WS1 Applying
Modern Genomic Tools to the Management and Characterization
of Plant Genetic Resources
A. Talks
at the workshop (more details below)
• Population genetic challenges
and the potential of modern genomics technologies for the
management
and characterization
of plant genetic resources (Dr. Loren H. Rieseberg)
• The management and characterization of plant genetic
resources in the age of genomics – chances
and challenges [Provisional title] (Dr. Christopher
M.
Richards)
• Towards a rational, secure and effective long-term
conservation strategy (Dr. Johannes M.M. Engels)
• DNA barcoding: An oversimplified solution to a
complex problem (Dr. David M. Spooner)
• Challenges of applying molecular techniques to
PGR management – a
Canadian perspective (Dr. Ken Richards)
• Prospects and challenges of Illumina and SOLiD
sequencing for PGR characterization [Provisional
title] (Dr. Nolan
Kane)
• Prospects and challenges of 454 sequencing for
PGR characterization [Provisional title] (Dr. Katrina
Dlugosch)
• Presentations by representatives of the private
sector
B. Workshop outline
As
new sequencing technologies become rapidly available,
the price for sequencing is predicted
to drop continuously. The human genomics community
in particular is pressing
hard for cheaper and faster sequencing
methods as they promise new and improved treatments
in the area
of medicine.
The great potential of these technologies
for the field of plant genetic resource management
have so
far remained
largely untapped. However, sequencing
large areas of the genome in order to obtain
information about
inter-and
intra-specific variability is about
to become a reality due to the ever decreasing cost
of sequencing
technologies.
Soon, germplasm will become distinguishable
on the level of varieties and land races with
standardized methods
that are fast, reliable and affordable.
Such methods
could include the use of massively parallel
sequencing to decipher the genetic code of whole
plastids and/or
chip based approaches that could survey
SNP variation at many nuclear loci for many individuals.
This
will allow researchers to tackle problems
such as landrace
genotyping, species level identification
of wild relatives in a genebank setting, the
detection of
duplicate accessions,
greater efficiency of germplasm management
and a standardized molecular characterization
protocol between
different
genebanks across the globe.
The great opportunities for plant genetic
resource management that arrive
with these new technologies
need to be explored.
Challenges of already established
methods, such as plant DNA-barcoding, should
be addressed and
limitations
of
such techniques should be discussed
in the context of plant genetic resource
management.
The diversity
of
crops regarding their reproductive
biology, agricultural management
and genetic make-up, poses a particular
challenge that needs special consideration
for the development
of global
standards. Furthermore, the generation
of tools, such as a centralized
database where standardized
methods
can be documented and characterization
results can be submitted,
ought to be a topic of discussion.
At this
workshop, we aim to discuss how
best to make use of these
emerging possibilities and how
to actively influence the development of accompanying
bioinformatics methods as to adapt
them
to suit the plant genetic
resource community’s needs. The debate about the usefulness
of many of these methods needs to be moved from the
informal setting of ‘institutional hallways’ to
an inter-institutional level in
order to work on a common strategy
to capitalize on these rapidly
emerging
opportunities
for the management of plant genetic
resources.
The workshop will consist of a series
of lectures, ranging from technical
and theoretical
viewpoints
to more applied
aspects. We are also planning
several ‘breakout
sessions’, in which the participants
will be able to get first-hand experience
with some of
the
new methods
and analysis techniques under the
guidance of experts in the field
and representatives of the private
sector. Furthermore a mediated discussion
forum
is envisioned,
where scientists can freely exchange
their ideas on this topic and debate
controversial issues.
C. Talk abstracts and details
(more soon)
Population genetic
challenges
and the potential of
modern genomics technologies
for the management and characterization
of plant genetic resources
- Loren Rieseberg
The development of molecular
diagnostic tools
for the management and characterization
of crop germplasm
such
as landraces, breeder’s varieties,
as well as populations of wild relatives
is useful for several
reasons. An appropriate
method could provide a standardized
means for identifying and categorizing
germplasm across species and across
institutions. It could also be used
to reduce unwanted
duplication in
germplasm repositories, assess genetic
relationships, develop a more stable
classification of domesticated
and wild populations, and detect
contaminated or admixed
samples.
Furthermore, if biologically relevant
molecular variation were assayed,
it might be feasible to
predict the
likely value of germplasm for breeding
and crop improvement. A variety
of different approaches are
currently being
employed to characterize germplasm
in different crops, ranging from
allozymes to microsatellites
to single
nucleotide polymorphisms (SNPs)
in nuclear loci. Also, DNA-barcoding
approaches, including whole plastome
sequencing,
are now being considered for analyses
of clonal and selfing
crops.
I will explore the strengths and
weaknesses of the primary
methods currently being employed
(or that have recently become technically
feasible) for germplasm characterization.
I will also discuss the population
genetic challenges
associated with the development
of a widely applicable, stable,
and cost-effective strategy for
analyzing
crops that vary in mating system,
ploidy level, and means
of propagation. When assessing different
approaches, I will
do so in the light of rapid advances
in sequencing and SNP genotyping
technologies that are providing
new technological
solutions to old problems.
Towards a rational, secure
and effective long-term
conservation strategy
- Johannes M.M. Engels (presenter) and
Robbert van Treuren
A rough analysis
of the history
of how most of the
existing
germplasm collections
have been established,
and comparing
the outcome of
this analysis with what
one would expect
that such collections
should
contain in terms
of genetic diversity
for
a given
genepool, allows
the conclusion
that the content
of existing ex
situ collections leaves
room for
improvement, especially
from a long-term
conservation
perspective. Many of these collections
have grown
out
of breeders’ working collections
that consisted of a selected set
of accessions and/or have been
established by countries and/or
national or institutional genebanks
with the aim of providing genetic
diversity, in
particular specific traits, to users
(i.e. predominantly plant
breeders) of those collections in
a given country. This approach
has resulted in considerable redundancy
and in genetic diversity gaps, both
from a genetic diversity as
well as from a geographic perspective.
A long-term global
or regional ex
situ germplasm
collection
for a
given crop
genepool should
contain an adequate
representation
of the total
existing genetic
diversity in that
genepool
(both, in situ
as well as ex
situ)
in
as few as possible
samples (i.e.
accessions) in
order
to be rational.
This principle
begs the question
if
a
long-term
conservation collection
should aim at
storing genotypes
or
genes/alleles.
Modern genomic
and information
management
tools allow
now more efficient
and effective
conservation
approaches
and methodologies
to be
applied
and this results among
others in:
o better monitoring
of routine
conservation activities
(e.g.
collecting and regeneration);
o attempts
to work
towards
more
adequately
composed
collections
for
long-term
conservation,
including
the
identification
of collection
gaps,
unwanted
duplicates
and
genetic
redundancy
(e.g.
proposed
approach
to establish
a
global
strategic
base
collection
for
cacao);
o better
coordinated
and
more
complementary
conservation
efforts
between
in situ
(natural
habitats
and
on-farm)
and
ex situ
conservation
programmes;
o more
efficient
collaboration
efforts
between
genebanks,
countries
as well
as between
regions
(e.g.
rationalizing
Allium,
predominantly
garlic
collections;
establishment
and
operation
of
a virtual
European
genebank
system,
i.e.
AEGIS;
rationalisation
efforts
of
the
Global
Crop
Diversity
Trust);
o More
rational
and
cost
efficient
global
or regional
conservation
efforts;
o Better
services
to users
(core
collection
and
core
selection
formation).
DNA
barcoding: An oversimplified
solution to a
complex problem - David
M. Spooner
DNA
barcoding (“barcoding”) has been proposed
as a rapid and practical molecular tool to identify
species via diagnostic variation in short orthologous
DNA sequences
from one or a few universal genomic regions. It
seeks to overcome the “taxonomic impediment” caused
by a greater need for species identifications than
the supply of taxonomic specialists.
A number of barcoding regions have been proposed
for plants, including the
internal non-transcribed spacer of nuclear ribosomal
DNA (ITS),
and the plastid markers trnH-psbA intergenic spacer,
matK, and other
plastid regions, with the first three being
the most variable. This study tests the utility
of barcoding
with these three regions in a complicated plant
group, Solanum sect. Petota;
wild potatoes. These DNA regions
fail to provide species-specific markers in sect.
Petota because
ITS has too much intraspecific variation and
the plastid markers lack sufficient polymorphism.
Wild potatoes
are not alone in failing to work with barcoding
regions. Addressing
the taxonomic impediment will require a
comprehensive and integrative program of research
and training using
a variety of data sets appropriate to different
species groups. Barcoding,
in contrast, is impeded by common
complicating biological phenomena, is a retroactive
procedure that
relies on well defined species to function, is
based solely on DNA
sequences that are often inappropriate at the species
level, has been poorly tested with
replicate samples, and ignores substantial practical
and theoretical problems in defining
species. |
