  importantly,
Arabidopsis genome sequence information  will be applicable to major crops,
such as  corn and soybeans, because  of the close evolutionary similarities
among  the genomes  of  all flowering  plants. An  international consortium
called The Arabidopsis Genome Initiative (AGI), which includes six research
groups  in Japan,  Europe  and the  USA, is  collaborating to  sequence the
genome. About  50% of the genome sequence  is currently available in public
databases  and a  large  proportion of  the genes  are also  represented by
partial  cDNA  sequences. It  is  currently anticipated  that the  complete
genome sequence will be available by the end of the year 2000.

The results  to date of the  Arabidopsis Genome Initiative  have revealed a
new world of scientific processes and opportunities in plants. With greater
than one-third  of the  genome sequence finished,  completely unanticipated
functions  have  been  found.  These  recent findings  reveal  our  present
ignorance of  the mechanisms  by which plants  grow and function,  but also
provide  the   exact  experimental   material  necessary  to   gain  a  new
understanding:  the genes  mediating  the newly  discovered processes.  New
technical capabilities such as gene chips and gene replacement technologies
now, for  the first time, allow us to proceed  rapidly and surely from gene
sequence to function. Thus, there is an unprecedented opportunity to follow
up on  these recent  genomic discoveries by  learning the functions  of all
plant  genes,   to  reveal  the  previously   unknown  processes  that  are
fundamental to the mechanisms of plant life.

Recent  unexpected discoveries  derived  from genomic  sequence information
include the identification of:

1) Glutamate receptor genes. Glutamate receptors are components of neurons,
where they  serve as ion channels  in rapid synaptic transmission. Recently
two glutamate receptor genes  have been found in Arabidopsis, each encoding
proteins with  all of  the signature domains  of the animal  proteins. What
role could  such previously brain-specific proteins  play in plants? Use of
channel inhibitors  shows that blocking the  plant channels seems to affect
the  ability of  the plants to  perceive light.  What role do  the channels
play? Several glutamate channel blockers used in brain research derive from
plants;  they were  previously  considered to  be used  in  defense against
herbivores.

Now  it appears  that these  compounds may  function in plants  to regulate
plant channels. How many  other bioactive plant compounds, such as caffeine
or nicotine, have direct roles in plants? What are the roles?

2) Receptor kinases. The Arabidopsis genome sequences to date reveal nearly
100  different  genes  that  appear  to  code  for  transmembrane  receptor
serine/threonine kinases,  implying that  the complete genome  will have on
the order  of 300 such genes. The mutant phenotype  of only three is known;
two  are involved  in regulation  of cell  division and  differentiation in
meristems, and one appears to be a hormone receptor. A similar gene in rice
mediates  response to  a  bacterial pathogen.  What  are the  roles of  the
hundreds of  these proteins?  Their existence implies a  massive network of
cell-cell and environment-plant communication,  via a series of ligands yet
to be  discovered. Understanding this network will  give us an entirely new
view   of  plant   development,  environmental  response,   and  organismal
integration.

3)  Nuclear architecture.  Use of modern imaging  technologies with nuclear
proteins (such  as photoreceptors and transcription  factors) discovered in
Arabidopsis reveals a series  of striking and novel subnuclear localization
patterns. What  are the nuclear microcompartments  that have been revealed,
and what is their role in gene expression and genomic function?

4)  Multiple drug resistance. ABC transporter genes. There are on the order
of 50  genes coding for ABC  transporters already found in  the Arabidopsis
genome project  and thus, 150 are expected in  the complete genome. What do
they transport? Some appear to be mitochondrial. What is the nature of this
mitochondrial  traffic,  and  the  role  it  plays  in  nuclear-cytoplasmic
interaction and energy metabolism?

5)  G-protein coupled  receptors.  It appears  that there are  already many
candidate  genes  that could  code  for  7-transmembrane G-protein  coupled
receptors  in   Arabidopsis .  There  is,  however,  only  a  single  known
heterotrimeric G-protein  alpha subunit.  Do all of  the putative receptors
act  through a  single G-protein,  or do  these plant  receptors act  in an
entirely  new signal  transduction pathway,  different from the  pathway in
which the cognate animal proteins act?

6)  Blue light  photoreceptors.  One  indication of  the amazing  degree of
conservation in biological systems  is the discovery of molecules in plants
that are important in human disease. For example, the conserved role of the
blue light  photoreceptor cryptochrome  in regulating both  circadian plant
growth and rhythmic sleep behavior in animals.

These unanticipated discoveries have opened a new world of experimentation
and understanding that we must explore now.



II. FUNCTIONAL AND INTEGRATIVE GENOMICS: THE NEXT DECADE OF PLANT RESEARCH

The  goal  of the  field  is  to understand  plant  biology completely.  In
particular, this  means being able to explain in  detail how all aspects of
plant growth  and development occur, how plants  respond to change in their
environment,  the  molecular basis  of  variation between  species and  how
plants respond in complex  communities (i.e., ecosystems). An integral part
of this  goal is to make the knowledge  broadly accessible. In this respect
our traditions for organizing  academic knowledge are no longer appropriate
to the task and will be even less so in the future.

In order to progress  toward that goal in the most efficient manner we need
to have  a sense of what kinds of discoveries are  likely to be most useful
so that  we can  allocate resources and  make the many  community decisions
that  shape  modern science  on  a daily  basis.  It is  also essential  to
identify the  factors that will facilitate  broad progress in understanding
plant biology  rather than only focusing  on one or two  model species. The
biomedical community  is largely focused on one organism  and is not a good
model for how plant biology should develop. The completion of the goals for
plant  biology  described in  our  mission statement  will enable  dramatic
increases  in  our  understanding  of  mechanistic aspects  of  plant  gene
function.

Assigning  Functions to  All  Plant Genes.  An important  and revolutionary
aspect of  the  proposal to understand the function  of  all plant genes by
the year 2010  - is that it implicitly endorses the allocation of resources
to attempts  to assign function to genes that  have no known function. This
represents a significant departure from the common practice of defining and
justifying  a  scientific  goal  based  on the  biological  phenomena.  The
rationale for  endorsing this radical change is that  for the first time it
is feasible  to envision  a whole system  approach to function.  This whole
system approach promises to  be orders of magnitude more efficient than the
conventional approach.  We envision that once  the efficiencies of genomics
have  been realized,  presumably within  the next  decade, there will  be a
renewed emphasis on problem-oriented approaches and an expanded emphasis on
understanding diversity.

In  order  to attain  this  level  of understanding,  a  set of  scientific
problem-oriented goals  were defined. The attainment  of these goals relies
heavily  upon  the  development  of  a set  of  process-oriented,  enabling
technologies  (tools   and  materials)   and  on  further   human  resource
development in the plant sciences.

A.  Scientific  Problem-Oriented  Goals:  The  natural  world   provides  a 
virtually  endless  source  of  biological  phenomena  that are amenable to
observation, description and explanation. However, experience suggests that
certain  problems yield insights of broad  relevance whereas others do not.
What are the problems that are likely to yield the greatest advances?

 Identification of the language of  transcriptional  control elements will 
allow  us  to  be  predictive  about  gene  expression (and to control gene 
expression).

 Elucidation of the molecular  mechanisms that  regulate pattern formation 
and morphogenesis will allow us to understand and control the morphological
diversity of higher plants.

 Structural  characterization of key  enzymes will allow us to efficiently 
identify genes and proteins responsible for chemical diversity in plants.

 Elucidation  of processes that are not found in Arabidopsis or  rice will 
provide a useful basis for future work in understanding plant diversity.

 Elucidation  of  basic  cellular  processes that  are  unique  to  plants 
or  which  differ  between  plants   and  animals  will  be   essential  to 
understanding the mechanisms underlying growth and development.

The  explicit  scientific  problems can  best  be stated in the form of the 
central unanswered questions in  the  areas of  cell biology, biochemistry/
genetics, development and evolution of plants. These questions can and must 
now be answered.

1) Cell  Biology. The function  and structure of cells determines
the architecture of the plant. We will endeavor to understand the
number  and function  of plant  cell types and  the physiological
contributions and interactions amongst them, including a detailed
molecular  understanding  of  each  cell type.  Major  unanswered
questions include:

 How  is cell shape, size, and density  regulated - how is plant
morphology determined?

 What is the  basis for broad structural diversity amongst plant
species?

  How  does  organ morphology  derive from  cell  physiology and
structure and result in adaptive characteristics?

 How are asymmetric growth signals coordinated?

 To  what extent  do pathway components  physically group within
cells?

 What are the subcellular signaling domains that control various
responses such as asymmetric cell elongation?

 How  does cell-cell  communication happen in plants  - what are
the   roles   of  plasmodesmata,   receptor  kinases,   adhesins,
structural cell wall components, and other small molecules?

 How does differentiation  of plant cell types take place in the
absence of cell migration?

    What  is  the  role  of   the  cytoskeleton  in  plant  cell
differentiation?

  What are the unique mechanical  properties of plants? How does
mechanosensing control differentiation?

 Cell wall  deposition - how does it happen - how does it relate
to expansion and division and differentiation?

 Intracellular dynamics of plant cells - how does it differ from
other systems?

 What  is the  function of cytoplasmic  streaming and how  is it
regulated?

  What  are  the  processes  that  control/coordinate  organelle
biogenesis?

  Short-  and long-range  signaling  -  how does  it happen  for
different stimuli?

  How do tissues  coordinate their  responses to a  diversity of
signals? -  light (quality, quantity,  photoperiod), water, ions,
gravity, microbes  (pathogens and symbionts and  epiphytes - both
rhizosphere and phylloplane-associated), and insects?

 What are the modes of signaling (chemical/
electrophysiological/ mechanical/ osmotic/ bulk flow)?

 Nuclear  topology/3-D chromatin structure -  how does it relate
to coordinate expression of sets of genes?

  How does  cell migration  occur in  cases such as  pollen tube
growth?

  Regulation of  apoptosis  (programmed cell  death), suspensor,
xylem  element  differentiation,  role  of  cell  death  in  leaf
morphology what are the signals  -how does pathogenesis relate to 
developmentally programmed cell death?

 What is the basis of non-host resistance?

 What  is the nature of  interorganellar communication - control
of nuclear gene expression by chloroplast (and mitochondria) - is
nuclear gene expression controlled by other organelles?

 Protein and oil  bodies - how are they structured? How does the
packing work?

2) Biochemical  and Genetic Functions.  While the  past ten years
has seen  major advances in our  understanding of the genetic and
biochemical basis for gene  function in a variety of plants, most
notably Arabidopsis,  major unanswered questions remain. Examples
of scientific questions to be addressed include:

 Sensing  and responding to environmental  cues including light,
cold, drought,  gravity and  many other abiotic  signals by which
plants interact with their surroundings.

 Interacting  with   an  enormous  (largely  unknown/unexplored)
variety of other organisms including bacteria, fungi, insects and
other plants via chemical and other signals.

 The  defining of pathways for  biosynthesis of numerous primary
and  secondary metabolites  and  for the  biogenesis of  cellular
membranes,  walls, and  organelles  including lipid,  protein and
polysaccharide biosynthesis.

 The nature of biotic signals and signal transduction mechanisms  
including  hormones,  light  and  a  variety  of stress producing 
stimuli.

 The  mechanisms of  gene expression,  including  transcription,
translation and regulatory networks controlled by kinase cascades
and other protein-protein interactions including the assembly and
destruction   of   macromolecular   complexes   via   chaperones,
proteosomes, etc.

 Epigenetic  effects   on   gene  expression,  cellular  memory, 
imprinting, gene silencing and paramutation.

 Genetic  mechanisms   of  repair,  replication,  recombination,
transposition,  meiotic and  mitotic  inheritance of  the genetic
material.

 Chromosome dynamics, kinetochore function.

 Functional discovery  by  sequence comparison  with prokaryotic
and eukaryotic genomes, such  as the discovery of novel universal
pathways of protein translocation.

3) Developmental  Biology.  The final form  of a higher  plant is
produced  through  a  complex  interaction  of  gene  expression,
preexisting  cellular  components and  the  environment. For  the
first time we will have a catalog of all of the genes of a higher
plant  as  a  starting  point for  developmental  analysis.  This
together  with  new  enabling  technologies  will  now  allow  an
understanding of  the fundamental events underlying developmental
processes. Identifying  the function  of all genes  will allow an
understanding of a diversity of plant process including:

 How  are whole sets of  genes coordinately regulated to produce
complex plant structures?

 How   can  genetic   differences  account  for  the  tremendous
diversity of angiosperms?

 How  do  plant cells communicate with each other,  and how does
this    communication     regulate    cellular    behavior    and
differentiation?

 How does communication between cells lead to regulation of gene
expression?

 What  is  the  nature  of  regulatory networks  responsible for
regulation of development?

 How  are  environmental  signals  perceived  and  how  are  the
perceived  signals  transduced  to  modulate gene expression  and
development?

 What are the nature of sequences responsible for the regulation
of gene expression?

 The nature  of  regulatory  transcription factors and  how they
interact with specific DNA sequences to regulate gene expression.

 The interplay between the genome, the cytoskeleton and the cell
wall and how this process mediates plant morphogenesis.

 How  plants measure  time and respond to  timing events (annual
and biennial regulatory processes, circadian rhythms).

4)  Genome  Evolution.  Although  flowering  plants have  evolved
during the  past 150 million years or  so, and might therefore be
expected  to be  very similar  at the genetic  level, substantial
developmental and  chemical diversity  is apparent. Understanding
the basis  for this  diversity is a  key to understanding  how to
effect rational  improvements in the productivity  and utility of
crop  species. Knowledge  of the  genetic basis  for intraspecies
variation  in specific  traits should  be useful in  selecting or
creating  useful  variation  within   a  species .   Examples  of
scientific questions to be addressed include:

 How  are genomes  similar within and between  families in which
chromosomal segments have been conserved (macro and micro)?

 How does higher order structure compare?

 What are the functional consequences of conservation?

 What are  the  interspecific differences - how  do  these arise
(duplication,   ploidy,   repetitive  DNA)   and  contribute   to
speciation?

 What are the intraspecies differences?

 How is allelic diversity defined and quantified?

 What is the complete gene repertoire of the plant kingdom?

 How  representative   is   the  genic  content   of   rice  and 
Arabidopsis?

 How   does  phylogenetic/ecological   diversity  predict  genic
novelty?

B. Process-Oriented  Goals:  For biologists to  fully realize the
benefit from  the availability of fully  sequenced plant genomes,
we must  facilitate a  dramatic change in  the current laboratory
landscape.  Current studies  of single  genes will  transition to
large-scale   analysis  of   entire  gene   regulatory  networks.
Moreover, with the expected  further reduction in the cost of DNA
sequencing  technologies, comparisons  of a  few genomes  will be
replaced  by  a  broad   sampling  of  plant  genetic  diversity.
Ultimately,  the future  plant biologist  will be  integrating an
array of tools that  will allow an appreciation of the complexity
which we can currently only imagine.

The proposal made about ten years ago to sequence the Arabidopsis
genome was  a process goal. It  was based on the  concept that it
would be  tremendously enabling for the  entire community to have
the complete sequence of the Arabidopsis genome.

 To assign  a function to all higher plant genes on the basis of
experimental  evidence by  2010. An  implicit assumption  is that
higher plants  share essentially the same  basic set of genes and
that   by   knowing   the  function   of   a   small  number   of
representatives,  it  will  be  possible to  infer  the  probable
function in  other species. We recognize  that in many cases, the
exact function of many  genes will remain elusive beyond the year
2010.  However,   we  believe   that  it  will   be  possible  to
experimentally  assign a  general  function to  each gene  in the
genome of  the model organisms or  to establish that inactivation
or overexpression of the  gene causes no observable effect on the
organism. In  order to establish gene  function, we believe that,
at the  very least, each gene  must be characterized with respect
to the  phenotypes caused by inactivation  or overexpression, the
mode and specificity  of regulation, the subcellular localization
of the gene product, the identity of interacting proteins and the
identity of  coregulated genes. By extending  the goal to include
all higher  plants, we intend that  research on diversity of gene
function must play an increasingly important role.

 To determine the complete sequence of a second plant,preferably 
rice. The sequencing of rice must  be  accompanied by  a  similar 
kind  of infrastructure  development  that  was  used  to advance 
Arabidopsis (e.g., maps, mutants and infrastructure).

 To  acquire deep EST coverage for  all plant species of utility
or academic  interest. This will be  very useful in many respects
but, in  particular, will help to  identify genes that are highly
divergent between Arabidopsis, rice and other plant species.

 To develop high  resolution genetic and physical maps of select
plant  species  in  particular  grasses (maize,  sorghum,  wheat,
barley),  legumes  (soybean),  Solanaceae  (potato, tomato),  and
other important crops.

 To  produce  low  resolution genetic/physical  maps and  sample
sequencing   of   a  variety   of   flowering  plants   including
gymnosperms, mosses,  and liverworts  (using ESTs, BAC  ends, low
coverage genomic sequencing).

 To  characterize  the expression of all  Arabidopsis and cereal
genes under all developmental and environmental circumstances.

 To develop new information management methods that will provide
universal access  to all  information about basic  plant biology.
The  large   amounts  of   data  that  are   being  generated  by
genome-related approaches  cannot be distributed  by print media.
There is  a pressing need for  the development of new information
retrieval and analysis approaches.  In the short term, these will
need to  be publicly supported in much  the same way the Internet
was subsidized. Eventually,  electronic databases will merge with
print   media  and   appropriate  cost/benefit  models   will  be
implemented.

There is a shortage  of people trained in the development and use
of bioinformatics. Support for graduate and postgraduate training
is needed.  Support for  the development of  academic programs is
also needed.

 To  develop  infrastructure and  community processes  that will
integrate basic and applied research in plant biology.

C. Enabling Technologies: To realize many of the process-oriented
goals,   the    following   enabling   technologies,   materials,
comprehensive data  sets and tools need  to be developed and made
available to the community:

 The  complete sequence  and inventory of  full-length cDNAs for
predicted open  reading frames  for model species.  These will be
essential  for correct  identification of  all coding  regions in
these genomes. These data sets can then be used as a standard for
comparison in  exploration of  other species for  novel genes not
found in the model species.

 A  complete set  of insertion mutants  in all plant  genes with
sequence of flanking regions for rapid mutant identification.

 An expression map of every gene by in situ and/or enhancer/gene
traps. Alternatively,  GFP or  similar fusion should  be produced
for every gene predicted by open reading frame.

 Tools for  parallel analysis  of the  expression of  all  plant
genes, using whole genome sequence information  (e.g., chip-based
technology).

 Tools for genome-wide,  rapid mapping for mutants, whole genome
chips with appropriate  sampling redundancy for identification of
all differences between two  genomes should be assembled and made
available. This  would enable direct  identification of mutations
in a single experiment.

 Tools  for genome-wide,  rapid  mapping of  QTLs,  to  identify
naturally occurring alleles  affecting quantitative traits (e. g.
chip-based technology for segregating populations).

 Tools  for  proteomics, such  as those currently  available for
yeast that  allow easy determination of  the identity of purified
proteins.

 Artificial  plant chromosome  vectors ,  to  enable the  facile
movement of large gene sets from plant to plant.

 Methods   for   efficient   gene  replacement   by   homologous
recombination,  to enable precise and  reproducible gene function
studies.

It  is  recognized that the  community will never  assemble these
tools  unless  concerted efforts  are  made.  Large consortia  of
investigators working  on each of these  topics, independently of
their  application, will  need to  be established. While  this is
perhaps not the most  immediate creative science, the benefits to
overall  progress clearly  justify  the investment  of resources.
Directed   assembly    of   these   tools    will   prevent   the
counterproductive "reinvention  of the wheel"  by all independent
labs  wishing  to  utilize  these new  technologies.  Independent
investigators  will then be  able to  focus their efforts  on the
biological questions at hand.

A key  concept for  all these methods/tools is  access. Access to
all  these   tools  must   include  means  of   dissemination  of
appropriate arrays, resources for their use, and means of storing
and  accessing data  generated by  their use.  The  investment in
their  development  will  only   be  worthwhile  if  it  includes
establishment  of effective  mechanisms for ensuring  the methods
and  data  will  be  available  to the  entire  biology  research
community. The mechanisms  for rapid dissemination of information
developed  by  the  U.S.  component  of the   Arabidopsis  Genome
Initiative,  whereby  even preliminary  genome  sequence data  is
rapidly disseminated, should serve  as a model for this. Under no
circumstances  should consortia  be established  under conditions
where    non-members   would    be   excluded    from   immediate
access/utilization of  the products of the  consortia. Efforts to
assemble these tools need to be established as soon as possible.

It is expected that  the application of these and related methods
will lead  to the assignment  of some degree of  gene function to
most  higher plant  genes. In  addition, parallel studies  of the
function of  all genes  in the other, non  plant, model organisms
will  contribute a  great  deal to  understanding gene  function.
Presumably,  this  comprehensive approach  to understanding  gene
function  will usher  in an  era of  true genetic  engineering in
which  rational  changes  can  be  devised  from  some  level  of
knowledge  of  the  entire   system,  rather  than  the  one-gene
tinkering that has marked the beginning of the era.



III. HUMAN RESOURCE DEVELOPMENT

The availability  of massive quantities of  plant genome sequence
data plus an increasing understanding of plant gene function will
bring  about rapid changes  in all  areas of plant  biology, from
biochemistry  and  molecular biology  to  ecology and  evolution.
Advances in  these areas  of basic plant biology  will be rapidly
transformed into practical benefits  that will change the face of
agriculture and  will trigger rapid growth  in the agriculturally
related biotechnology  industry. These  anticipated advances will
require a  new generation  of basic and  applied plant biologists
who  possess  new  combinations  of skills,  both  among  college
graduates  and among  those  who pursue  more advanced  training.
Providing these highly skilled  plant scientists will require the
coordinated  efforts   of  colleges,  universities,  and  federal
funding  agencies,  with  appropriate  support from  the  private
sector and professional societies.

The most important characteristic  of the new generation of plant
scientists is that they  will need to be broadly trained in plant
biology.   Regardless  of   whether   they  are   biochemists  or
ecologists, they will need to have basic training in all areas of
plant biology  and must be  able to work as  effective members of
multi-disciplinary teams. Although  a solid foundation in biology
will be  the most  important requirement, the  next generation of
plant scientists  will also need  to be highly skilled  in a wide
array  of  genomic  techniques   including  the  ability  to  use
information technology to access  and analyze large quantities of
biological data.

Although  the  training of  future  plant  biologists will  occur
primarily in colleges  and universities, federal funding agencies
will be important partners  in this effort. New training programs
are needed  at all  levels; i.e. baccalaureate,  M.S., Ph.D., and
post-doctoral.  New  interdisciplinary training  programs at  the
undergraduate  level  will  require  changes  in  the  curriculum
requirements  in many  traditional  majors. At  the graduate  and
postdoctoral   levels,   new  and   expanded  financial   support
mechanisms  are   needed.  Funding  for   graduate  students  and
postdoctoral associates has traditionally been tied to individual
research  grants, which  often limits the  training possibilities
available to the trainees. New funding mechanisms, including both
expanded training grants  and fellowships to individual students,
are  needed.  These mechanisms  should  provide  trainees with  a
maximum of  flexibility to  pursue their training  in top quality
labs and to gain the various experiences and expertise needed.

Training Goals:

Establish new  individual predoctoral and postdoctoral fellowship
programs in plant biology.

Expand  existing training  grant programs,  with a focus  on high
quality   programs  that   provide   multi-disciplinary  training
experiences  for both  predoctoral  and postdoctoral  trainees in
plant biology.


IV. BENEFITS OF THE RESEARCH

The availability  of  the  sequence of Arabidopsis, together with
the  comprehensive data  sets and  tools outlined above  will not
only dramatically  accelerate research on this  species, but also
will facilitate studies on other plants and higher eukaryotes. As
noted  above, the  availability  of a  comprehensive set  of gene
knockouts can be used  to make rapid progress on analysis of gene
function  for currently  "unknown"  genes. The  majority of  such
genes are  common to all plants, and  a large fraction are common
to all  higher eukaryotes. Thus, much of  the work on Arabidopsis
will  be  directly  applicable   to  these  other  systems,  and
Arabidopsis  will  be the  system  of choice  for answering  many
questions on  gene function. In  addition, syntenic relationships
are  already  being  established   between  the  chromosomes  of
Arabidopsis and a variety  of crop species. Exploitation of these
relationships    will     dramatically    facilitate    molecular
identification of genes associated with specific desirable traits
in  crops. The  perceived viability  of this approach  is clearly
evidenced by the significant  investment of the private sector in
Arabidopsis/crop comparative genomics.

On  the biochemical  and cell  biological side,  proteomics tools
will  enable rapid  identification  of proteins  from very  small
samples.   This  will   engender  a  resurgence   in  biochemical
approaches   to   biological   questions.   Small-scale   protein
purification and determination of  the nature of the protein will
be  a  routine  method  of  gene  identification.  Obtaining  and
examining the knockouts of  the identified genes will immediately
lead   to  further   characterization  of   biological  function.
Similarly, partners  of proteins, or other  components of protein
complexes will be more easily identified and analyzed.

On the  genetic side, isolation of  genes and understanding their
molecular/biochemical  function will  no longer be  a bottleneck.
For example,  allowing the immediate ability  to compare sequence
similarities between members of  gene families. This will lead to
a renewed focus on  genetic screens - "rational genetics" - aimed
at understanding  gene function at a  tissue or organismal level.
Researchers  will  be  able  to afford  to  invest  more time  on
relatively complex  screens, including  those that might  yield a
lot of "false hits".  They will be able to afford to discard many
of the  mutants coming from these screens  because of the ease of
isolation and analysis. Genetic screens are still one of the most
effective  tools to identify  gene function,  even in the  age of
cDNA arrays, and are  unlikely to be superseded soon by in silico
analyses.

In  addition to  analysis  of small  sets of  genes  or proteins,
genome-wide   analysis  will   be  enabled.  For   example,  such
approaches have already led  to identification of new, previously
undetected  regulatory   sequences  in  yeast.   The  ability  to
simultaneously study  regulation of whole sets  of genes, or even
of  all genes,  will  enable unprecedented  insight into  complex
biological  processes.  If  properly  implemented, it  should  be
possible to  assemble a  database of expression  profiles of each
condition, as  it is determined. Other  researchers could draw on
and add to this database as they perform their own analysis. This
should  form the basis  of a  comprehensive map of  regulation of
genes  during  development   and  in  response  to  environmental
conditions.

In the  long term, such  a database could be  integrated with the
growing body  of biological  information on gene  function, plant
form and plant biochemistry.  The eventual goal would be assembly
of a virtual plant - click on a leaf at three days of age and get 
a list of all  genes  up-regulated in a variety  of physiological
conditions; click on a root and watch it grow with a dynamic list
of  changes at  the  molecular level  accessible. Thus,  the data
would  be accessible  to  all researchers  in an  easily utilized
form.

The development and application  of genome sequences and enabling
technologies will  lead to the removal  of a series of roadblocks
to  progress, putting the  answers to  all of these  questions in
reach. For example,  genomic technology will enable the discovery
of:

 Novel  plant  functions  previously  obscure  to   conventional
genetic  and  biochemical analysis

 Novel  signaling molecules,  including peptide and  other small
molecules   responsible  for  intracellular,   intercellular  and
interorganismal interactions

 Interactions among and between metabolic pathways

 Integrative approaches  to  complex cellular  functions such as
cell growth,  division and morphogenesis by  parallel analysis of
regulatory networks in many different areas (e.g., metabolism and
hormone signaling)

The  whole  range  of   plant  developmental  processes  will  be
understood  at  a   molecular  level,  enabling  manipulation  of
specific development processes  including the regulation of plant
size,  the time  to  flowering, the  mechanisms controlling  seed
dormancy  and  embryogenesis.  Understanding  of  the  mechanisms
regulating plant development using genomic technology will enable
rational  alteration  of  this  process in  agronomically  useful
directions by allowing:

 The identification of candidate genes underlying traits

 Gene prospecting (looking for novel variants)

 Engineering novel alleles/traits

 Rapid characterization and managing germplasm resources

The  ability to  study  gene expression  and genetic  function in
parallel for  multiple genes,  networks, and their  products will
revolutionize   mechanistic  approaches   to   plant  physiology.
Understanding the plant  genome structure will enable mechanistic
dissection  of  chromosomal biology,  including  the assembly  of
complete,   interacting  pathways   for  biosynthesis   of  novel
compounds,  and will  allow whole  genome analysis  of epigenetic
mechanisms  and  their relationship  to  genome organization  and
combinatorial  approaches  to  genetic  analysis  via  functional
libraries.

Rapid   methods   for  comprehensive   analysis  of   coordinated
regulation of gene expression  will enable new means of discovery
of gene function through  rapid analysis of mutants, as moving to
a gene will no longer be a bottleneck. Moreover, these tools will
allow testing  of models  of functions of single  genes, and even
construction and  reintroduction of novel  assemblies of multiple
genes.



V. APPLICATION OF THE INTELLECTUAL ADVANCES: POTENTIAL BENEFIT TO
APPLIED SCIENCE

A. Molecular  Analysis of Traits:  Molecular genetics has to this
point been  dominated by the identification  of single genes that
control  phenotypes of  interest.  However, this  approach is  of
limited value  in understanding  the molecular basis  for complex
phenotypes that  are complicated integrals of  the action of many
genes.  For instance,  yield, although exceedingly  important, is
relatively undefined at  the biochemical and physiological level.
This lack of definition stems not only from the complexity of the
phenotype,  but   also  from  the  limited   number  of  specific
biochemical or physiological measurements that can be made.

The identification  of every  gene in a  particular plant species
gives  the  possibility to  analyze  expression of  each gene  in
particular varieties or genotypes, in different environments, and
in   response   to   various   stresses.  In   addition,   modern
chromatographic methods,  coupled with on-line  detection by mass
spectrometry, are allowing the resolution of increasingly complex
mixtures of  small molecules  and proteins. As a  result of these
parallel developments, the assignment of surrogate end-points for
detecting complex phenotypes will become increasingly commonplace
and facile.

Understanding patterns  of gene regulation will  directly lead to
the ability  to express genes at  appropriate places and times in
development  or in  response  to specific  extra-organismal cues.
This knowledge will be applicable to genes engineered into plants
from any source, including those outside the plant kingdom.

The result of understanding  how complex properties are regulated
will  be  an ability  to  breed  crops that  are improvements  of
current varieties, as well as new crops that make altered amounts
or  types of  certain  components of  that crop's  output  (e.g.,
starch, oil, protein). Moreover, the ability to precisely control
gene expression and redirect  metabolic output will make possible
the  production  of novel  materials  in  plants at  economically
attractive levels.

B. Molecular  Breeding: As the resolution  of genetic maps in the
major crops  increases, and  as the molecular  basis for specific
traits or  physiological responses becomes  better elucidated, it
will  be  increasingly  possible  to associate  candidate  genes,
discovered  in model  species,  with corresponding  loci in  crop
plants. Appropriate relational databases will make it possible to
freely associate  across genomes  with respect to  gene sequence,
putative function, or genetic  map position. Once such tools have
been implemented,  the distinction  between quantitative genetics
(breeding) and  molecular genetics will  become blurred. Breeders
will  routinely  use  computer  models  to  formulate  predictive
hypotheses to  create phenotypes of interest  from complex allele
combinations,  and then  construct those combinations  by scoring
large populations for very large numbers of genetic markers.

The vast resource comprising breeding knowledge gathered over the
last several  decades will become directly  linked to basic plant
biology, and  enhance the  ability to elucidate  gene function in
model organisms. For instance,  traits that are poorly defined at
the biochemical level but well established as a visible phenotype
can  be  associated  by  high  resolution mapping  with candidate 
genes. Orthologous genes in a model species, such as  Arabidopsis 
or  rice,  may not have  a  known association with a quantitative 
trait like that seen in the crop, but might  have been implicated 
in  a  particular  pathway  or  signaling  chain  by  genetic  or 
biochemical experiments. This kind  of  cross-genome  referencing 
will lead  to  a  convergence  of  economically relevant breeding  
information  with  basic  molecular  genetic   information.   The  
specific phenotypes  of  commercial interest that we expect to be 
dramatically  improved   by   these  advances  include  both  the  
improvement   of   factors  that  traditionally  limit  agronomic  
performance (input traits) and the alteration  of  the amount and  
kinds  of  materials that crops produce (output traits). Examples 
include:

 Abiotic stress tolerance (cold, drought, salt)

 Biotic stress  tolerance (fungal, bacterial, viral, chewing and
sucking insect feeding)

 Nutrient use efficiency (N,P,K)

 Manipulation of plant architecture and development (size, organ
shape,   number,  and   position,  timing  of   development,  and
senescence)

  Metabolite partitioning  (redirecting   of  carbon flow  among
existing pathways, or shunting into new pathways)



C. Rational Plant Improvement:  The implications of genomics with
respect to  food, feed and fiber  production can be envisioned on
many  fronts.  At the  most  fundamental level,  the advances  in
genomics will greatly accelerate the acquisition of knowledge and
that, in turn, will directly impact many aspects of the processes
associated with  plant improvement. Knowledge of  the function of
all plant  genes, in conjunction with  the further development of
tools for  modifying and interrogating genomes,  will lead to the
development of  a genuine  genetic engineering paradigm  in which
rational  changes   can  be  designed  and   modeled  from  first
principles.



APPENDIX I: ROSTER OF WORKSHOP PARTICPANTS

     Roger N. Beachy, Ph.D.
     Donald Danforth Plant Science Center
     7425 Forsythe Blvd.
     Box 1098
     St. Louis, Missouri
     Email: rnbeachy@danforthcenter.org
     Tel: (314) 935-9782
     FAX: (314) 935-8605

     Joseph R. Ecker, Ph.D.
     University of Pennsylvania
     Department of Biology
     415 S. University Ave
     Philadelphia, PA 19104-6018
     Email: jecker@atgenome.bio.upenn.edu
     Tel: (215)898-9384
     FAX: (215)898-8780

     Charles S. Gasser, Ph.D.
     University of California, Davis
     Molecular and Cellular Biology
     1 Shields Ave.
     Davis, CA 95616
     Email: csgasser@ucdavis.edu
     Tel: (530)752-1013
     FAX: (530)752-3085

     Steve A. Kay, Ph.D.
     The Scripps Research Institute
     Department of Cell Biology
     10550 North Torrey Pines Rd.
     La Jolla, CA 92037
     Email: stevek@scripps.edu
     Tel: (619)784-2360
     FAX: (619)784-2368

     Kenneth Keegstra, Ph.D.
     MSU-DOE Plant Research Laboratory
     Michigan State University
     East Lansing, MI 48824
     Email: keegstra@pilot.msu.edu
     Tel: (517)353-2270
     FAX: (517)353-9168

     Rob Martienssen, Ph.D.
     Cold Spring Harbor Laboratory
     1 Bungtown Road
     Cold Spring Harbor NY 11724
     Email: martiens@cshl.org
     Tel: (516)367-8322
     FAX: (516)367-8369

     Susan R. McCouch, Ph.D.
     Cornell University
     Department of Plant Breeding
     418 Bradfield Hall
     Ithaca, NY 14853
     Email: srm4@cornell.edu
     Tel: (607)255-0420
     FAX: (607)255-6683

     Elliot Meyerowitz, Ph.D.
     California Institute of Technology
     Division of Biology 156-29
     1200 East California Boulevard
     Pasadena, California 91125, USA
     email: meyerow@cco.caltech.edu
     Tel: (626)395-6889
     FAX: (626)449-0756

     Chris Somerville, Ph.D.
     Carnegie Institution of Washington
     Stanford University
     260 Panama Street
     Stanford, CA 94305
     email: crs@andrew.stanford.edu
     Tel: (650)325-1521, ext 203
     FAX: (650)325-6857

     Eric Ward, Ph.D.
     Novartis Agribusiness Biotech Research, Inc.
     3054 Cornwallis Road
     Research Triangle Park, NC 27709-2257
     Email: eric.ward@nabri.Novartis.com


     Susan Wessler, Ph.D.
     University of Georgia
     Dept. of Genetics
     Life Sciences Bldg.
     Athens, GA 30602
     Email: sue@dogwood.botany.uga.edu
     Tel: (706)542-1870
     FAX: (706)542-3910



Observers:

     David Meinke, Ph.D.
     BIO/DBI
     National Science Foundation
     NSF Plant Genome Research Program
     4201 Wilson Boulevard
     Arlington, VA 22230
     Email: dmeinke@nsf.gov
     Tel: (703)306-1470
     FAX: (703)306-0356

     Paul Gilna, Ph.D.
     BIO/DBI
     National Science Foundation
     4201 Wilson Boulevard
     Arlington, Virginia 22230
     Email: pgilna@nsf.gov
     Tel: (703)306-1469
     FAX: (703)306-0356

     Roger Hangarter, Ph.D.
     National Science Foundation
     BIO/IBN
     4201 Wilson Boulevard
     Arlington, Virginia 22230
     Email: rhangart@nsf.gov
     Tel: (703)306-1422
     FAX: (703)306-0349

     Judith A. Verbeke. Ph.D.
     National Science Foundation
     BIO/IBN
     4201 Wilson Boulevard
     Arlington, Virginia 22230
     Email: jverbeke@nsf.gov
     Tel: (703)306-1422
     FAX: (703)306-0349



APPENDIX II: Workshop Agenda

"New Directions in Plant Biological Research"

Carnegie Institution of Washington

Department of Plant Biology

Stanford, California

November 23-24, 1998

Host

Chris Somerville, Carnegie-Stanford

Chair

Joe Ecker, University of Pennsylvania

	Monday, November 23

9:00 a.m. Welcome-Meeting Logistics-Chris Somerville

9:15 a.m. Introduction-Charge of the Workshop-Joe Ecker

9:30 a.m. Begin Participant Perspectives: "The Future of Plant Research"

9:30 a.m. Elliot Meyerowitz

10:00 a.m. Chris Somerville

10:30 a.m. Break

10:45 a.m. Steve Kay

11:15 a.m. Chuck Gasser

11:45 a.m. Sue Wessler

12:15 p.m. Lunch

1:30 p.m. Rob Martienssen

2:00 p.m. Susan McCouch

2:30 p.m. Roger Beachey 

3:00 p.m. Ken Keegstra

3:30 p.m. Eric Ward

4:00 p.m. Break

4:15 p.m. David Meinke

4:45 p.m. Paul Gilna

5:15 p.m. General discussion of issues/questions raised: All participants

7:15 p.m. Dinner

	Tuesday, November 24

9:00 a.m. General Discussion of the Direction of Future of Plant Research: Entire group

12:00 p.m. Lunch

1:30 p.m. Formation  of  break out groups  (3 persons/group)  responsible  for  further  
	  development of a specific recommendations (1 page each)

3:00 - 3:15 Break

3:15 p.m. Assembly of entire group for discussion of break-out group reports

5:15 p.m. Wrap-up session- writing assignments

5:30 p.m. Workshop adjourns

6:00 p.m. Reception/Dinner