ACPFG Annual Report

ACPFG Annual Report

Contents
Chairman’s Report 1
CEO’s Report 2
Board and EMG 4
Structure 8
Nodes 9
ACPFG II 10
Collaborations 11
Visitors 12
IP and Patents 13
Symposium: Genomics of Drought 15
Research 16
Drought 17
Salinity 19
Nutrients 22
Boron 24
Cold and Frost 26
Technology Platforms 28
Transcriptomics 32
Bioinformatics 34
Positional Cloning 36
Education 37
Student List 38
Communication 41
Publications 42
Summary of Contributions 44
Contacts and Acronyms 45
ACPFG Mission Statement
To create and commercialise cutting edge knowledge to significantly
enhance grain quality and yield in our challenging environment.
Australian Centre for Plant Functional Genomics (ACPFG) uses
functional genomics to improve the resistance of wheat and barley to
hostile environmental conditions such as drought, salinity, frost and
mineral deficiencies or toxicities. These stresses, known as abiotic
stresses, are a major cause of cereal crop yield and quality loss
throughout the world.

Chairman’s Report
On behalf of my fellow Directors, I am pleased to present
the fifth annual report of the Australian Centre for Plant
Functional Genomics Pty Ltd (ACPFG).
There were two very important activities in 2007 for ACPFG.
The first of these was the development of a successful
re‐funding proposal to create ACPFG II. The second was
the development of a proposal to admit a new Shareholder,
UniSA. Both of these matters involved intense effort from
management and Directors. The refunding plan and
the proposal to admit UniSA were put to Shareholders
and Stakeholders for their consideration at the Annual
General Meeting in May 2007 and were followed up at a
subsequent Shareholders Meeting in October 2007. I am
pleased that Shareholders and Stakeholders accepted the
Board’s recommendations on both matters. Discussions
and negotiations occurred throughout 2007 to ensure
suitable agreements were in place with all Shareholders and
Stakeholders to fund the ACPFG into its second phase
(ACPFG II) and to allow the admittance of UniSA. UniSA will
deliver additional expertise in plant bioinformatics.
Other significant events were:
»» As with previous years, ACPFG hosted many visits
from politicians, international visitors, school students,
community groups and other interested parties.
»» We continued and extended our existing close links with
the Australian grain and farming community through
regular attendance at industry briefings, events and field
days around Australia.
»» We licensed intellectual property associated with frost
tolerance to Green Blue Print International.
»» A license was negotiated for ACPFG to use technology
associated with nitrogen use efficiency.
»» ACPFG’s Vector magazine continued to attract interest from
Australia and overseas as a prime source of information on
plant genomics.
»» ACPFG met with and briefed politicians, government
bureaucrats and their advisers from around Australia
on matters of scientific interest in the area of plant
functional genomics, particularly as it applies to cereal
crop improvement.
»» Senior ACPFG management regularly travelled interstate
and overseas to attend conferences, present scientific
papers, represent the ACPFG, and to meet with current
industry and scientific partners, or potential scientific or
commercial partners.
»» ACPFG continued discussions and consultation with
Shareholders and Stakeholders, industry and other
potential participants on a national delivery pathway
for new technologies.
»» ACPFG scientific teams at all nodes have been
outstandingly successful in attracting grant funds for
work within the ACPFG.
On behalf of my fellow Directors, I thank our Shareholders
and Stakeholders for their support of ACPFG’s activities
and for their support in ensuring our work will continue
into ACPFG II. I also thank our scientists, staff, national and
international visitors and students who have worked within
the nodes of the ACPFG around Australia, on the campuses
of the University of Adelaide, the University of Melbourne,
La Trobe University and the University of Queensland.
Their dedication and efforts in maintaining what is generally
acknowledged as one of the world’s most desirable
environments to undertake grain abiotic stress research,
continues to be the invaluable cornerstone of the ACPFG’s
success so far. As a team, we have consolidated the name
and profile of the ACPFG in global scientific and commercial
markets for environmental stress tolerance improvement in
cereal crops. Finally, I sincerely thank my fellow Directors for
their efforts, dedication and continued wise counsel.
»»
»»
We organised our fourth successful annual international
conference in Adelaide, South Australia, this time on
drought tolerance; the conference was again a sell out,
with many attendees from interstate and around the globe.
ACPFG made representations in support of the removal of
the moratoria on the commercial production of GM crops
in various states in Australia. Late in 2007, the New South
Wales and Victorian Governments lifted their moratoria on
the commercial production of GM canola in those states.
Nicholas Begakis AM
Chairman
2007 ACPFG ANNUAL REPORT
1

CEO’s Report
This report marks a major phase transition for our centre.
ACPFG was originally established with a very broad brief.
While the focus was to develop and deliver genomics
technologies for the Australian grains industry, Stakeholders
had diverse expectations that have, not surprisingly, changed
over the life of ACPFG. Our strong international and domestic
collaborations and high quality science have reduced our
original commercial drive, reflecting the path of cereal
improvement in Australia, which remains largely in the public
sector. While these shifts have translated into changes in
the strategic plan for ACPFG, the scientific premises of the
organisation have remained constant. When ACPFG was
established plant genomics was seen as providing a new set of
technologies, which offered opportunities to tackle previously
intractable problems. The target identified – abiotic stress
tolerance – was ambitious given the available resources, but
allowed the development of capabilities and was clearly of
prime importance to cropping in Australia. The severe climatic
conditions in Australia over the past few years and political
awareness of climate change have confirmed the importance
of tackling abiotic stresses.
Over the past five years we have been establishing the
capabilities, resources and linkages needed to provide a
plant genomics platform of the highest international standard.
There were several assumptions made in developing the
strategy. Firstly, we assumed we could apply the technologies
developed largely for humans and model organisms to species
with highly complex genetic and genomic makeups. For
example, is it practical to apply the techniques of transcript,
protein and metabolite profiling to species where little of the
genome is sequenced? Our second assumption was that we
could exploit the extensive genetic information and genetic
populations for wheat and barley to target individual genes.
By and large both assumptions have proved valid. Technology
platforms have been established and used to tackle a wide
range of traits. Positional cloning, albeit combined with
clever bioinformatics, transcript profiling and yeast screening,
resulted in the isolation of the major boron tolerance locus
from barley. Similarly, by combining forward and reverse
genetics, the genes involved in aluminium tolerance from
rye and the major genes involved in sodium exclusion from
durum wheat have been isolated.
2 2007 ACPFG ANNUAL REPORT

ut we must quickly position ourselves to capitalize on these
developments. Perhaps the biggest challenge will be the
development of pathways for delivery of outputs to growers.
In particular, the issues surrounding GM delivery will need
to be tackled. ACPFG hopes to conduct its first field trials of
GM wheat and barley in 2008, and trials are likely to expand
in subsequent years. New phenomics and metabolomics
capabilities will present huge opportunities, but will also
present challenges related to incorporating the technologies
into ACPFG programs. Our new activities at UniSA in
phenomics and bioinformatics will be important in optimising
use of the new capabilities.
The past five years have also highlighted areas where there
were significant bottlenecks in advancing genomics research.
The most significant has been in phenotypic evaluation
of plant collections and populations, through which
natural variation in attributes such as drought tolerance
could be identified, characterized and exploited in cereal
improvement programs. Initially ACPFG proposed to develop
linkages with high-throughput phenotyping capabilities
overseas but this proved too costly. Therefore, we developed
collaborations with breeding programs in Australia and
overseas to gain access to field phenotyping. However, the
most significant event in tackling the phenotyping bottleneck
has been the successful proposal developed under the
Australian National Collaborative Research Infrastructure
Strategy (NCRIS) by Mark Tester and Geoff Fincher, in
collaboration with colleagues at CSIRO and the ANU,
to establish the $40 million Australian Plant Phenomics
Facility. The new facility is planned for completion in mid
2009 and will not only provide a fully automatic system for
analysing a wide range of plant characteristics under normal
and stressed growth conditions, but will also provide a
platform for the development of next generation phenotyping
technologies. This facility is expected to revolutionise the
types of experiments we, and others, can undertake.
The ACPFG metabolomics group at Melbourne University, led
by Tony Bacic, have been successful in obtaining support from
NCRIS to greatly expand Australia’s metabolomics capability.
The new facility, Metabolomics Australia, will help address the
high demand for metabolite profiling from ACPFG and other
groups. Importantly, the new funding highlights the broad
recognition in Australia and overseas of the power of these
techniques in analysing developmental and stress responses in
biological systems.
Research in the next phase of ACPFG will focus on drought
and salinity tolerance. Excellent recent progress in the genetics
of these two stresses will be critical to our immediate research
plans. Mark Tester’s salinity group has successfully used cell
and tissue specific expression to enhance tolerance, while
we have shown enhanced drought tolerance by modulating
expression of regulatory genes. These advances provide clear
paths for developing tolerance to these two key stresses.
The education program in ACPFG is also undergoing
transition. Our main emphasis over the next few years will
be in the training programs for postgraduate students and
post-doctoral staff, although we are maintaining the highly
successful school programs developed in collaboration with
the Molecular Plant Breeding CRC.
In the last five years we have built the research and
education base for a strong functional genomics program
in wheat and barley. In the next phase, we will continue
to build on these established strengths while tackling the
challenge of producing tangible outcomes for the farming
community. Finally, we need to look beyond ACPFG II, by
identifying opportunities to capitalise on our expertise and
evaluating opportunities for expanded research activities and
collaborations. We must ensure that we remain in a strong
position to take advantage of the inevitably rapid advances in
functional genomics and related technologies.
Peter Langridge
CEO
While the challenges of the first five years of ACPFG’s
operation were substantial, new challenges will undoubtedly
present themselves in the next phase. The technologies, of
course, continue to advance rapidly and there is a real chance
that the full genome sequences of barley, and possibly wheat,
will become available in the next five years. This would
greatly accelerate our map based cloning work and would
offer new possibilities in proteomics and network analysis,
2007 ACPFG ANNUAL REPORT
3

ACPFG Board
Mr Simon Drilling, Professor Geoff Fincher (Deputy CEO),
Mr Nicholas Begakis AM (Chair), Professor Vicki Sara, Professor Peter Langridge (CEO),
Ms Maggie Dowling and Mr Michael Gilbert (Company secretary).
Executive Management Group
Professor Kaye Basford, Mr Michael Gilbert, Professor Mark Tester,
Professor Tony Bacic, Professor Geoff Fincher (Chair).
Absent: Professor Peter Langridge and Professor German Spangenberg.
4 2007 ACPFG ANNUAL REPORT

Tony Bacic
Kaye Basford
Nicholas Begakis
Maggie Dowling
Professor Tony Bacic leads the
ACPFG team at the University of
Melbourne and is a member of
the EMG. He holds a Personal
Chair in the School of Botany.
He is Director of the Plant
Cell Biology Research Centre,
Platform Convenor of the
NCRIS-funded Metabolomics
Australia and Interim Director
of the Bio21 Molecular Science
and Biotechnology Institute for
2008. He is on Management
Committees of Bioplatforms
Australia, the Australian
Proteomics Computational
Facility, the Integrative
Neuroscience Facility Platform
and the Maud Gibson Trust
of the Royal Botanic Gardens
in Cranbourne. He is a
Monitoring Editor for Plant
Physiology, an Associate Editor
for Glycobiology and is on the
Editorial Boards of Planta and
Plant and Cell Physiology. In
2007 he was on the Scientific
Committee and a speaker for
the XIth Cell Wall Meeting in
Denmark. He was also on the
Organising Committee for the
XIXth International Symposium
on Glycoconjugates held
in Cairns, Australia where
he was a Keynote Speaker.
His research is focused on
the structure, function and
biosynthesis of plant cell walls
and their biotechnological
application as well as the
application of functional
genomics tools to abiotic stress
and productivity in cereals.
Professor Kaye Basford is a
member of the EMG. She leads
the ACPFG bioinformatics
program and oversees the
Queensland node. Kaye is
Head of the University of
Queensland’s School of Land,
Crop and Food Sciences
and Professor of Biometry.
Her teaching and research
is at the forefront of statistics
and quantitative genetics
through the development
and dissemination of
methodology for the analysis
and interpretation of genotypic
adaptation in large-scale
plant breeding trials. She
has published widely in
this area, including two
monographs. Kaye is a Fellow
of the Australian Academy
of Technological Sciences
and Engineering (ATSE).
She is currently Honorary
Secretary of the Queensland
Division of ATSE and also
the immediate Past President
of the Statistical Society of
Australia Inc. Her awards
include the 1998 Medal of
Agriculture from the Australian
Institute of Agricultural
Science and Technology
and a 1986 Fulbright
Postdoctoral Fellowship
to Cornell University.
Chair of the Board, Nick
Begakis AM, has an electronic
engineering degree and more
than 30 years experience in
senior management roles in
manufacturing industries; as an
entrepreneur creating his own
enterprises; in venture capital,
investment and merchant
banking; in corporate recovery
roles and as an independent,
non-executive Chairman and
Company Director. Nick is
involved in creating intellectual
property and capturing value
as Chairman of ACPFG. He has
also established enterprises and
encouraged entrepreneurial
activities as Chairman of
Enterprise Development Inc;
prudently invested funds and
created wealth as a Director
of Statewide Superannuation
Trust (SA); encouraged
exports as Chairman of the
Council for International
Trade and Commerce SA Inc;
and represented business
and industry interests at the
state and national level as
a Member of the Premier’s
Food Council (SA). Nick is a
Director of Business SA and of
the Canberra-based Australian
Chamber of Commerce
and Industry. He supports
the non-profit sector as a
Member of Flinders University
Council and as Chairman of
the Women’s and Children’s
Hospital Foundation (SA). Nick
co-owns, and is Chairman of
Bellis Fruit Bars, an Australian
supermarket food brand with
interests in China that exports
to Europe, the USA and NZ.
He is a Fellow and past Deputy
Chair (SA and NT) of the
Australian Institute of Company
Directors and a Member of
the Multicultural Forum (SA).
Maggie Dowling, ACPFG
Director, has more than
20 years experience in the
grains industry. She has
been a Manager at AusBulk
and ABB Grain, as well as
Director of Grains Industry
Development for the South
Australian Government.
Maggie has been on Advisory
Committees; nationally for
Molecular Plant Breeding, and
for the SA Government on
Genetically Modified Crops.
She has been on National
Steering Committees for the
implementation of intellectual
property royalty systems in
agriculture and GRDC’s Partners
in Grain project. She has also
been on the SA Premier’s
Science and Research Fund
Selection Panel. Maggie has
qualifications in business,
management and company
directorship, and has been
Chair or Director of several
grains-focused companies. She
is currently General Manager
at the CRC for Contamination
Assessment and Remediation
of the Environment.
2007 ACPFG ANNUAL REPORT
5

Simon Drilling
Geoff Fincher
Michael Gilbert
Peter Langridge
ACPFG Director Simon
Drilling is trained as a
Chartered Accountant and an
Investment Research Analyst
with Thornton Group. He has
previously been Director of
Kirribilli Wines, Director of
the Deloitte Touche Tohmatsu
Policy Board, member of
the Deloitte Consulting Asia
Pacific Africa Management
Committee and member
of the Deloitte Consulting
Worldwide Board. His
previous roles include Project
Director for BioInnovation SA,
CEO for Deloitte Consulting
Australasia and leader of
Deloitte Consulting Utility
Industry Group in Australasia.
Professor Geoff Fincher is
Deputy Chief Executive Officer
of ACPFG, where he chairs the
Executive Management Group
and takes specific responsibility
for new projects and initiatives.
Geoff’s research interests are
in the enzymology, molecular
biology, structural biology,
genetics and biochemistry of
plant cell wall metabolism.
Geoff is also Director of
University of Adelaide’s Waite
Campus and has been Director
of a GRDC-funded program
on the functional genomics of
growth and end-use quality
in cereals for seven years. He
is an editor for the Journal
of Cereal Science and the
BioEnergy Journal, and is a
long-serving member of the
editorial board of Planta. He
chairs the Scientific Advisory
Committee of Biomime, the
Swedish centre for wood
functional genomics. In 2007,
Geoff was a plenary speaker at
the annual Arabidopsis meeting
in Beijing and an invited speaker
at the Fungal and Plant Cell
Wall Meeting in France, the
International Triticeae Mapping
Initiative meeting in Israel, the
Royal Australian Chemical
Institute Cereal Chemistry
Division’s annual meeting
in Melbourne, the European
Plant Cell Wall meeting in
Copenhagen, and at the
University of Helsinki in Finland.
ACPFG General Manager,
Company Secretary and EMG
member Michael Gilbert is on
the Board of Ausbiotech and
is Chair of its Risk and Audit
Committee. In 2006, Michael
was also appointed to the
Federal Government’s Advisory
Council on Intellectual Property
(ACIP), which advises the
Federal Minister for Innovation,
Industry, Science and Research
on intellectual property matters
and the strategic administration
of IP Australia. Michael
graduated as a Mechanical
Engineer then worked in
research and development
for lens manufacturer
SOLA International both in
Australia and overseas. He
became General Manager of
a South Australian group of
manufacturing companies,
then began working for himself
in 1998 after completing
an MBA at the University
of Adelaide. His company,
Adelaide Consulting, included
clients such as Haigh’s
Chocolates and Laubman and
Pank as well as professional
firms seeking to restructure
underperforming businesses.
Michael worked increasingly
with the University sector and
was the project manager for
the start-up of ACPFG in 2002.
In 2003 Michael officially
joined ACPFG, where his
responsibilities include finance,
reporting and intellectual
property management as well
as board secretarial matters.
ACPFG’s CEO, Professor Peter
Langridge, is on the Advisory
Boards of the European
Union BioExploit Program,
the Australian Research
Council Centre for Integrative
Legume Research and the
National Science Foundation
Wheat Genomics Programs
in the USA. He is also on the
Research Advisory Committee
of the Consultative Group
on International Agricultural
Research’s Generation
Challenge Programme. He has
been a member of the Gene
Technology Technical Advisory
Committee of Australia’s
Office of the Gene Technology
Regulator since 2001. In 2007
Peter was appointed Chair of
the Biological Sciences Panel
for the Australian Research
Quality Framework. He is
currently a Director of LifePrint
Australia Pty Ltd, a plant
DNA diagnostic company,
and chairs the management
committee of the International
Triticeae Mapping Initiative
(ITMI). Peter is an Honorary
Fellow of the Scottish Crop
Research Institute and in
2007 was appointed Fellow of
Food Standards Australia and
New Zealand. Peter is often
approached by the media to
talk about scientific advances
for agricultural development. In
2007, he published 17 papers
in international journals and
gave several presentations,
notably at Clermond-Ferrand
in France, the University of
Regensburg in Germany,
the Scottish Crop Research
Institute and the John Innes
Centre in the UK. He was the
Keynote Speaker at the MapNet
Conference in New Zealand,
and an invited speaker at both
the ITMI workshop in Israel and
the Abiotic Stress workshop at
the Plant and Animal Genome
Conference in the USA. Peter
co-supervises 10 PhD students
and is on three journal editorial
boards: Theoretical and Applied
Genetics, Plant Methods and
International Journal of Plant
Genomics. His research has
focused on the development
and application of molecular
biology to crop improvement.
6 2007 ACPFG ANNUAL REPORT

Vicki Sara
German Spangenberg
Mark Tester
ACPFG Director, Professor
Vicki Sara, is Chancellor of
the University of Technology
Sydney. Vicki is Chair of the
Board of the Australian Stem
Cell Centre and a member
of the Advisory Board of the
Rio Tinto Foundation for a
Sustainable Minerals Industry.
She was Vice-Chair of the
OECD’s Global Science Forum
in 1999, a member of the
Advisory Board of the APEC
R&D Leaders’ Forum in 2002,
and Consul General for Sweden
in Sydney in 2006. She has
been Chair and CEO of the
Australian Research Council,
on the CSIRO board, member
of the Prime Minister’s Science
Engineering and Innovation
Council (PMSEIC), Dean of
Science at the Queensland
University of Technology (QUT)
and Director of the Cooperative
Research Centre for Diagnostic
Technologies. Before moving
into management Vicki held
various research positions
at the Karolinska Institute,
Stockholm, where she moved
with a UNESCO postdoctoral
fellowship. There she led the
Endocrine Pathology Research
Laboratory and received awards
for isolating a growth factor
responsible for regulating foetal
brain development. In Australia
she has been awarded the
Centenary Medal, an Honorary
Doctor of Science from both
the University of Southern
Queensland and the Victoria
University, and an Honorary
Doctor of the University from
Queensland University of
Technology. Vicki is a Fellow
of the Australian Academy of
Science and the Australian
Academy of Technological
Sciences and Engineering.
Professor German Spangenberg
is a member of the EMG. He
is Executive Director of the
Biosciences Research Division
in the Victorian Department of
Primary Industries and Adjunct
Professor with the School of
Botany at La Trobe University,
Melbourne. He is Director
of the Centre for Sustainable
Plant Production, Chair of
the Victorian Microarray
Technology Consortium,
Node Leader of the Victorian
Bioinformatics Consortium,
Director and Chief Scientific
Officer for Phytogene Pty.
Ltd., and Chief Scientist of the
Molecular Plant Breeding CRC.
In 2006 he was recipient of
the Australian Thinker of Year
Award and in 2007 he was
elected Fellow of the Australian
Academy of Technological
Sciences and Engineering, for
his inspiring and innovative
research in agricultural
biotechnology and as a
world leader in pasture plant
genomics and gene technology.
He received his PhD from
the University of Heidelberg
and Max-Planck-Institute of
Cell Biology in Ladenburg
b. Heidelberg, Germany. He
was a postdoctoral researcher,
then Associate Professor at
the Max-Planck-Institute of
Cell Biology and the Institute
of Plant Sciences at the Swiss
Federal Institute of Technology
(ETH) in Zürich, Switzerland.
Professor Mark Tester is a
member of the EMG. He
completed a PhD in biophysics
at the University of Cambridge
in 1988, where he was a
lecturer for 11 years, before
moving back to South Australia
as a Federation Fellow at the
University of Adelaide. Mark
oversees ACPFG’s salinity
tolerance research, using both
forward and reverse genetics
approaches. In 2007, this team
showed the value of cell-type
specific manipulations of
targeted genes for increasing
salinity tolerance in model
species. Transferring these
technologies to wheat and
barley started in 2007. Mark
co-supervises 12 PhD students
and is an enthusiastic science
communicator who is regularly
involved in ACPFG media
coverage. He is involved in
leading the development of
the Australian Plant Phenomics
Facility, being built near the
ACPFG headquarters on the
Waite Campus in late 2008.
In 2007, Mark published
10 papers in international
journals and gave several
presentations, notably at Oxford
and Cambridge Universities
and at Rothamsted Research
in the UK, and at POSTECH in
Korea. He was also a session
chair at the 14th International
Workshop on Plant Membrane
Biology, Valencia in June
and was a plenary speaker
at the International Congress
on Plant Genomics, Tenerife
in October. Mark is on six
journal editorial boards: Plant,
Cell and Environment; Plant
Signalling and Behaviour;
Functional Plant Biology;
Molecular Plant; Rice; and
the Journal of Integrative Plant
Biology. Currently he is cochair
of the Gordon Research
Conference on drought and
salinity, to be held in Montana
in September 2008, and is
on the Steering Committee
for both Interdrought III in
Shanghai in 2009 and the 15th
International Workshop for
Plant Membrane Biology, which
will be in Adelaide in 2010.
ACPFG has a small,
non-representational
Board that works
with the management
team to set the
strategic direction
of the company.
The Board relies on
the scientific advice
of the Executive
Management Group.
2007 ACPFG ANNUAL REPORT
7

ACPFG Structure
RESEARCH FOCUS GROUPS
Drought
Salt
Nutrients
Boron
Cold and Frost
BOARD
MANAGEMENT
EXECUTIVE
MANAGEMENT
GROUP
TECHNOLOGY
PLATFORMS
RESEARCH
SUPPORT
ALIGNED
PROGRAMS
Technology Platforms
Bioinformatics
Positional Cloning
Transformation Systems
Metabolomics
Transcriptomics
Proteomics
Antibody Production
In situ Analyses
Promoters Isolation
Mutant Populations
Genomic Resources
Research Support
Information Technology
Intellectual Property
Regulatory Compliance
Education
Communication
Commercialisation
Finance
Aligned Programs
Grain Quality
Nitrogen Use Efficiency
Barley Transgenesis
8 2007 ACPFG ANNUAL REPORT

ACPFG Nodes
NT
Qld
WA
SA
NSW
Vic
Tas
The University of Adelaide
The Waite Campus is Australia’s largest crop research centre
with extensive teaching and research activities as well as
various breeding programs. For the ACPFG, close links to
the Waite barley and wheat breeding programs have been
important in accessing key germplasm and providing delivery
mechanisms for research outcomes. In Adelaide, the ACPFG
has facilities for plant production and screening. Other
activities include the transformation of various cereals and
model plants, germplasm screening and evaluation, genetic
analysis, positional cloning, protein expression and structural
analysis, antibody production and the construction and
screening of large insert libraries.
The Adelaide node also houses all support capabilities
including communication and education, intellectual property
and commercialisation, business and financial management,
information technology and administration. These support
capabilities are accessed by various related research programs
within the Plant Genomics Centre.
The University of Queensland
The University of Queensland node has developed a highquality
bioinformatics capability for ACPFG and provides
bioinformatics support for research projects across the
organisation. ACPFG in Queensland is developing internal
biological databases and is working with national and
international partners to develop large-scale database
infrastructure. In the future, there will be an increasing
emphasis on integrating advanced bioinformatics strategies
with the abundant data being produced.
The University of Melbourne
The University of Melbourne node has access to current
functional genomics technologies through the Victorian Centre
for Plant Functional Genomics. These technologies include
proteomics, metabolomics, glycomics and bioinformatics
which are needed to support high throughput analysis.
ACPFG’s research team at the University of Melbourne is
using these technologies to study responses to different
abiotic stresses in cereals, such as drought, salinity, frost,
mineral deficiencies and toxicities, aiming to identify novel
mechanisms of stress adaptation and tolerance.
The DPI at La Trobe University
ACPFG’s DPI node is housed in the Victorian Agri-Biosciences
Centre at the La Trobe University R&D Park in Melbourne. The
Centre includes nodes of the Victorian Microarray Technology
Consortium, the Victorian Bioinformatics Consortium and
the Victorian Centre for Plant Functional Genomics, as well
as the headquarters for the Molecular Plant Breeding CRC.
This gives ACPFG scientists access to a comprehensive
suite of technology platforms for plant genome and
transcriptome analyses. These include: four complementary
microarray systems; a large capacity in ultrahigh throughput
DNA sequencing and genotyping, with both capillary
electrophoresis and picoplate pyrosequencing systems; as
well as capacity in wheat transgenesis. Underpinning this
is an advanced bioinformatics platform for data mining and
integration from genome to phenome. These facilitate the
DPI node’s role in determining mechanisms of abiotic stress
tolerance in indigenous and Antarctic extremophile grasses.
2007 ACPFG ANNUAL REPORT
9

ACPFG II
Following the major review in 2006, a research strategy
for the next five years was developed and refined during 2007.
In the new research plan, further development and
enhancement of technologies will continue and activities will
be targeted at understanding the genetic and molecular basis
of two key stresses; drought and salinity. These stresses are
of fundamental importance to Australia and are predicted to
grow in significance both here and overseas.
The new research program has been made possible by
three elements:
»» ACPFG’s strong technology base;
»» gene discovery work that has occurred over the past five
years; and
»» new national and international linkages.
In devising the research strategy through to 2012 it has been
necessary to consider the strengths established in ACPFG,
the likely technological and resource advancements that may
occur over the next five year period and the most effective
methods for smoothly integrating ACPFG into broader aspects
of Australian cereals research and the extensive international
programs underway or in development.
Funding requests were made in 2007 to the ARC, GRDC and
SA Government and there were negotiations with UA, UM,
UQ, Vic DPI and UniSA. Shareholders and the ARC have now
committed $36.6m in cash funding to ACPFG II and a further
notional in-kind contribution of $45.6m. A total of $82m has
therefore been committed.
A key component of ACPFG’s role includes fundamental
scientific research of the highest international quality.
Relatively long-term and flexible funding has enabled
ACPFG to tackle difficult scientific problems such as the
highly complex genetic, biochemical and physiological
basis for tolerance to drought and salinity. The strength of
the fundamental research, as measured for example by
publications, will underpin our ability to understand and
define complex biological systems and processes and will
ACPFG II Cash Funding
2008 2009 2010 2011 2012 TOTAL
ARC* $2,223,986 $2,223,986 $2,313,835 $2,360,112 $2,407,314
GRDC $2,000,000 $2,000,000 $2,000,000 $2,000,000 $2,000,000
SA $1,750,000 $1,772,000 $1,816,500 $1,862,000 $1,908,500
UA $1,000,000 $1,000,000 $1,000,000 $1,000,000 $1,000,000
UM $150,000 $150,000 $150,000 $150,000 $150,000
UQ $50,000 $50,000 $50,000 $50,000 $50,000
UniSA $300,000 $300,000 $300,000 $300,000 $300,000
$7,473,986 $7,495,986 $7,630,335 $7,722,112 $7,815,814 $38,138,233
remain essential for the development of strategies to enhance
tolerance in Australian cereals to the ravages of drought and
rising salinity.
The establishment of clear delivery paths for the outcomes
of genomics research will become a major activity during
the next five years. While the processes for delivery of
conventional germplasm and molecular markers are well
established in Australia, the pathway for delivery of genetically
modified wheat and barley has yet to be developed. ACPFG
will continue to exploit those traditional delivery paths for
markers that arise from the gene discovery programs. In all
cases, the highest priority for ACPFG will be to ensure rapid
and broad adoption of emerging technologies in Australia.
Opportunities for revenue generation will be explored,
particularly in overseas markets, but will be secondary to the
delivery of benefits to the Australian cereal industry.
ACPFG has established the commercial contacts necessary
to ensure “freedom to operate” and has been developing
strategies and options for the delivery of enhanced cereal
varieties to Australian producers. These will now be
implemented and fully tested.
The strategic plan envisages the first GM field trials will be
conducted in 2008 and applications have been made to the
OGTR for these. Although these early trials will be largely
directed at establishing systems and processes needed to
manage such trials, it is planned to have barley and wheat
engineered for enhanced tolerance to salt, boron and grain
quality in trials in 2009, with trials of lines with enhanced
drought and frost tolerance planned for 2010.
ACPFG will continue to expand its education and community
programs. The “Get into Genes” and “Gene Juice Bar”
programs, run with the Molecular Plant Breeding CRC, are
currently delivered in South Australia and Victoria. Expansion
into Queensland and Western Australia is planned over the
next two years. An ambitious target
envisages that by 2012 over half of the
senior biology students at secondary
schools in the states concerned
will have attended these programs.
Postgraduate training will be extended
through a new masters program at
Adelaide, taught largely by ACPFG
staff. PhD student numbers will be
held at around 30.
*Assumes indexing at 2%
10 2007 ACPFG ANNUAL REPORT

Collaborations
ACPFG has a wide range of collaborations with public and
private sector organisations. A $537,000 grant was won
in 2007 to link in with the European Union Framework 7
program in the area of wheat and barley genome analysis.
In 2007, ACPFG was able to strengthen its relationship
with Pioneer Hi-Bred International Inc. using its funding
to leverage, through the University of Adelaide, a further
$900,000 from the ARC in the area of nitrogen use efficiency.
This came on the back of the $689,000 won in 2006 to work
on cellulose biosynthesis.
ACPFG staff have been working hard with colleagues in the
CSIRO Division of Plant Industry and the ANU to establish
the Australian National Plant Phenomics Facility. The Facility
will include an automated, high throughput phenotyping
glasshouse worth in the vicinity of $25 million, which
will be constructed at the Waite Campus using funding
from the Federal Government’s National Collaborative
Research Infrastructure Strategy, the State Government of
South Australia and the University of Adelaide. The Waite
component is known as the Plant Accelerator and will be
the most sophisticated and largest facility of its type in the
public sector, anywhere in the world. In addition to serving
the national phenotyping requirements, it will also provide
state-of-the-art infrastructure for many of the forward genetics
projects within the ACPFG.
An exciting new development has been our role in the
formation of a new National Collaborative Research
Infrastructure (NCRIS) national metabolomics platform
through Metabolomics Australia. The University of Melbourne,
through the ACPFG and the Victorian Centre for Plant
Functional Genomics at the School of Botany, and the
Bio21 Molecular Science and Biotechnology Institute, will
form the hub of a national service centre also involving the
Universities of Western Australia, Murdoch and Queensland
and The Australian Wine Research Institute. This will provide
approx. $9.6 million of funding, as well as employing
10–12 new personnel. Furthermore, through the Australian
Bioinformatics Facility, we will have 4–5 new informaticians
and IT support people to provide a vital resource for data
mining, analysis and interpretation. ACPFG, along with other
groups in Australia, will have access to the new NCRIS facility
for Metabolomics at the University of Melbourne. This will
enhance the technical capabilities of the metabolite analysis
group and should increase throughput
ACPFG has been developing, and will continue to develop,
strong international collaborations. Such collaborations
leverage significant advantages for the ACPFG, including:
»» Ensuring and/or facilitating access to the latest
technologies, wherever they are developed.
»» The potential to broaden the funding base for ACPFG.
»» Access to high value markets for our research outcomes.
»» A role in setting international research agenda, through
which problems and issues of relevance to the Australian
Industry are tackled.
»» Benchmarking for ACPFG scientific, commercial and
educational activities.
A major achievement in 2007 was the negotiation of a license
for well-developed nitrogen use efficiency (NUE) technology
from Arcadia BioSciences Inc. in California. ACPFG, in
collaboration with CSIRO, acquired an exclusive license
for developing the technology in wheat and barley crops
for Australia.
In 2007 ACPFG signed collaboration agreements with Vibha
Seeds, India, and also Regione Puglia, Italy, to share research
outcomes in durum and bread wheats.
ACPFG has an active role in the Consultative Group on
International Agricultural Research and in the Genomics
Taskforce and Generation Challenge programs. It has received
funding for its collaborations with CGIAR centres.
Within Australia, ACPFG is a contributor to the GRDC’s
“Pre-Breeding Alliance” and has made significant
contributions in developing a new framework for sharing
research outcomes nationally. The NSW Department of
Agriculture has agreed to fund a series of projects linking
ACPFG in with the CSIRO, including a project to look at
the effect of drought on grain quality.
2007 ACPFG ANNUAL REPORT
11

Visitors to ACPFG
Name
Assistant Professor Mary Tierney
Associate Professor Chris Cobbett
Associate Professor Yoshihiko Hirai
Dr Alan McKay
Dr Andrew Southcott MP
Dr Brian Smith
Dr Celeste Linde
Dr Cynthia Bottema
Dr David Poulsen
Dr Duncan McFetridge
Dr Giles Oldroyd
Dr Greg Rebetzke
Dr Gustav Vaaje-Kolstad
Dr Michael Francki
Dr Narayana Upadhyaya
Dr Rana Munns
Dr Rob Bramley
Dr Simon Robinson
Dr Steven Thomas
Dr Sunita Gupta
Dr TJ Higgins
Dr. Sibylle Rösel
Emeritus Professor David Catcheside
His Excellency Rear Admiral Kevin Scarce
Hon Iain Evans
Iowa delegation
Manitoban delegation
Mr Martyn Evans
Mr Avi Menashe
Mr Bill Porter
Mr Bruno Julien
Mr Dirk Vanderhirtz
Mr Matthias Eberius
Mr Michael Gallagher
Mr Peter Carr
Mr Tom Kenyon MP
Mr Tony Kent
Ms Corinne Turner
Ms Heike Wolff
Ms Iben Sorensen
Ms Katja Geipel
Ms Miriam Frey
Ms Suzanne Matschi
Ms Vera Sprothen
Professor Alan Cooper
Professor Bob Gibson
Professor Chris Lamb
Professor Christine Foyer
Professor David Adelson
Professor Dirk Inze
Professor Grant Cramer
Professor Gustavo Slafer
Professor Marilyn Ball
Professor Peter Sharp
Professor Robert Henry
Professor Robert Waugh
Professor Roberto Tuberosa
Professor Steven Smith
Professor Tim Flowers
Professor William Lucas
Organisation
Department of Plant Biology, University of Vermont, USA
Department of Genetics, University of Melbourne
Okayama University, Japan
South Australian Research and Development Institute
Federal Member for Boothby
The Walter and Elisa Hall Institute of Medical Research
School of Botany and Zoology, ANU
Animal and Agricultural Science, University of Adelaide
Queensland Department of Primary Industries and Fisheries
Liberal Member for Morphett
Department of Disease and Stress Biology, John Innes Centre, UK
CSIRO Plant Industry, Canberra
Department of Chemistry, Biotechnology and Food Science Norwegian University of Life Sciences, Norway
Molecular Plant Breeding CRC, Perth
CSIRO Plant Industry, Canberra
CSIRO Plant Industry, Canberra
CSIRO Land and Water, Canberra
CSIRO Plant Industry, Adelaide
NSW Department of Primary Industries
Postdoctorate visitor, India
CSIRO Plant Industry, Canberra
Lifeprint, Germany
School of Biological Sciences, Flinders University
Governor of South Australia
SA Member for Davenport
Iowa Economic Development Board, USA
Canada
Former South Australian politician
Avi Menashe Consulting Engineers, Israel
BioChambers, Canada
European Union Ambassador
Lemnatec, Germany
Lemnatec, Germany
Group of Eight universities
Carr Consulting and Services
Member for Newland, South Australia
LongReach Plant Breeders, Australia
CSIRO Mathematical and Information Sciences
Wolff and Partners, Germany
Department of Biology, Copenhagen University, Denmark
Leibniz Institute for Solid State and Materials Research Dresden, Germany
Student, Germany
Student, Germany
Correspondent for WirtschaftsWoche business news magazine, Germany
Australian Centre for Ancient DNA, Adelaide
Nutrition and Functional Food Science, University of Adelaide
John Innes Centre, UK
School of Agriculture, Food and Rural Development, Newcastle University, UK
Bioinformatics, University of Adelaide
Department of Plant Systems Biology, University of Ghent, Belgium
Department of Biochemistry, University of Nevada, USA
Department of Crop and Forest Sciences, University Lleida, Spain
Research School of Biological Sciences, ANU
Plant Breeding Institute, University of Sydney
Australian DNA Plant Bank, Southern Cross University, Lismore
Scottish Crop Research Institute, UK
University of Bologna, Italy
Plant Energy Biology, University of WA
Department of Biology and Environmental Science, University of Sussex, UK
Plasmodesmata laboratory, UC Davis, USA
12 2007 ACPFG ANNUAL REPORT

IP and Patents
Stephanie Agius
Dr Stephanie Agius is ACPFG’s Intellectual Property Manager. She has a
Masters degree in Science and Technology Commercialisation from the
University of Adelaide and a PhD in Plant Physiology from Lund University,
Sweden. Her expertise covers intellectual property management and strategy,
commercial assessment of technologies, commercialisation strategy, product
development, research and development plans, developing business cases,
risk management, and communication. Stephanie teaches intellectual
property management and technology commercialisation at the University of
Adelaide and Flinders University, and is on the SA Committee of Ausbiotech.
2007 has been an exciting year for ACPFG inventors with new discoveries
made in the areas of boron, gene promoters, plant cell walls and grain quality.
Presently we have 15 patents in the areas of frost and salinity tolerance, grain
quality, gene promoters, micronutrient transporters, transcription factors in
addition to various research and development tools and methods.
In the ACPFG patent portfolio there are four patent applications in national
Phase, eight in PCT phase and three provisional patent applications.
Freezing tolerance
Ice recrystallisation inhibition protein
or antifreeze proteins from deschampia,
lolium and festuca species of grass
WO 2005/049835A1, national phase
Description:
»» Genes encoding ice recrystallisation
inhibition proteins (IRIPs).
»» IRIPs inhibit the growth of ice crystals.
Applications:
»» Improve plant frost tolerance.
»» Medical applications (cryosurgery).
»» Food technology (frozen food industry).
Gene promoters
Plant egg cell transcriptional control sequences
WO 2007/092992 A1, PCT
Description:
Plant egg cell specific promoter.
Applications:
»» Induce female sterility in plants.
»» Produce hybrid cereals increasing yield up to 20%.
»» Engineer the apomixis trait.
Plant seed active transcriptional control sequences
provisional
Description:
Endosperm and aleurone specific promoter in a plant seed.
Applications:
»» Increase grain yield.
»» Manipulate grain quality.
»» Manipulate grain size.
Specific expression using transcriptional
control sequences in plants
WO 2007048207A1, PCT
Description:
Endosperm specific cell promoter in a plant seed.
Applications:
»» Increase grain yield.
»» Manipulate grain quality.
»» Manipulate grain size.
Transcriptional control sequences
PCT
Description:
Plant egg cell and pollen specific promoter.
Applications:
»» Engineer male reproductive sterility.
»» Induce female sterility in plants.
»» Produce hybrid cereals increasing yield up to 20%.
»» Engineer the apomixis trait.
2007 ACPFG ANNUAL REPORT
13

Transcriptional regulators for reproduction
associated plant part tissue specific expression
WO 2007/137361 A1, PCT
Description:
Plant endosperm and male specific promoter.
Applications:
»» Increase grain yield.
»» Engineer male reproductive sterility.
Hydroponics
Hydroponic support medium of plastic pellets
WO 2007/056794A1, PCT
Description:
A hydroponic support medium of plastic pellets.
Applications:
Research and development tool.
Grain quality
Polysaccharide synthases
WO 2007014433A1, national phase
Description:
Genes encoding polysaccharide synthases producing (1,3):1,4)
β-D-glucans encoded by members of the Csl F gene family.
Applications:
»»
Functional foods (high β-glucan level).
»»
Human disease prevention (high β-glucan level).
»»
Improve growth performance (low β-glucan level).
»»
Enhance beer processing (low β-glucan level).
»» Molecular marker.
Polysaccharide synthases
(H), provisional
Description:
Genes encoding polysaccharide synthases producing (1,3):1,4)
β-D-glucans encoded by members of the Csl H gene family.
Applications:
»»
Functional foods (high β-glucan level).
»»
Human disease prevention (high β-glucan level).
»»
Improve growth performance (low β-glucan level).
»»
Enhance beer processing (low β-glucan level).
»» Molecular marker.
Polysaccharide transferase
WO 2008/011681 A1, PCT
Description:
»» Genes encoding polysaccharide transferases (xyloglucan
endotransglycosylases).
»» Can potentially influence the strength, flexibility and
porosity of plant cell wall.
Applications:
»» Agro-industrial processes (paper and pulping).
»» Malting and brewing.
»» Bioethanol production.
»» Functional food (dietary fibre and ruminant digestibility).
Micronutrient transporters
Boron transporter
PCT
Description:
»» Genes encoding boron transporters.
»» Essential for protecting plants from boron deficiency
and toxicity.
Applications:
»» Increase or decrease boron levels in plants.
»» Molecular marker.
Zinc transporter
WO 2007/070936 A1, PCT
Description:
Genes encoding plant zinc transporters.
Applications:
»» Increase or decrease zinc levels.
»» Molecular marker.
Salt tolerance
Vascular plants expressing Na+ pumping ATPases
WO 2006037189A1, national phase
Description:
»» Genes encoding sodium pumping ATPases.
»» A sodium efflux system.
Applications:
Improve plant salinity tolerance.
Tools and methods
Targeting vector
WO 2006/135974 A1, national phase
Description:
»» DNA constructs for cloning genes of interest into
target chromosomal loci in plants.
»» Determining unknown gene function.
Applications:
Research and development tool.
Transcription factors
Modulation of plant cell wall deposition
provisional
Description:
Homeodomain/leucine zipper polypeptide which
modulates plant cell wall deposition including secondary
cell wall deposition.
Applications:
»» Increase or decrease stem strength.
»» Decrease lodging.
»» Biofuel production.
2007 ACPFG ANNUAL REPORT

Symposium: Genomics of Drought
ACPFG’s annual symposium was held from October 22nd
to 24th in Adelaide, with a special focus on the genomics of
drought. Around 130 delegates travelled from more than
15 countries for the event, which illuminated many important
aspects of internationally recognised drought research.
The accessible location and newsworthy topic meant the
symposium attracted media attention and government
personalities. In addition to the scientific presentations,
we heard from the SA Minister for Science and Information
Economy, Paul Caica, and SA Minister for Agriculture,
Rory McEwen, who gave a talk at the conference dinner
highlighting the difference between political decision making
and science, emphasising that scientists need to engage with
the public. Don Gunasekera from the Australian Bureau of
Agricultural and Resource Economics (ABARE) spoke about
the economic impact of drought and the lead the scientific
community should take to overcome this issue. Abstracts of
scientific presentations and lists of speakers at the symposium
can be downloaded from the ACPFG website.
In early September, 35 people involved in pre-breeding
research from all Australian grain growing areas met for a
GRDC workshop on drought.
ACPFG’s Thorsten Schnurbusch helped organise the event,
along with John Passioura from CSIRO Plant Industry in
Canberra, Richard Brettel from GRDC in Canberra and
Richard Trethowan from the University of Sydney. The meeting
aimed at improving coordination and communication
between scientists in the pre-breeding area and cereal
breeders, with a special emphasis on future drought research.
2007 ACPFG ANNUAL REPORT
15

Research
Drought
Salinity
Nutrients
17
19
22
Boron
Cold and Frost
Technology
Platforms
24
26
28
Transcriptomics
Bioinformatics
Positional Cloning
33
35
37
16 2007 ACPFG ANNUAL REPORT

Drought
Thorsten Schnurbusch
Thorsten graduated in agronomy and plant breeding from the University of Göttingen
in Germany. He completed a PhD and Postdoctorate in wheat molecular genetics and
durable disease resistance in Zurich, Switzerland. In February 2004 he received a Feodor-
Lynen-Research Fellowship from the Alexander-von-Humboldt Foundation in Germany,
to start working with Peter Langridge at ACPFG. Since April 2005 he has been head of
the Drought Focus Group, as well as being actively involved in ACPFG’s boron, mapbased
cloning and transcriptomics research.
DROUGHT
Background
In 2007, South Australia experienced a second year
of devastating drought, with some of the toughest water
restrictions on record. Dry conditions meant crop production
was significantly lower than expected (ABARE Australian
Crop Report #144, 2007). Australian agriculture is dependent
on introduced cereal species which were originally poorly
adapted to local conditions. Plant breeding has developed
plants better able to cope with Australia’s environment
and these plants have a range of strategies to enable them
to survive the multiple elements of drought and other
stresses. An understanding of the genetic, biochemical and
physiological basis of these strategies allows us to introduce
novel protective systems and enhance existing tolerance
mechanisms into commercially important cereal species such
as wheat and barley.
The Drought Focus Group works to identify mechanisms for
extending the drought tolerance of commercially-valuable
crops beyond the levels seen in existing germplasm. Detailed
knowledge of these mechanisms for drought adaptation
under Australian growing conditions is being developed. This
knowledge is used to develop new strategies for enhanced
drought tolerance in barley, wheat, rice and Arabidopsis, with
a view to developing plants tolerant to multiple components
of drought (osmotic and oxidative stress, heat and
dehydration). Benefits are being delivered to the Australian
grains industry in the form of drought-tolerance markers
for the selection of adapted lines in conventional breeding
programs, and we aim to develop transgenic cereal lines
carrying adaptive genes from a range of sources.
Research and activities
In 2007, the ACPFG drought research focused on three
integrated approaches aimed at improving drought tolerance
of cereal crops: (1) analyses of drought tolerant germplasm,
(2) characterising drought responsive genes, and (3) improving
oxidative stress protection systems.
Analyses of drought tolerant germplasm
One of the group’s core activities is centred on crosses
involving elite bread wheat germplasm, showing segregation
in grain yield under drought conditions. The central objective
of working with this germplasm is the identification of
quantitative trait loci (QTLs) that influence drought-related
traits and grain yield stability under local drought conditions.
Germplasm selection, population and genetic linkage map
construction and field trialling all rely on collaborations with
the Molecular Plant Breeding CRC and the wheat breeding
company, Australian Grain Technology (AGT). We have
chosen two crosses with a view to producing 300 doubled
haploid lines (DHs) and 3,000 recombinant inbred lines (RILs)
from each. Their detailed physiological, genetic and metabolic
analyses will form the basis for future discoveries of droughtrelated
genes.
Characterising drought responsive genes
Plant adaptation to drought is controlled by: cascades of
molecular networks that regulate signalling pathways, the
expression of proteins conferring stress tolerance; and the
accumulation of stress-related metabolites. We have identified
drought tolerance-related proteins operating at each of these
2007 ACPFG ANNUAL REPORT 17

DROUGHT
levels of plant response and are manipulating their
expression/localisation to improve drought tolerance.
The transcriptional response of plants to water stress is
controlled by numerous transcription factors (TFs), including
members of the dehydration responsive element (DREB) and
the plant-specific homeodomain-leucine zipper (HD-ZIP)
protein families. Isolated DREB proteins from drought tolerant
lines are being investigated for their drought response at
flowering and during grain development. In addition, we are
studying the processes regulating DNA binding of HD-ZIP TFs,
with a view to manipulating HD-ZIP regulation to improve
drought tolerance.
Improving oxidative stress
protection systems
In plants, numerous antioxidant defence systems have evolved
to combat the production of reactive oxygen species (ROS).A
redox-active protein class with an emerging role in the
oxidative defence mechanism of plants includes thioredoxins.
Thioredoxins are ubiquitous proteins that have been shown to
play a central regulatory role in the oxidative stress response
of both prokaryotes and eukaryotes through redox signalling,
or as electron donors for ROS scavenging enzymes. We are
currently using a number of transgenic, molecular biological
and biochemical methods to investigate the role of cytosolic
thioredoxins in cereal’s oxidative stress signalling and defence
responses. Expression, targeting and regulatory properties of
thioredoxins and interacting proteins are to be manipulated to
improve the oxidative stress tolerance of wheat, barley and rice.
Experiment highlights
James Edwards spent several months at CIMMYT Obregon,
Mexico, phenotyping drought mapping populations under
flood irrigation and water stress; he was hosted and supervised
by Matthew Reynolds. The field trials produced high-quality
and valuable phenotypic data for QTL discovery.
A water status experiment, conducted in the glasshouse by Ali
Izanloo, revealed that osmotic adjustment might play a major
role in the drought adaptation of the wheat lines Excalibur and
RAC875. The input of Tony Condon from CSIRO Plant Industry
in Canberra in this experiment is gratefully acknowledged.
Dry conditions in 2007 allowed ACPFG scientists, in
collaboration with AGT, to collect another set of valuable
phenotypic data from five field sites (Roseworthy, Booleroo,
Minnipa, Piednippie and Robinvale), which are helping to
identify more drought tolerant germplasm.
Staff changes
Juan Juttner left the group to take up a position with the
GRDC in Canberra as project manager in biotechnology and
pre-breeding. Juan was a major contributor in the successful
establishment of the wheat-drought stress-series, which is
an invaluable resource for current and ongoing drought
research at the ACPFG. Thorsten Schnurbusch left the group
in late 2007 to take on an independent research group leader
position at the Leibniz-Institute of Plant Genetics and Crop
Plant Research (IPK) in Gatersleben, Germany. The search
for a suitable new leader for the Drought Focus Group will
continue in 2008.
18 2007 ACPFG ANNUAL REPORT

Salinity
Stuart Roy
Stuart Roy has a Bachelor of Science with Honours in Plant and Environmental Biology
from the University of St Andrews, Scotland. He obtained a PhD at the University of
Cambridge, where he designed quantitative assays to measure enzyme activities in sap
extracted from single plant cells. In 2001 he received a Broodbank Research Fellowship
to continue his work in Cambridge, developing techniques for carrying out microarray
analysis on mRNA extracted from single plant cells. Stuart arrived at the ACPFG in 2004
and leads the Salt Focus Group. His current research involves identifying QTLs and genes
for sodium exclusion in Arabidopsis.
DROUGHT
salinity
Background
Salinity is a global problem; in Australia alone
approximately 20,000 farms are affected, with an estimated
820,000 hectares of Australian farmland unusable (Salinity
on Australian Farms 2002, Australian Bureau of Statistics).
The main toxic component of salt is the sodium ion (Na+).
In high concentrations, Na+ can interfere with cellular
metabolic functions, because it competes with potassium and
inhibits enzyme activities and protein synthesis. High Na+
concentrations can also cause osmotic damage.
Generally, the best yielding crop plants in saline soils
accumulate the lowest concentrations of Na + in their shoots.
If the mechanisms of Na + movement between the roots and
shoots of a plant are understood, these pathways can be
modified to increase crop salt tolerance.
Some wild relatives of crops can accumulate Na + in their
leaves, presumably by sequestering the ion in storage
organelles such as the vacuole; these plants are referred to as
tissue tolerant. A complete understanding as to how plants
compartmentalise Na + into non-vital organs and cellular
compartments would undoubtedly present opportunities to
enhance salt tolerance in commercially important cereals.
Research and activities
The aim of the Salt Focus Group is to improve the salt tolerance
of Australian cereal crops by generating plants that can survive
and produce viable yields on saline soils. To achieve this it
is vital to understand how salt gets into a plant and how the
plant then deals with the salt. The genes and cellular processes
involved in salt tolerance must be identified, both in our current
crops and in other resistant plant lines, so that these traits can
be introduced into commercially available crops. As a result we
are identifying novel genes involved in salinity tolerance and
introducing candidate genes into transgenic plants to investigate
if we have improved their ability to grow in saline soils.
Identifying novel genes involved
in salinity tolerance
We have screened different varieties, lines and accessions of
wheat and barley for their ability to exclude Na + from their
leaves, so we can identify the genes involved. We are using
lines of interest to generate mapping populations. These
populations then allow us to identify which chromosomal
regions are linked to Na + accumulation (quantitative trait
loci, QTLs).
From a single, but strong, QTL discovered in a Barque ×
CPI 71284 barley mapping population, we have identified
a candidate gene involved in Na + compartmentation.
Experiments have shown that this gene is up-regulated in
barley plants under salt stress; we are working to characterise
the gene and understand its function further. Another QTL has
been identified from a different barley mapping population
(Clipper × Sahara) and two potential candidate genes have
been identified. We are now testing to identify which of the
two genes is responsible for low shoot Na + accumulation.
Analysis of wild relatives of cultivated cereals continues to
provide exciting results. The species Triticum monococcum
contains significant differences to the A genome found in
both durum wheat (T. durum) and bread wheat (T. aestivum).
Many T. monococcum accessions have evolved in saline
environments, away from selective pressures induced
by humans. Their genomes therefore contain a source of
untapped genetic variation that could potentially be used to
identify genes or alleles involved in Na + exclusion, osmotic
tolerance and tissue tolerance.
2007 ACPFG ANNUAL REPORT 19

salinity
The importance of such research can be illustrated from
experiments carried out in 2007 at ACPFG. Lines of
T. monococcum and T. urartu (the likely donor of the wheat A
genome) have been screened for the presence of two genes,
Nax1 and Nax2, which are important in Na + exclusion. Only T.
monococcum lines have the genes present, while T. urartu lines,
and therefore cultivated wheat, are lacking these important
genes. Work in collaboration with CSIRO is continuing to
introgress the Nax1 and Nax2 genes into durum wheat.
Experiments have commenced that will identify useful
mapping population parents for discovering genes important
in tissue and osmotic tolerance in T. monococcum. We
are using a LemnaTec Scanalyser to obtain non-destructive
measurements of plant growth and tissue damage of lines
growing under salt stress. These measurements are to be used
to construct indices for both tissue and osmotic tolerance and
these will be used in future QTL mapping calculations.
Arabidopsis thaliana is being used as a model plant for the
identification of candidate genes, which may lead to improved
salinity tolerance in Australian crops. Previously, an exciting
QTL was identified in the test lines of a novel mapping
population. Further experiments on the whole mapping
population confirmed that a significant QTL for Na + exclusion
could be found on chromosome 2. Fine mapping has reduced
the number of genes under the QTL from 1400 to 35, one of
which is a potential candidate involved in an abiotic stress
signalling pathway. In the coming year the candidate gene will
be confirmed and characterised further.
Using candidate genes to
increase salinity tolerance
Genes that were identified as important in Na + exclusion
are being investigated, the two most notable being PpENA1
and HKT.
PpENA1 derives from the moss, Physcomitrella patens.
The PpENA1 gene is involved in the transport of Na + out of
cells, and allows the moss to survive in saline conditions.
In 2007 constitutive over-expression of PpENA1 was
conducted in a number of plant species, including barley,
rice and Arabidopsis, to demonstrate that the amount of Na +
accumulating in the shoots of these individuals can be altered.
Rice plants with high expression of PpENA1 had significantly
reduced Na + accumulation in the shoot. We also observed this
in subsequent generations of transgenic plants.
The HKT gene family can be divided into two subgroups
which either transport Na + alone or Na + and potassium ions
together. The regulation of these subgroups during salt stress
appears to be important in a plant’s ability to survive that
stress. We previously established that there is a correlation
between the levels of expression of the Arabidopsis AtHKT1;1
gene and the difference in accumulation of Na + in two
ecotypes of Arabidopsis. Sequencing of the gene and its
regulating promoter from both ecotypes has now taken
place, allowing identification of several regions that may be
responsible for the differences in levels of expression. In rice,
work has also progressed in characterising the expression
patterns of the HKT gene family in cultivars which are salt
sensitive and others which are salt tolerant. While rice has
nine OsHKT genes, it appears that only a few are important
in salinity tolerance. These crucial genes are now being
investigated further.
Studies of a previously identified locus (Nax2) led to the
isolation of a gene involved in Na + transport in wheat. In
2007 we characterised the function of the gene using two
methods, to further establish its role in salinity tolerance.
We did so using gene silencing technology and by expressing
the gene in yeast and Xenopus oocytes, where its Na +
transport characteristics were investigated.
We achieved a breakthrough with the candidate gene work
using ACPFG’s unique tools to monitor expression of genes
in specific cell types. These tools mean we can target the
particular tissues and cells in which the proteins of interest are
produced. Previously, the importance of this approach was
demonstrated in work with Arabidopsis where the specific
expression of the gene AtHKT1;1 in stelar root cells resulted
in reduced shoot Na + accumulation, while constitutive
expression throughout the plant resulted in an increase in
shoot Na + . Experiments confirmed that those plants with
stelar specific AtHKT1;1 are better at retrieving the Na +
being transported from the root to the shoot in the plant’s
transpiration stream, so retain more salt in their roots than
wild type plants. These are important results as they show the
advantages of expressing a gene in a specific tissue/cell over
constitutive gene expression that can be detrimental.
Building on the success of the Arabidopsis work, we created
lines of rice that express members of the rice OsHKT
gene family and the moss PpENA1 gene in specific root
cells. Due to the long generation time of rice plants, seeds
of homozygous lines are only now ready for analysis.
Nevertheless, results from initial transformants have been
promising, with cell type-specific root expression of Na +
transporters resulting in lower shoot salt accumulation. With
the positive results of cell type-specific expression in both
Arabidopsis and rice, we are now developing a system for
cell type-specific expression in barley. This will be crucial for
developing transgenic cereal crops that are salt tolerant.
In addition to controlling the spatial location of a gene’s
expression, controlling the temporal expression of a gene is
now a target, so that it is only active when required. Initial,
but promising, work involved the creation of rice plants which
activated a gene when supplied with an external chemical.
This system is being developed by looking for the transcription
factors responsible for activating a gene under salt stress, so
we can have greater control over transgenes.
We have established a collaboration with New York University
to identify genes that are differentially regulated in specific
cell types of rice and Arabidopsis plants undergoing salt stress.
We have isolated RNA from specific root cell types in both
species and microarray analysis has identified a number of
genes that are differentially regulated between cell types.
It has been an exciting and productive year in the Salt
Focus Group. Significant steps have been taken towards the
development of crops better adapted to the saline soils.
20 2007 ACPFG ANNUAL REPORT

Genes that were identified as important in
Na + exclusion are being investigated, the
two most notable being PpENA1 and HKT.
salinity

Nutrients
nutrients
DROUGHT
Chunyuan Huang
Chunyuan Huang specialises in plant physiology, molecular biology and genetics.
His main research interests are molecular mechanisms of plant responses to
nutrient stresses, particularly phosphate and zinc, genetic variations in plant
tolerance to nutrient stresses and improvement of nutrient stresses through genetic
manipulation. Other research interests include root traits related to nutrient
acquisition and drought tolerance. At ACPFG he is improving the phosphate
efficiency and zinc deficiency tolerance in cereal crops.
Background
Australian farmers are heavily dependent on fertiliser
application, because most soils in Australia are deficient in
almost all essential plant nutrients. For example, over 70% of
Australian cropping soils are low in phosphate (P). For wheat
and barley production alone, P fertilisers cost Australian
farmers $400 million annually. Transporter genes are involved
in the adaptation of plants to low nutrient levels. Plants better
able to transport ions such as P and zinc (Zn) can partially
overcome low concentrations of ions in soil solution.
Mineral toxicity can also cause significant losses in crop
yields. For example, acid soils account for 40% of the
world’s arable land and represent a major limitation to crop
production. These limitations are manifested through the
release of soluble aluminium (Al 3+ ) at low soil pH and the
subsequent toxic effects of aluminium (Al) on plant growth.
In Australia, aluminium toxicity affects 1.5 million hectares of
cropping land and causes yield losses worth approximately
$180 million annually. Al tolerant genotypes that can release
higher levels of organic acids at the root tip reduce the effects
of high levels of Al in soil solution on plant growth.
Research
In 2007 we have been focused on defining genetic variations
in P efficiency root system architecture, understanding the
roles of transporter genes and root morphology in tolerance
to low available P and Zn, and characterising genes involved
in the transport of P and Zn ions and the secretion of organic
acids. The aim of this research program is to define tolerance
mechanisms and thereby to improve P and Zn efficiency and
Al tolerance in cereals.
We are using both existing cereal mapping populations and
specifically designed populations to identify quantitative
trait loci (QTL) controlling nutrient stress tolerance of
cereal varieties. Map-based cloning techniques are being
used to isolate genes, transcriptomics and metabolomics to
understand the molecular basis of the tolerance mechanisms
to low P and Zn and high Al, and transgenic approaches to
characterise the functions of candidate genes.
Barley is used as a model system for cereals in plant
adaptation to low P and Zn. Cereal rye (Secale cereale) is used
for Al tolerance studies, because it is the most Al tolerant of
the cultivated cereals and Al tolerance genes from rye could
potentially be transferred to other cereals through standard
breeding technologies.
Subcellular localisation of HvZIP7::GFP
in onion epidermal cells. (a) cytoplasmic GFP
control (b) plasma-membrane control (HMA2::GFP)
(c) organelle control (Trx5::GFP) and (d) plasmamembrane
localisation (HvZIP7::GFP).
Scale bar = 100µm.
22 2007 ACPFG ANNUAL REPORT

Zinc deficiency
Aluminium tolerance
A map-based cloning approach has been used to isolate rye
Al tolerance genes at an Al tolerance locus (Alt4). While the
Almt1 (aluminium-activated malate transporter-1) gene is
single-copy in wheat, we found that an Al tolerant rye line
contains a cluster of Almt1 gene homologues that are located
at the Alt4 locus. We have characterised a cluster of five genes
in the tolerant parent and a cluster of two genes at the same
locus in the intolerant parent. Two out of five genes were
expressed in the root tips of the tolerant parent, whereas only
one was expressed in root tips of the intolerant parent. Full
cDNA sequences as well as splice variants of mRNA were
determined. Organic acid analyses suggested that the Alt4
locus may control secretion of malate as well as citrate, in
contrast to the wheat ALMT1 transporter that transports only
malate. We also determined the chromosome position of
ALMT1 homologue in barley, which differs from that in wheat
and rye. We are characterising the function of rye Almt1
genes by the transformation of barley and electrophysiology
in collaboration with Steve Tyerman and Matthew Gilliham,
from The University of Adelaide.
Transgenic technologies have been used to investigate the
function of a putative barley Zn transporter (HORvu;ZIP7)
gene in Zn deficiency tolerance. We have shown that
this protein is plasma-membrane localised (see photo
2). We obtained transgenic T2 homozygous lines which
constitutively express HORvu;ZIP7. Preliminary uptake
experiments showed that the transgenic HORvu;ZIP7 lines
could take up more Zn than control lines. We also produced
transgenic rice lines overexpressing HORvu;ZIP7 so that
we could study of HORvu;ZIP7 function in cells. We also
generated antibodies specific for HORvu;ZIP7 for detailed
analyses of the gene in plants. In addition, we demonstrated
the importance of root hairs in Zn uptake, in collaboration
withYusuf Genc from the Molecular Plant Breeding
Cooperative Research Centre. The results indicate that root
morphology can contribute to Zn efficiency.
nutrients
Phosphate deficiency
Two new members of the high-affinity P transporter (Pht1)
genes (HORvu;Pht1;9 and HORvu;Pht1;10) were identified
in barley. Transcript analyses revealed genetic variations in the
expression of not only high-affinity HORvu;Pht1 genes but
also in low-affinity HORvu;Pht1 genes, and the variations are
closely related to P efficiency in the tested barley genotypes.
We characterised the electrophysiology of both high and
low-affinity barley P transporters in X. laevis oocytes in
collaboration with Steve Tyerman and Matthew Gilliham.
Primary results show that a low-affinity HORvu;Pht1
transporter has an anion channel activity. We are investigating
the potential functional significance of high- and low-affinity P
transporters in P homeostasis and P efficiency. In addition, we
have used a transgenic approach to define the function of the
arbuscular mycorrhiza (AM) responsive phosphate transporter
gene (HORvu;Pht1;8). Overexpression of HORvu;Pht1;8
improved P uptake into excised roots under both low and
high P conditions. We are now investigating P uptake in these
over-expression lines, both at the whole plant level in soil and
in the presence of AM fungi. We have produced transgenic
knock-down lines for HORvu;Pht1;8 to investigate the role of
HORvu;Pht1;8 in AM fungal colonisation.
2007 ACPFG ANNUAL REPORT
23

Boron
BORON
Tim Sutton
Tim Sutton has a Bachelor of Agricultural Science with Honours from the
University of Adelaide. He obtained a PhD in molecular genetics working with
Peter Langridge at the Waite Campus of the University of Adelaide, focusing on
the molecular aspects of chromosome pairing in polyploid wheat. He joined
ACPFG as a Research Fellow in 2003, working on the positional cloning of boron
tolerance genes from barley and wheat. He is leader of the Boron Focus Group
and a member of the Map-Based Cloning Group.
Background
Boron is essential for healthy plant growth and
reproduction. Of all plant nutrient elements, boron has
the narrowest range between deficient and toxic soil
concentration, and both boron toxicity and deficiency
severely limit crop production worldwide. Whilst deficiency
may be addressed easily through the application of boron
rich fertilisers, boron toxicity is more difficult to manage
agronomically. Boron levels are generally higher in subsoils
than in the surface root zone, so it is difficult to address the
problem simply through soil management.
In southern Australia 30% of soils in grain growing regions
have levels of boron considered toxic to plant growth. Yield
penalties of up to 17% between adjacent areas of barley have
been attributed to differences in shoot boron concentration,
and similar figures have been reported for wheat.
Under adequate boron supply, uptake from the soil into plant
roots via the plasma membrane is a passive process, one that
occurs rapidly. In vascular plants, boron moves from the roots
within the transpiration stream and accumulates in the tips
of older leaves. A sharp concentration gradient is observed
within the leaf, and toxicity symptoms are directly correlated
with boron distribution.
Variation in tolerance to boron toxicity exists both between
and within species, and this has been investigated at the
genetic, molecular and physiological levels. A common
trait for tolerant genotypes is the accumulation of lower
concentrations of boron in plant tissues compared to
intolerant genotypes, suggesting that exclusion rather than
internal tolerance mechanisms are operating. Currently the
exact molecular basis for boron toxicity tolerance is unknown.
Research and activities
The boron group adopts an integrated strategy to investigate
the genetic and molecular basis for boron tolerance in barley
and wheat. We have forward genetics programs specifically
targeting regions of the wheat and barley genomes that we
know contain the genes for tolerance. The foundation for
much of this work is a strong knowledge base, developed at
the Waite Campus, in the area of boron tolerance genetics.
QTL in barley and wheat are known; in barley these loci
are on chromosomes 2H, 3H, 4H and 6H, and in wheat
they are on chromosomes 4 and 7. These projects rely on
the conservation of gene order and colinearity for close
marker development in the intervals of interest. The regions
identified by fine mapping are recovered and sequenced from
large insert BAC libraries containing the alleles of interest
(constructed in-house from adapted germplasm). In addition,
we have reverse genetic projects in which we are adopting a
candidate gene approach.
We are also investigating the mechanisms involved in boron
toxicity tolerance at the protein level. Proteomics technology
platforms at the University of Melbourne provide unique data
that can be complementary to other gene discovery projects.
Proteomics identifies adaptive shifts in the plant’s response
to boron, or in the regulation of specific pathways in boron
tolerant germplasm.
We are analysing the function of candidate genes derived
from gene discovery projects using the Waite Campus
Transformation Facility. These experiments use either overexpression
or silencing of candidate genes in the barley
cultivars Golden Promise and Flagship.
24 2007 ACPFG ANNUAL REPORT

The barley 4H boron tolerance gene Bot1
In barley, research has been focused on the characterisation of
the boron tolerance gene Bot1. We identified the gene using
a high resolution mapping approach that exploited the close
genetic relationship between barley and rice. A tolerance
allele (from the Algerian landrace Sahara 3771) accounts for
approximately 65% of the reduction in boron accumulation in
leaves of tolerant, compared to intolerant, barley genotypes.
Sahara contains approximately four times as many Bot1 gene
copies as intolerant genotypes, produces dramatically more
Bot1 transcript and encodes a BOT1 protein with a higher
capacity to efflux boron and provide tolerance in yeast. Bot1
transcript levels in barley tissues are consistent with a role
in limiting net entry of boron into the root and the disposal
of boron from leaves via hydathode guttation. This work was
published in the November issue of Science. We are now
working to demonstrate an agronomic impact of the gene in
unadapted germplasm, so we can implement the findings into
breeding programs in Australia.
BORON
Boron tolerance gene on
barley chromosome 6H
The gene underlying the chromosome 6H QTL is also under
investigation, in the Clipper x Sahara doubled haploid
mapping population. An F 2
mapping population was
developed and the locus mapped to a 1.8 cM interval by
progeny testing recombinant lines. In a parallel approach to
the genetic mapping, we mapped several candidate genes to
the chromosome level and found that one gene co-segregated
with the boron tolerance locus in this population. Functional
characterisation of the gene in yeast suggests a role in boron
transportation in barley, and the gene remains a strong
candidate for explaining the 6H boron tolerance locus.
Boron tolerance gene on
wheat chromosome 7BL
In wheat, we made good progress in our high resolution
mapping of the chromosome 7BL boron tolerance gene Bo1.
We mapped a population of 1700 F2 individuals from a
Cranbrook x Halberd cross. This allowed the separation of
Bo1 from previously co-segregating markers and delimited
the intervals in rice and Brachypodium to less than ten and
fifteen genes, respectively. We are investigating the function of
wheat orthologues of those genes with a possible role in boron
tolerance. Given the difficulties associated with positional
cloning in wheat, we also used random mutagenesis to tackle
the task of identifying Bo1. Mutagenised populations were
developed in two genetic backgrounds: boron tolerant Halberd
and boron intolerant BobWhite. Using high throughput
screening methods, more than 12,000 plants were analysed for
either gain- or loss-of-function in relation to root growth and
boron accumulation under boron toxic conditions. A number
of phenotypic mutants are being analysed using Southerns
and DArT markers, and we are mapping the genomic location
of deletions in these lines. These mutant populations will also
provide a valuable resource for other research projects at ACPFG.
Iron nutrition and proteomics
Proteomic approaches investigating boron tolerance
continued to produce interesting data. During 2007, our
work focused on unravelling the relationship between iron
nutritional status and boron uptake in barley. We published
a paper describing a proteomic identification of elevated
levels of proteins involved in siderophore production, and a
unique siderophore profile in boron tolerant plants in Plant
Physiology. Siderophores are components of a pathway
associated with iron acquisition from soil.
2007 ACPFG ANNUAL REPORT
25

Cold and Frost
cold and frost
Ulrik John
Ulrik John has broad experience in molecular and cellular biology and in functional
genomics in a range of organisms from yeasts through to fruit flies and wheat. Ulrik
obtained his PhD from the University of Adelaide, and has worked at the Plant
Breeding Institute in Cambridge, UK (now the Cambridge Laboratory at the John
Innes Institute), the Wellcome/Cancer Research Council Institute and the Peter
MacCallum Cancer Institute. His research focus at DPI Victoria, and within ACPFG,
is the molecular mechanisms of abiotic stress tolerance in indigenous and Antarctic
grasses with adaptations to extreme environments.
Background
Frost leading to cereal crop damage is a consistent
problem in south-eastern Australia and in Western Australia.
The sporadic nature of frost means it can have a devastating
impact on specific regions, farms or even particular fields
in certain years. Taking into account financial costs from
indirect losses due to delayed sowing, down grading or crop
protection, the total economic impact of frost on wheat and
barley production in Victoria and South Australia is estimated
at $95.8m and $33.6m per annum, respectively. Thus, even
modest increases in cold and frost tolerance in cereals have
the potential to deliver tens of millions of dollars of benefit to
the cropping industries of southern Australia.
Research and activities
The Cold and Frost Program has focused on the isolation
of novel genes and gene variants from barley, Arabidopsis,
and Antarctic hair grass (Deschampsia antarctica). We have
investigated functions of the genes and their promoters and
have defined properties of proteins and cellular metabolites
correlated with cold and frost tolerance. We have also defined
the molecular structure and function of key cold and frost
tolerance conferring proteins and the gene promoters that
drive their expression, and we have used this information to
engineer novel and more efficient variants.
Map based cloning
We are using map based cloning to isolate the gene(s)
controlling reproductive frost tolerance on barley
chromosome 2H. Variation in frost tolerance exists
across barley genotypes, with germplasm of Japanese
origin harbouring significant tolerance to frost damage of
reproductive tissues. This project builds upon earlier work
at the Waite Campus in which a major QTL for reproductive
frost tolerance was mapped. The experimental approach
exploits co-linearity between related regions in the barley
and rice genomes to generate PCR markers close to the Fr-2H
locus. This, in combination with phenotyping, is being used to
define and refine the interval in mapping populations, which
allow segregation of the trait.
Three loci influencing flowering related traits, earliness
per se (eps-3), clystogamy (cly) and rachis internode length
(ril), are clustered close to the putative reproductive frost
tolerance locus on chromosome 2H. In 2007 we have been
investigating whether one or more of these loci can account
for the original ‘frost tolerance’ QTL effect, or whether they
are unrelated to frost tolerance. Additional markers were
developed in the region, extending coverage of markers to
the entire 2H long arm, and additional inversions and breaks
in co-linearity with rice were discovered. We genotyped
recombinants for the 3cM eps-3 interval for: tiller height;
rachis internode length; and time of awn emergence revealing
all of these traits to be essentially co-segregating at the
same locus. Twenty genes are present in the corresponding
rice interval, one of which has a barley orthologue that is a
credible co-segregating candidate for the controlling gene.
We are isolating and defining the functions of candidate cold
and freezing tolerance conferring genes from Deschampsia
antarctica (the only grass species native to Antarctica) and
assessing their potential to enhance tolerance in sensitive
species. A gene discovery and functional genomics program
in D. antarctica has produced 10,704 high quality ESTs,
representing 4,811 non-redundant unigenes. We will test the
phenotypic consequences of gain-of-function expression of
candidate genes, including those encoding variants of ice
26 2007 ACPFG ANNUAL REPORT

CBFs is regulated by a constitutively expressed transcription
factor ICE1. We have generated Arabidopsis plants putatively
transgenic for over-expression or RNAi-mediated silencing of
a novel Arabidopsis DREB/CBF regulator. These plants have
been subjected to molecular analysis and tested for freezing
stress tolerance. Similar analyses will be applied to a series
of barley plants, transgenic for over-expression of the barley
orthologue of the novel DREB/CBF regulator and for reporter
genes driven by its promoter. We are currently characterising
barley HvCBF2 over-expression lines, imported from the USA.
recrystallisation inhibition proteins (IRIPs), using transgenic
systems, particularly in Arabidopsis. Homologues of IRIP
genes isolated from D. antarctica encode proteins with
structural complementarity to ice crystal faces. The transcript
abundance of these proteins increases markedly in response
to cold acclimation. Expression in heterologous bacterial
and plant expression systems demonstrate that IRIPs confer
recrystallisation inhibition activity.
A programmable convective refrigeration chamber and
a custom built frost chamber have been used to develop
protocols for assaying plants for freezing tolerance. The
protocols were used to test lines transgenic for constitutive
expression of DaIRIPs. An anti-IRIP antibody was used to
demonstrate that IRIP levels are highly dynamic in leaves in
response to cold acclimation and de-acclimation, and closely
correlated with IRIP transcript abundance. Root and shoot
samples from non-acclimated, cold-acclimated or subzeroacclimated
plants were analysed, using transcriptomics and
metabolomics, to identify additional potential molecular
determinants of cold and freezing stress tolerance. An
experiment to assay survival following exposure to a range
of sub-zero temperatures of D. antarctica plants sampled
from cold acclimation and de-acclimation time courses, and
non-acclimated plants revealed high levels of survival down
to -22°C.
We are isolating and defining the functions of barley
homologues of the ICE and DREB/CBF genes and associated
regulatory factors, and assessing their role in cold tolerance.
Dehydration responsive element binding/CRT binding factors
(DREB/CBFs) are evolutionarily conserved transcription
factors that regulate many cold-responsive genes in model
and crop plants. Constitutive gain-of-function expression of
DREBs/CBFs confers enhanced cold and frost tolerance to
transgenic plants. In Arabidopsis, the expression of DREBs/
Validation of a distinct
frost tolerance QTL
We analysed frost tolerance in the Amagi Nijo × WI2585 F5
family 103-1-2-117, which was homozygous for the flowering
time eps-3 locus, but segregating for the putative frost tolerance
QTL region located proximal of eps-3. Individuals containing
the tolerance (Amagi Nijo) allele at the putative frost tolerance
locus showed approximately 25% less frost induced sterility
than those carrying the sensitive allele, suggesting that a frost
tolerance locus separable from any earliness effect does exist.
Genomic sequences of two candidate genes from near the
frost tolerance QTL has been obtained from Haruna Nijo BAC
clones containing these genes.
Molecular engineering of enhanced IRIPs
An engineered version of the IRIP repeat domain of a DaIRIP
with 32 repeat motifs, expressed in bacteria, has 10 or more
times the ice recrystallisation inhibition activity of the wild
type 16 repeat version. Testing of Arabidopsis transgenic
for constitutive expression of DaIRIPs revealed lines that
can survive temperatures 1–2°C lower than non-transgenic
control lines.
Novel barley transcriptional
regulators isolated
We identified two novel barley cDNA clones encoding DREBrelated
proteins from a yeast 1-hybrid screen of a frost stressed
barley expression library, with DRE element baits. Barley
plants transgenic for over-expression of the barley orthologue
of the novel DREB/CBF regulator for enhancement of freezing
stress tolerance are being tested.
Cold and frost
2007 ACPFG ANNUAL REPORT
27

Technology Platforms
Technology Platforms
Andrew Jacobs
Andrew Jacobs has a Bachelor of Science with Honours from Flinders University and
a PhD from the University of Adelaide. He has worked for CSIRO Plant Industry and
the Max-Planck-Institute for plant breeding research in Cologne, Germany, where he
isolated the gene responsible for the formation of callose at sites of fungal infection in
Arabidopsis leaves and characterized the effects of mutations in this gene. Andrew
joined ACPFG in 2003 and leads the Technology Platforms Program. His current research
projects focus on abiotic stress tolerance with an emphasis on salinity tolerance and
developing improved tools and greater resources for the analysis of these genes.
Background
This program is developing and refining technologies
necessary for the analysis of gene function, identification
of important genes and for the characterisation of abiotic
stress responses. The core technologies being developed in
this program are: plant transformation; positional cloning
of candidate genes; bacterial artificial chromosome (BAC)
production; promoter isolation; and high throughput
genomics technologies, including proteomics, transcriptomics
and metabolomics. These technologies, coupled with
powerful computing and bioinformatics capabilities, underpin
ACPFG’s research activities. The core technologies are
also being made available to the wider Australian research
community and have been important in attracting research
funding with national and international collaborators.
The technology platform program involves the ongoing
acquisition of state-of-the-art equipment, staff training in the
use of the equipment, and the development and maintenance
of the technologies. The investment and knowledge can be
subsequently leveraged to attract further research funding
and support other collaborative projects with Australian and
international scientists.
Plant growth resources
A new polytunnel shade house (30m x 6m) was built
adjacent to the Plant Genomics Centre in Adelaide and
houses ACPFG’s barley mutant and other populations. This
complements the shared, existing physical containment
glasshouse in which the bulk of ACPFG’s transgenic plants are
housed, and the three glasshouse areas ACPFG rents from the
South Australian Research and Development Institute (SARDI)
at the Plant Research Centre.
The Lemna-Tec scanalyser is situated in one of the SARDI
glasshouses and has been used by several scientists to
quantitatively measure the effects of abiotic stress on plant
biomass. The system is becoming increasingly important as
scientists seek non-destructive ways to measure the effects of
stress on plant growth. We built many hydroponics systems for
plant growth studies for ACPFG staff and collaborators during
2007 and some units were sold to other research institutions.
We produced 16 trolley-mounted systems that flood and drain
through an 80 litre reservoir, along with 12 smaller units that
operate in a similar fashion. We produced a further 26 units
that keep the roots constantly in the growth solution. A large
system for maize (2x750L) was developed for the nitrogen use
efficiency group and a similar large maize system was shipped
to our collaborators DuPont-Pioneer in the USA.
Transformation systems
Barley transformation
We have direct access to a barley transformation facility that
is supported through separate funding from the GRDC. Within
that program, Dr Rohan Singh and his colleagues transformed
the barley variety Golden Promise with 93 constructs,
including many from ACPFG projects, during 2007. The elite
malting quality variety Flagship and two other elite lines were
also transformed at high frequencies, using Agrobacteriummediated
transformation. Sinorhizobium-mediated
transformation of Golden Promise produced a single putative
transformant and transformants were recovered without the
use of selectable marker genes.
28 2007 ACPFG ANNUAL REPORT

Wheat transformation
In 2007 we established efficient and reproducible biolistic
wheat genetic transformation. We successfully transformed
model wheat cultivars BobWhite and Apogee, as well as the
commercial cultivars Drysdale, Frame, Gladius, Krichauff
and Yitpi. A total of 32 gene constructs were used in stable
transformation experiments and this produced more than 700
independent transgenic events with good fertility. Analysis
of T 0
and T 1
generation transformants using polymerase
chain reaction (PCR), Northern and Southern blotting, and
β-glucuronidase (GUS) histochemical staining, confirmed
their transgenic nature. We analysed the function of several
new wheat promoters using transient transformation with
GUS and green fluorescent protein (GFP) markers. We also
developed a GFP-based transient test system to optimise
wheat Agrobacterium-mediated transformation.
Rice transformation
Demand for rice transformation increased significantly in
2007, with approximately 1500–2000 lines produced for the
salt, nutrients and reproductive genomics focus groups. Most
of the lines were generated in the genetic background of the
Gal4 enhancer trap lines, which enable cell type-specific
expression of genes of interest. However, many constitutive
over-expressing and promoter:reporter gene transformants
have also been produced.
Arabidopsis transformation
Scientists used the Arabidopsis thaliana transformation
pipeline to introduce a range of constructs related to boron
tolerance, cell wall synthesis and for the analysis of promoter
activity. The overall number of constructs received in 2007
was lower than in past years and this enabled us to develop
other Arabidopsis transformation capabilities, including
protoplast transformation and transient assays in detached
leaves. A number of honours and PhD students learnt the
floral dip transformation procedure.
Moss transformation
A yeast contamination problem early in the year necessitated
the complete disposal of existing Physcomitrella patens
cultures and the import of two new moss strains. We modified
techniques for the culture of the moss and we now use an
altered transformation procedure to introduce foreign DNA
into this species. The transformation protocol was changed,
following discussions with collaborators in the USA, and six
constructs designed to alter the cell wall structure of the moss
are being used to test the new transformation protocol.
Mutant populations
Barley transposon-tagged population
Work on this project was scaled back in 2007 because most
of the initial objectives had already been met. The population
has been produced in the barley cultivar Golden Promise.
A combination of TAIL-PCR amplification, DNA sequencing,
restriction length polymorphism (RFLP) analysis and PCR was
used to identify T-DNA integration sites in the genome. To
date, we have located 30 integration sites by genetic mapping
of flanking sequence tags using several barley mapping
populations. Insertions are found on all chromosomes. The
30 single insertion lines, with known genomic locations, can
be used as launch pads for future targeted tagging of genes
in the vicinity of the insertion sites. A number of lines are
being back-crossed into the cultivar Flagship. This work will
continue to generate a set of BC 2
lines.
In 2007 we demonstrated the transposition capability of our Ds
element, by Southern blot analysis of 340 F 2
lines derived from
three different Ds/Ac combinations. These results indicate the
transposition system is functional and that new mutants can be
generated in the existing population. The Ds construct used has
the added feature that it acts as an enhancer-trap or gene-trap
through the use of a reporter gene (GUS). We screened 576 T1
seedlings, of which 22 had unique GUS staining patterns and
six showed a consistent pattern when re-screened. The results
highlight the additional capacity of this system to operate as a
promoter discovery tool.
Technology Platforms
2007 ACPFG ANNUAL REPORT
29

Technology Platforms
Whilst extensive phenotyping of the population has not been
possible with current staffing levels, it is apparent that there
are a number of mutants with altered phenotypes when
compared to wildtype material. For these lines we have begun
analyses of Ds insertion sites through generation of flanking
sequence tags.
Barley TILLING population
We generated a barley targeted induced local lesions in genome
(TILLING) population in 2007, by ethane methyl sulfonate (EMS)
mutagenesis of 10,000 barley (cv. Flagship) seeds. We sowed
500 M1 families of ten individuals, grew the plants to maturity
and documented any obvious mutant phenotypes. Seed from
individual plants was retained for further plantings and pooled
leaf tissue was taken for DNA isolation from the three healthiest
family members. Four thousand M2 families, consisting of
three individuals, were planted. DNA is being extracted from
all individuals and will be stored for characterisation of DNA
lesions. The seed that forms the mutant population is now ready
for screening.
Genome Structure Resources
We have now completed two large insert barley (var. Morex)
HindIII BAC libraries, as part of the international barley
physical mapping project. One contains 115,200 BAC
clones, with an average insert size of 115 kb, while the other
contains 153,600 clones, with an average insert size of
143 kb. Together, these two libraries cover approximately six
equivalents of the barley genome. In 2007, we produced a
BamHI BAC library with an average insert size of 120 kb. This
library contains 300,000 clones and covers seven equivalents
of the barley genome. We produced eight filter copies for
hybridisation screening of the barley HindIII BAC library, as
well assix filter copies for hybridisation screening of the rye
HindIII BAC library, and four filter copies for hybridisation
screening of the phalaris HindIII BAC library.
In addition to the barley BAC libraries constructed, we also
helped colleagues at CSIRO Plant Industry construct a lupin
BamHI BAc library. This library contains inserts around 100 kb
and has ten times genome coverage.
Promoter isolation
Promoters are DNA elements that are important in the
spatial and temporal control of gene expression in an
organism. Scientists use these promoters in the production of
constructs for plant transformation, so that the transgene can
be expressed in specific tissues, at specific developmental
stages, or in response to specific stress treatments. We isolated
promoter elements from Arabidopsis and rice enhancer trap
lines, and for Arabidopsis we were able to replicate the
patterns of cell-specific gene expression seen in the lines from
which the promoters were isolated. In addition, we isolated
promoters from rice and wheat. Five of the rice promoters
enabled drought stress inducible expression of a reporter
gene in transgenic barley, and another cold stress inducible
expression. We also modified three transformation vectors for
use in the plant transformation process.
Heterologous Expression
As a result of funding priorities for ACPFG II changing,
support for this technology platform ceased in 2007. Several
heterologous expression techniques have been implemented,
including the magnICON system developed by ICON Genetics.
A number of genes were expressed in Nicotiana benthamiana
leaf tissue using the magnICON system and were extracted and
found to be active. These included the control GFP and the cell
wall modifying enzymes EII, XEB and XTH.
Proteomics and
protein analysis
APCFG’s proteomics platform is located at the School of
Botany, University of Melbourne node. Protein abundance
and activity can be regulated through multiple mechanisms at
the level of gene transcription, translation, post translational
modification and protein degradation. In 2007, methods have
been refined to enable quantitative comparisons between
protein abundance in different tissue extracts. Robust
capabilities were established using two complementary
approaches to undertake this type of experiment; two
dimensional gel electrophoresis coupled with difference in gel
electrophoresis (DIGE) dyes and iTRAQ peptide labeling.
The iTRAQ methodology was successfully applied to the
comparison of protein abundance in B tolerant and intolerant
barley lines, and this resulted in a publication in Plant
Physiology. This approach was also applied to examining the
changes in protein abundance in the roots of barley plants
following salt stress. This study highlighted consistent changes
in proteins involved in glycolysis following extended exposure
to elevated salt, and the physiological implications of this are
being investigated.
The 2D-DIGE was used to monitor changes in protein
abundance in rice suspension culture cells, following
exposure to elevated levels of NaCl and abscisic acid. A
number of proteins with altered abundance have been
identified following these treatments. Coupled with these
studies have been the ongoing identification of proteins from
2D gels and the construction of 2D spot libraries. To date,
over 100 spots have been identified in reference 2D gels.
We also used the targeted analysis of simple protein mixtures
to identify the post-translational modification status of a
number of thioredoxin proteins. These targeted studies have
been used as a preliminary component of the antibody
production pipeline, to monitor the efficacy of protein antigen
expression levels.
30

In situ hybridisation/
Immunolocalisation
The expression patterns of the barley HvBo4 gene, which
is a transporter that confers tolerance to high levels of
boron were revealed by in-situ hybridisation. The results
were published as part of the paper in Science (Sutton et al.
2007, 318:1446). Concurrently, a new fixation method to
overcome problems with in-situ hybridisation in root tissue
was developed. A new staining method to study hydathodes,
a specialised tissue in leaves that may be involved in boron
excretion, was also developed.
Several gene expression markers for different barley grain
tissues were discovered by in-situ hybridisation, including
markers for nucellar projection, endosperm transfer cells,
embryo, and the embryo-surrounding region.
In-situ hybridisation of a HD-ZipII-1 homeodomain leucine
zipper protein from wheat was improved by development
of a method to reduce background hybridisation. The salt
tolerance gene HKT1 was investigated by in-situ hybridisation
and laser dissection in Arabidopsis and rice. We are also
developing new probe labelling and detection methods to
increase sensitivity for in-situ detection of problematic lowexpression
genes such as HKT1.
Collaboration with Steve Tyerman’s laboratory resulted in
excellent RNA in-situ and protein immunolocalisation data for
an expressed gene in grapevine.
Progeny screens of BG-1 transgenic barley has begun, using
immunolocalisation of β-glucan antibody on resin-embedded
leaf and stem.
Antibody production
Negotiations with Adelaide-based biotechnology companies
MAbSA and Neubody have resulted in agreements to market
and distribute existing (10) and future antibodies produced
at ACPFG. In 2007, we successfully raised antibodies to
zinc transporter proteins and phosphate transporters of
barley. Of the ongoing projects from 2006, antibodies to
ice recrystallisation inhibition proteins (IRIP) proteins from
freezing tolerant Antarctic hairgrass were raised, while the salt
transporters, HKT and PpENA1 remain works in progress.
A boron transporter protein from barley was the target of
another antibody project in 2007. Hybridoma cultures for
this target were developed and further testing is planned to
identify a functional monoclonal antibody. We also raised an
antibody to a nitrogen transporter from maize, as part of the
ACPFG-Pioneer collaboration.
Metabolomics
The metabolomics platform of ACPFG is located at the
School of Botany in The University of Melbourne, and is
an important component of a large number of research
programs of ACPFG. Metabolomics, which is defined as the
analytical, non-targeted and high-throughput identification
and quantification of metabolites in a biological system, is
increasingly applied for an in-depth investigation of metabolic
responses to different abiotic stresses in cereals, mainly barley
and wheat. The technology relies on gas chromatographymass
spectrometry (GC-MS) for the analysis of a large range of
metabolites. Two GC-MS instruments are used for metabolite
profiling. Extraction techniques for metabolites from plant
tissues have been established and validated. Semi-automated
data evaluation is now a routine procedure.
In 2007, a new liquid chromatography-mass spectrometry
(LC-MS/MS) system was commissioned, funded though
an ARC Linkage, Infrastructure, Equipment and Facilities
(LIEF) grant application. A method is being developed for
the quantitative analyses of compounds of interest, such as
free amino acids and sugar nucleotides. An exciting new
development has been the formation of a new metabolomics
platform, through the National Collaborative Research
Infrastructure Strategy (NCRIS). The University of Melbourne,
through ACPFG and the Victorian Centre for Plant Functional
Genomics at the School of Botany, and the Bio21 Molecular
Science and Biotechnology Institute, will form the hub of a
national metabolomics service centre that will also involve the
Universities of Western Australia, Murdoch and Queensland
and The Australian Wine Research Institute. The centre will
provide approx. $9.6 million of funding, while employing
10–12 new personnel. Furthermore, through the Australian
Bioinformatics Facility, four or five new bioinformaticians and
IT support people will provide assistance in data mining, data
analysis and interpretation.
In the last year we have completed the metabolite analysis
of three wheat cultivars exhibiting different tolerance levels
to cyclic drought conditions. Results with transcriptomics
and proteomics data are being correlated from the same
experiment. We also compared the metabolite responses of
barley, wheat and Arabidopsis to salinity. A key objective of
this project is to identify responses common between species
and species-specific metabolite alterations. For the work in
wheat, ACPFG collaborated with Dr Rana Munns, CSIRO
Plant Industry, Canberra.
In 2007, ACPFG established collaborations with Flinders
University, Adelaide, and CSIRO Plant Industry, Brisbane and
Canberra, as well as internationally with the University of Cape
Town, South Africa, and Lincoln University, New Zealand.
Technology Platforms
2007 ACPFG ANNUAL REPORT
31

Transcriptomics
transcriptomics
DROUGHT
Ute Baumann
Ute Baumann completed her undergraduate studies in genetics at the University
of Freiburg, Germany, then moved to Australia for a PhD in plant molecular biology
at the University of Adelaide. She moved to the UK for a Postgraduate Certificate
in Bioinformatics at the University of Manchester, before returning to Australia to
work for ACPFG, where she leads bioinformatics at the Adelaide node and
transcriptomics nationally.
Background
When plants are subjected to an abiotic stress they
respond and adapt by altering the expression levels of
hundreds of genes. These transcriptional changes cause
adjustments of cellular, physiological and biochemical
processes that have evolved to help plants cope with a
range of environmental stresses.
Global gene expression studies, or transcriptome analyses,
can help unravel possible mechanisms of stress tolerance,
and also provide insights into why some cultivars are more
stress tolerant than others.
Research and activities
Transcriptomics research at ACPFG involves profiling the
transcriptomes of cereal genotypes differing in their tolerance
to various stresses, identifying candidate genes potentially
involved in stress tolerance, and developing the ACPFG’s
QPCR stress series. Our focus in 2007 was on the analysis of
microarray data generated in 2006 and on the use of QPCR to
confirm microarray results.
Investigating salt and boron
tolerance with microarrays
In 2007 there were some exciting results. In rice, salt
microarray data provided clues to why the rice cultivar FL478
is salt-tolerant; this work is now being prepared for publication.
Analysis of gene expression in barley grown under elevated
levels of boron revealed a likely candidate for the 3H boron
tolerance locus, and several candidates for the 2H boron
tolerance locus that are currently under investigation.
Investigating drought tolerance
in wheat with microarrays
The wheat drought stress experiment is part of ACPFG’s
involvement in CGIAR’s Generation Challenge Project,
Programme #15. The bioinformatics work involves comparative
transcriptomics, specifically comparing the response of the
wheat, maize and rice transcriptomes under drought stress.
To achieve this, we firstly need to distinguish orthologues,
paralogues and homeologues. No genome sequence is
available for wheat and maize, so expressed sequence tag (EST)
data from public sequence databases was used. The ESTs were
clustered and assembled into consensus sequences, which
were subsequently used for orthologue identification.
In 2007 we worked with plant material grown and collected
in 2006, in which one of the worst droughts in Australian
history was recorded. Three wheat cultivars were used,
namely the drought resistant cultivars Excalibur and RAC875,
and the drought sensitive Kukri. We completed the microarray
experiments for Excalibur leaf, and the remaining experiments
will be completed in 2008. The microarray platform employed
is the Wheat Long Oligo Chip, which was designed in an
international collaboration in 2004.
QPCR stress series
ACPFG’s QPCR stress series is a collection of cDNA samples
that allow scientists to rapidly examine transcript levels of
specific genes in a range of tissues that have been exposed to
different abiotic stresses.
In 2007 we added a barley drought stress series and a wheat
ABA stress series to our collection.
32 2007 ACPFG ANNUAL REPORT

Of the plant material collected for the wheat microarray work
mentioned above, some will be used to produce an extensive
wheat drought stress series. As with the other series, we
took extra tissue for proteomic and metabolomic analyses,
providing scientists with a comprehensive resource that
should provide insights into the cellular and genetic processes
involved in drought.
QPCR Integrated Network Suite (qINs)
We generated 590 Mb of raw data from QPCR experiments
in 2007. In order to store, manage and analyse these data, we
have developed a three-tier distributed software application
called qINs. This provides secure storage of raw data in a
central repository, and extracts, normalises and combines
the gene expression data employing uniform statistical and
normalisation procedures. Automated workflow processes
ensure complete data capture and integrity. ACPFG scientists
can access and query the data via a graphical user interface.
transcriptomics
This year we focussed on improving data standards, data
quality and data capture. For the former, we have created
cross-references of relevant tables with the Plant Ontology
Standard, which will facilitate data exchange with other
databases in the future. For the latter, the application was
extended to include a web-based interface for primer
submission, and a protocol that verifies both primer and
amplification sequences by searching against public
databases, such as NCBI.
2007 ACPFG ANNUAL REPORT
33

Bioinformatics
Bioinformatics
Dave Edwards
Following his PhD studies at the University of Cambridge, Dave worked in the Genetics
Department of the University of Cambridge on rice genome structure, before joining
Long Ashton Research Station, Bristol, UK. During his time in Bristol, he developed
cereal microarrays for both high throughput transposon mutagenesis and gene expression
profiling, along with computer based tools for sequence data analysis and molecular
marker discovery. He then moved to the Victorian Department of Primary Industries
in Melbourne, establishing a new bioinformatics research team. During this time, he
managed groups sequencing genomes and researching molecular markers in Brassica
and Strawberry, as well as a transcriptomics research group. He recently moved to
ACPFG’s University of Queensland node where he is establishing a new team to support
bioinformatics within ACPFG, as well as developing systems for genetic and genomic
analysis for a number of crop systems.
Background
Biological research is becoming increasingly data
intensive. DNA sequencers are now capable of reading
thousands of millions of bases in a single run, microarrays can
measure the expression of tens of thousands of genes, marker
systems can interrogate tens of thousands of polymorphisms,
and the latest automated phenotyping systems can screen
thousands of plants with little human intervention. Combined
with the internet, which enables the open sharing of this data
between international groups, data overload can generate
a significant headache for scientists. While bioinformatics
cannot provide an easy answer to this problem, it can
promote quality research by making data accessible for
integration and interrogation.
Transcriptome classification
The algorithms used in the transcriptome classification project
were improved in 2007, and we are now able to analyse
higher dimensional microarray data. The algorithms were used
on high (≥7) dimensional computer generated data, with and
without added noise, and were able to successfully identify
higher order correlations. They were subsequently used on a
selection of publicly available Arabidopsis tissue series data,
and again identified a number of sets of genes with apparent
correlations. The annotation of these sets is being analysed.
Regulatory elements in untranslated
regions of messenger RNAs (mRNAs)
The search for conserved upstream open reading frames
(uORFs) was extended in 2007 to include Arabidopsis,
and identified additional novel mRNAs in our dataset. The
results have been submitted for publication. In the second
half of 2007, experimental validation of the computationally
identified sequence-conserved uORFs was undertaken.
Generation Challenge Programme
A phylogenomic software tool that reliably detects
orthologues, paralogues and homologues in wheat, barley,
rice and maize is being developed. This software will be
used to analyse data collected for our project within CGIAR’s
Generation Challenge Programme. This project, named the
‘GrassKin project’, has progressed well and involved:
a.
b.
c.
d.
the cultivar-specific clustering of expressed sequence tags
(EST) in maize, wheat and barley;
automated homologous cluster generation;
automated phylogenetic analysis of these clusters; and
the development of a public interface and database.
The first two steps are complete and a procedure for the
phylogenetic analysis has been developed. This is semiautomated,
which will be more reliable and useful than
full automation. Development of the public interface and
database commenced towards the end of the year.
34 2007 ACPFG ANNUAL REPORT

Proteomics
Current state-of-the-art measurement of protein performance
within plants has been hampered by an inability to measure
changes in the amount of protein present in biological
samples. At the University of Melbourne ACPFG node we
were able to measure changes in abundance of identified
proteins over time-course experiments for barley under
salt stress. Software was developed to efficiently analyse
identified proteins, and integrate products that would
otherwise not integrate to produce reliable results. As part of
this program we collaborated with the Australian Proteomics
Computational Facility, with a view to:
»» improving automation by developing a clustered
proteomics pipeline;
»» integrating the most modern proteomics technology
available into ACPFG proteomics; and
Bioinformatics
»»
developing software projects where common
requirements can be identified.
Australian Wheat Pedigrees Database
The database system (http://gwis.lafs.uq.edu.au) delivers
comprehensive datasets with Australian wheat pedigrees
and ancestry information. It has been maintained and
updated with historical information on Australian triticale
and durum wheat pedigrees obtained from the CIMMYT
(International Centre for the Improvement of Wheat and
Maize) library in Mexico.
Wheat reference microarray experiment
This project came to a close in 2007 with the completion of
the “Comparator” software application, enabling comparison
of expression profiles of homologous wheat and barley genes.
Molecular marker discovery
The discovery of molecular genetic markers from available
sequence data is the most cost effective approach for high
resolution genetic studies. We have pioneered methods for
SSR and SNP discovery from sequence data, and continue
with development of pipelines, databases and web interfaces
for the discovery and annotation of markers from the latest
high throughput sequence data.
2007 ACPFG ANNUAL REPORT 35

Positional Cloning
Positional Cloning
Nick Collins
After a Bachelor of Science from Monash University, Nick moved to Adelaide to
do his PhD in the laboratory of Bob Symons, working on the genetics of barley
yellow dwarf virus resistance in barley and rice. He then joined Tony Pryor at the
CSIRO Division of Plant Industry in Canberra to isolate rust resistance genes from
maize. His second postdoctoral position was in the group of Paul Schulze-Lefert
in the Sainsbury Laboratory (UK) researching mechanisms of cell-wall penetration
resistance to powdery mildews in barley. Nick then returned to Adelaide to join
ACPFG and lead the positional cloning group.
Background
Plant genotypes possess varying levels of tolerance to
abiotic stresses, and the genes controlling such differences
can be genetically mapped on the chromosomes with
sufficient precision to allow the controlling DNA sequences
to be identified. Genes and gene functions identified using
such map-based (positional) cloning approaches contribute
to our understanding of the molecular basis of natural
stress tolerance mechanisms, and can potentially be used
for enhancing the trait of interest through GM or non-GM
approaches. Thus, the sequences of isolated genes can be
used as perfect markers for selection, or as templates in
searches for superior alleles in wild germplasm.
Sequencing the barley genome
Libraries of large-insert bacterial artificial chromosome
(BAC) clones have been constructed from several species of
grasses, and in 2007 we contributed a barley BAC library to
the international effort to produce a BAC clone scaffold – or
physical map – of the barley genome. The physical map
represents the first step in sequencing the barley genome.
Until sequences of the large cereal genomes become available
we will continue to use the smaller, sequenced rice and
Brachypodium distachyon genomes and take advantage of
the conservation in gene content and the order between these
smaller genomes, barley and wheat.
Salt tolerance
In a collaborative PhD student project with CSIRO Plant
Industry we are characterising the high affinity potassium
transporter (HKT)1;5 genes, which represent candidates for
the wheat Nax2 and Kna1 salinity tolerance loci. Curiously,
homologues of Bot1, ALMT1 and HKT1:5 genes were all
located in positions that were not co-linear between rice and
the target species, despite good overall levels of co-linearity
in the regions surrounding these loci. Further data will be
needed to determine if abiotic stress tolerance genes in
general tend to show less co-linearity across the cereals than
other classes of genes. Attractive candidate genes for QTL
controlling sodium exclusion were also identified. Two loci
are being examined in Arabidopsis and two in barley. The
respective candidates represent four different classes of genes.
Mapping for drought
and frost tolerance
Genetic mapping also plays an important role in dissecting
the multiple components of tolerance to drought and frost
during flowering. Differences in heading date can influence
both traits by allowing plants to avoid stress exposure. We
have identified a locus controlling heading date in the
vicinity of the reproductive frost tolerance QTL on barley
chromosome 2H, but preliminary results suggests there is also
a locus nearby conferring genuine frost tolerance. Likewise,
loci controlling heading date have been mapped in the
wheat drought mapping populations, but there are at least
some loci that also influence grain yield independently of
heading date in drought-affected field trials. Loci controlling
genuine drought and frost tolerance are of special interest and
represent potential targets for positional cloning.
36 2007 ACPFG ANNUAL REPORT

Education
Community Outreach
ACPFG was represented at dozens of community outreach
events in 2007, including a Siemens Science Day at
Roseworthy Campus, a presentation on careers in science at
North Ingle Primary School, a booth at the Royal Adelaide
Show and a booth at the University of Melbourne careers
fair. These events complemented “Get into Genes” sessions
around the country.
Hypothetical
Belinda Barr, Jenna Malone, Alex Smart and Heath White,
through their involvement in the Ausbiotech Students
Association (ABSA) committee, helped coordinate the event
‘Biotechnology means just working the lab’, a hypothetical,
held on the 28th March 2007. This event featured Maryanne
Demasi (ABC, Catalyst presenter/producer), Justin Coombs
(POF), Anne Collins and Ian Dry (CSIRO). More than 70
students attended and ACPFG provided $500 sponsorship
for this event.
Get into Genes (GiG)
Two new PCR stations have been developed for GiG.
These stations have been developed following requests
from teachers. Each station includes new posters, activities,
worksheets and a complementary power point presentation.
ARC Centre of Excellence in Plant Energy Biology signed a
licensing agreement and are now delivering GiG in Western
Australia. This is a positive collaboration and is part of the
national roll out of GiG. In May, the GiG team hosted 20
visiting Singaporean students at the University of Melbourne.
The Year 10 students and their teachers were on a 3-day
visit to the university and participated in tours, talks and
workshops in many science-related disciplines including
engineering, maths and various streams of science. The
GiG session “was one of the most successful aspects of the
program” and the students “raved about it for the rest of the
day”. The GiG evaluation has now been completed. The 68
page document has helped identify regions of value and
suggests some areas for improvement and growth to make
the product better.
Transformation Workshop
Lab to Land
ACPFG have collaborated with the ARC Centre for Plant
Energy Biology to develop a series of farmer workshops called
“Lab to Land”. The first of these sessions was held at Kadina
through the Rural Business Skills course administered by Rural
Skills, a training provider of PIRSA. It was then delivered in
Laura to 14 women doing the Rural Business Management
course with Rural Skills Training. The three hour workshop
received excellent feedback – the participants particularly
enjoyed seeing the male and female parts of wheat /
barley, the root smash experiment and the DNA extraction
experiment. Lab to Land was also presented to the South
Yarawonga Land Care Group, the Corowa Women’s Ag and
Chat Group, Rand Land Care group and the Yarawonga Ag
Group in July.
Hydro to Go
In collaboration with MPBCRC, we launched a new
pilot education package called ‘Hydro to Go’. This new
resource has been developed to link with the SACE stage
II Agriculture and Horticulture curriculum. The package
consists of a PowerPoint presentation that introduces the
concept of experimental design and scientific rigour. This is
complemented with a hydroponics kit that the schools can
purchase – the kit consists of Clipper and Sahara barley seeds,
ACPFG growth solution and two hydroponics tanks. Students
can then monitor the growth of the barley varieties under a
control, and treat and determine the effects of boron on plant
growth. After presenting this concept to teachers at the 2007
agricultural educators’ conference, there were more than 30
orders placed for the kit. ACPFG and MPBCRC sponsored the
conference held on the 15th and 16th of March at the Clare
Country Club.
Science Engagement and
Extension at a Distance
ACPFG and MPBCRC are involved in the Science Engagement
and Extension at a Distance project, through the Australian
Schools Innovation in Science, Technology and Mathematics
initiative. This involves linking regional schools with resources
in the metropolitan community. ACPFG contributes in-kind
education resources.
The 2007 Transformation Workshop was held from 16 to 20
July 2007, and was fully subscribed with 14 participants.
Several people indicated they would like to be notified early
for 2008 registration to ensure that they do not miss out.
2007 ACPFG ANNUAL REPORT
37

Student List
ADELAIDE PhD projects
Hassan, Mahmood A genomic approach to boron stress tolerance in wheat. 2003 Baumann, Sutton, Oldach
Jones, Craig Computational approaches to the functional annotation of expressed sequence tags (ESTs). 2003 Brown, Baumann
Richardson, Vanessa Ice recrystallisation inhibition protein characterisation in cereals exposed to cold stresses. 2003 Fincher, Langridge
Sheikh-Jabbari, Jafar Functional Analysis of novel genes involved in the interaction of Rhynchosporium secalis and barley. 2003 Langridge, Oldach
Carter, Scott Non specific cation channels of plants and yeast. 2004 Kaiser, Tester
Dolman, Fleur Functional characterisation of plant cytosolic thioredoxins. 2004 Baumann, Juttner, Comis
Drew, Damian Characterisation and functional analsys of putative salt tolerance genes, monodehydroascorbate reductase and PpENA1 from the moss,
Phsycomitrella patens 2004 Fincher, Tester, Hrmova
Elsden, Joanne Map based cloning of a malt quality QTL loci in Barley 2004 Chalmers, Collins, Langridge, Eglinton
Grace, Emily ‘The control of phosphate transport in barley by micchorizal infection…’ 2004 S.Smith, Tester, A.Smith
Ilanzoo, Ali Genomics of drought tolerance in Cereals. 2004 Langridge, Tester, Schnurbusch, Collins
Malone, Jenna Analysis of signal pathway protein-protein interactions in signal pathways shared by biotic and abiotic stresses. 2004 Oldach, Comis
Plett, Darren Cell specific manipulation of gene expression in rice to increase salinity tolerance. 2004 Tester, Jacobs, Johnson
Reinheimer, Jason Breeding for frost tolerance in winter cereals. 2004 Eglington, Collins
Rivandi, Alireza Cloning and the physiological characterisation of a sodium exclusion gene from barley. 2004 Collins, McDonald, Tester, Schnurbusch
Rusinova, Irina Discovery of functional relationships among genes using microarray data. 2004 Schreiber, Baumann
Tran, Michael Investigating the role of untranslated regions in mRNA that may be involved with stability translation and localisation in abiotic
stress. 2004 Schultz, Baumann
Byrt, Caitlin Salinity Tolerance in Durum Wheat. 2005 Tester, Munns
Chen, Andrew Positional Cloning of a reproductive frost tolerance gene on barley chromosome 2H. 2005 Collins, Fincher, Baumann
Edwards, James Genetic mapping of drought related traits in Hexaploid wheat. 2005 Schnurbusch, Langridge, Kuchel, Jefferies
Hall, Sharla Mapping QTL’s Associated with Root Traits in wheat. 2005 Huang, Schurbush
Lombardi, Maria Early vigour in cereal seedlings. 2005 Burton, Fincher
Morran, Sarah Characterisation of AP2 domain transcriptional factors from early wheat grain. 2005 Lopato, Langridge
Pillman, Katherine Transcription Factors Involved in Cold and Salt Tolerance in Barley and Arabidopsis. 2005 Jacobs, Langridge, Lepato
Smart, Alex Stress Response and Characterisation of the Thioredoxin h family in cereals. 2005 Juttner, Langridge
Student name Project title. Year commenced Supervisors
38 2007 ACPFG ANNUAL REPORT

Buchanan, Margaret Stem Strength Determinants in Cereal Crops. 2006 Fincher, Burton
Sundstrom, Joanna Regulation of HKT gene expression in plants. 2006 Tester, Cotsaftis, Roy
White, Heath Identification of Kinase Substrates in Critical Stress-Signalling Pathways and Modulated Expression for Improved Drought
Tolerance. 2006 Lopato, Juttner, Langridge
Bennett, Dion Drought and heat tolerance. 2007 Langridge, Schnurbusch
Dow, Michael Characterisation of transcription factors important in regulating salinity tolerance. 2007 Tester, Jacobs
Krishnan, Mahima Cell-specific expression of Sodium transporters in cereals. 2007 Jacobs, Tester, Johnson
Preuss, Christian Phosphorus use efficiency and drought resistance in wheat: Through an understanding of root traits. 2007 Huang, Schnurbusch, Tyerman
Rajendran, Karthika Mapping for salinity tolerance in Triticum monococcum. 2007 Roy, Tester
ADELAIDE Honours projects
Ramsey, Courtney Na+ exclusion and salinity tolerance – A comparison of hydroponics and field trials. 2007 Tester, Shavrukov
Tiong, Jingwen Functional characterization of barley ZIP7 zinc transporter. 2007 Huang
melbourne PhD projects
Widodo A proteomic study of barley root plasma membrane. 2004 Submitted 2007 Patterson, Bacic, Tester, Newbigin, Roessner
Dawei, Liu The study of the biology of abiotic stress in cereals using functional genomics. 2005 Bacic, Patterson
Susma, Ramesh Differential proteomic analysis of abscisic acid responses in rice. 2005 Bacic, Patterson
Bowne, Jairus The study of the metabolic response of cereals to abiotic stress. 2006 Bacic, Roessner
Erwin, Tim The development and application of bioinformatics tools for the analysis of high throughput metabolomic data. 2006 Bacic, Roessner, Likic
melbourne masters projects
Shah, Maria Ulfa Md Investigation of abiotic stress responses in Physcomitrella patens using metabolomics. 2006 Bacic, Roessner
melbourne Honours projects
Love, Charles “Changes in protein abundance after salt stress in barley”. 2007 Patterson, Bacic
Queensland PhD projects
Appleby, Nicola Identification and characterisation of molecular genetic markers from DNA sequence data. 2004 Edwards, Basford
Woon, Peter Genome diversity and response of organisms to environmental factors.
2006 Brusic, Basford
Duran, Chris The development and application of bioinformatics tools for the integration and analysis of crop genetic and genomic data. 2007 Edwards, Basford
Imelfort, Mike To establish and apply novel genome sequencing and assembly methods as well as novel genome annotation and interrogation tools, with
specific application to cereal genomes. 2007 Edwards, Basford
2007/2008 Summer scholarship students
Forrester, Jade The University of Adelaide Fleury
Golder, Helen The University of Adelaide Burton
McBride, Rebecca The University of Adelaide Roy
Shi, Jun Yan The University of Adelaide Hrmova
Wright, Jordan The University of Adelaide Lopato
Student name Project title. Year commenced Supervisors
2007 ACPFG ANNUAL REPORT
39

40 2007 ACPFG ANNUAL REPORT

Communication
Magazine
In 2007, issues 5 and 6 of Vector magazine were released
and distributed to a growing distribution list. More than 1000
hard copies of each issue were sent out, with a further 1000
distributed at events. Copies are also available on the website.
ACPFG’s Wheat and Barley booklet was finalised in February
and has filled a gap in ACPFG’s publications portfolio,
providing an overview of why and how ACPFG operates.
Posters
We launched a new promotional stand, which features five
research case studies, at the GRDC Crop Update at the
Adelaide Convention Centre in February. Stand alone posters
have been developed and experiment stations adjacent to
each poster covered hydroponics and boron, salinity and
drought root growth experiments.
Writing and editing training
ACPFG hosted two science editing workshops in 2007.
The March 8 workshop focused on the topic of editing for
science communicators, and was presented in collaboration
with Australian Science Communicators. Another workshop
on successful science writing and editing was held the
following day.
The 2006 Annual Report was completed and distributed
electronically to all Shareholders and Stakeholders on
March 31st.
Website
A design for a new ACPFG website was approved in 2007
and will be developed and launched in 2008.
DVD
Progress was made on the ACPFG promotional DVD, with
voiceovers completed by Dr Rob Morrison in April. Editing
and production of this DVD will take place in 2008.
World Conference of Science Journalists
ACPFG hosted a breakfast at the 5th World Conference
of Science Journalists in Melbourne, 16 to 19 April. The
conference brought together more than 600 science
journalists and communicators from around the world
to discuss issues relevant to science reporting and
communication. It also gave science organisations the
opportunity to present their research.
The breakfast featured three ACPFG scientists, Rachel Burton,
Darren Plett and James Edwards. It gave these scientists an
opportunity to brief 50 journalists from Australia and overseas
about their particular research areas. The briefings produced
many questions from the journalists and led to international
media coverage. Tony Bacic and John Patterson were also
interviewed by journalists at the conference through the
University of Melbourne booth. Eleven new ACPFG research
fact sheets were developed, with input from ACPFG scientists,
in time to be distributed at the conference.
Media releases in 2007
Australian scientists identify boron tolerance gene in barley
30 November
New research links made with Italy
30 October
Nitrogen-efficient wheat and barley – the ‘NUE’ thing.
11 October
When will we have a serious debate about GM?
24 August
Funding to secure Adelaide’s largest plant genetics
research centre
19 August
SA Government provides $6.3 million to further support
plant research
7 June
Vibha Agrotech Ltd. Hyderabad, India signs a research
agreement with Australian Centre for Plant Functional
Genomics, Adelaide
29 May
Drought – a challenge for farmers and scientists
25 January
2007 ACPFG ANNUAL REPORT
41

Publications
5. Able JA, Langridge P and Milligan AS. 2007. Capturing diversity
in the cereals: many options but little promiscuity. Trends in
Plant Science, 12(2): 71-79
6. Appleby N, Edwards D and Batley J. 2008. New technologies
for ultra-high throughput genotyping in plants. Ed. Somers D,
Langridge P, and Gustafson JP. Methods in Molecular Biology,
Humana Press (USA) In Press
7. Ayliffe MA, Pallotta M, Langridge P and Pryor AJ. 2007. A
Barley Activation Tagging System. Plant Mol. Biol. 64:329-47
8. Batley J and Edwards D. 2008. Mining for Single Nucleotide
Polymorphism (SNP) and Simple Sequence Repeat (SSR)
molecular genetic markers. Bioinformatics for DNA Sequence
Analysis. Ed. David Posada Methods in Molecular Biology,
Humana Press (USA) In press
9. Batley J and Edwards D. 2008. Bioinformatics: Fundamentals
and Applications in Plant Genetics and Breeding. Principles and
Practices of Plant Molecular Mapping and Breeding. Eds. Kole C
and Abbott AG. Science Publishers, Inc., (USA) In Press
10. Batley J, Hopkins CJ, Cogan NOI, Hand M, Jewell E, Kaur J,
Kaur S, Li X, Ling AE, Love C, Mountford H, Todorovic M, Vardy
M, Walkiewicz M, Spangenberg GC and Edwards D. 2007.
Identification and characterisation of Simple Sequence Repeat
(SSR) markers from Brassica napus expressed sequences.
Molecular Ecology Notes 7: 886-889
11. Batley J, Jewell E and Edwards D. 2007. Automated discovery
of Single Nucleotide Polymorphism (SNP) and Simple Sequence
Repeat (SSR) molecular genetic markers. Plant Bioinformatics.
Ed. Edwards D. Methods in Molecular Biology, Humana Press
(USA), pp. 473-494
12. Boden SA, Shadiac N, Tucker E, Langridge P and Able JA. 2007.
Expression and functional analysis of TaASY1 during meiosis of
bread wheat (Triticum aestivum). BMC Molecular Biology 8:65
13. Brownfield L, Ford K, Doblin M, Newbigin E, Read S and Bacic
A. 2007. Proteomic and biochemical evidence links the callose
synthase in Nicotiana alata pollen tubes to the product of the
NaGSL1 gene. Plant Journal 52, 147-156
14. Byrt CS, Platten JD, Spielmeyer W, James RA, Lagudah ES,
Dennis ES, Tester M and Munns R. 2007. HKT1;5-like cation
transporters linked to Na+ exclusion loci in wheat, Nax2 and
Kna1. Plant Physiology, 143, 1918-1928
15. Callahan DL, Roessner U, Dumontet V, Perrier N, Wedd AG,
O’Hair RAJ, Baker AJM and Kolev SD. 2008. LC-MS and
GC-MS metabolite profiling of nickel(II) complexes in the
latex of nickel-hyperaccumulating tree Sebertia acuminata and
identification of methylated aldaric acid as a new nickel(II)
ligand. Phytochemistry. In press
16. Chen Z, Pottosin II, Cuin TA, Funglsang AT, Tester M, Jha
D, Zepeda-Jazo I, Zhon M, Palmgren MG, Newman IA
and Shabala S. 2007. Root plasma membrane transporters
controlling K+/Na+ homeostasis in salt stressed barley. Plant
Physiology, 145 (4):1714-1725
17. Collins NC, Rients EN and Schulze-Lefert P. 2007. Resistance
to cereal rusts at the plant cell wall – what can we learn from
other host-pathogen systems? Australian Journal of Agricultural
Research, 58, 476 - 489
18. Collins NC, Shirley NJ, Saeed M, Pallotta M, Langridge P
and Gustafson JP. 2008. An ALMT1 Gene Cluster Controlling
Aluminium (Aluminum) Tolerance at the Alt4 Locus of Rye
(Secale cereale L.). Genetics. In press
19. Davenport RJ, Munoz-Mayor A, Jha D, Essah PA, Rus A and
Tester M. 2007. The Na+ transporter AtHKT1 controls xylem
retrieval of Na+ in Arabidopsis. Plant, Cell and Environment 30,
497-507
20. Drew DP, Lunde C, Lahnstein J and Fincher GB. 2007.
Heterologous expression of cDNAs encoding
monodehydroascorbate reductases from the moss,
Physcomitrella patens and charaterizations of the expressed
enzymes. Planta 225, 945-954
21. Duran C, Edwards D and Batley J. 2008. Genetic maps and
the use of synteny. Plant Genomics. Ed. Somers D, Langridge P,
and Gustafson JP. Methods in Molecular Biology, Humana Press
(USA) In Press
22. Edwards D. 2008. Bioinformatics. The World Wheat Book. Eds.
Bonjean A, Angus W and Van Ginkel M. Lavoisier (France) In
Press
23. Edwards D. 2008. Bioinformatics and plant genomics for staple
crops improvement. Breeding Major Food Staples for the 21st
Century. Eds. Kang MS and Priyadarshan PM. Blackwell. In Press
24. Farrokhi N, Hrmova M, Burton RA and Fincher GB. 2008.
Heterologous and Cell Free Protein Expression Systems. In:
Methods in Molecular Biology: Plant Genomics, Humana Press
Inc., Totowa, NJ, USA (Somers D, Langridge P, Gustafson P, eds).
Invited review. In Press
25. Genc Y, Huang CY and Langridge P. 2007. A study of the role
of root morphological traits in growth of barley in zinc-deficient
soil. Journal of Experimental Botany 58: 2775-2784
26. Genc Y, Langridge P and Huang C-Y. 2007. A study of the role
of root morphological traits on growth of barley in zinc-deficient
soil. Journal of Experimental Botany, doi:10.1093/jxb/erm142
27. Genc Y, McDonald GK and Tester M. 2007. Reassessment of
tissue Na+ concentration as a criterion for salinity tolerance in
bread wheat. Plant, Cell and Environment 30: 1486-1498
28. Glassop D, Roessner U, Bacic A and Bonnett G. 2007. Changes
in the sugarcane metabolome with stem development. Are
they related to sucrose accumulation? Plant Cell Physiol. 48,
573-584
29. Hrmova M and Fincher GB. 2007. Dissecting the catalytic
mechanism of a plant ß-D-glucan glucohydrolase through
structural biology using inhibitors and substrate analogues.
Invited review. Carbohydrate Research 342, 1613-1623
30. Hrmova M and Fincher GB. 2008. Functional genomics and
structural biology in the definition of gene function. In: Methods
in Molecular Biology: Plant Genomics, Humana Press Inc.,
Totowa, NJ, USA (Somers D, Langridge P, Gustafson P, eds).
Invited review. In Press
31. Hrmova M, Farkas V, Lahnstein J and Fincher GB. 2007. A
barley xyloglucan xyloglucosyl transferase covalently links
xyloglucan, cellulosic substrates and (1,3;1,4)-ß-D-glucans.
Journal of Biological Chemistry 282, 12951-12962
32. Imelfort M, Batley J, Grimmond S and Edwards D. 2008.
Genome sequencing approaches and successes. In: Plant
Genomics. Ed. Somers D, Langridge P, and Gustafson JP.
Methods in Molecular Biology, Humana Press (USA) In Press
33. Jacobs A, Lunde C, Bacic A, Tester M and Roessner U. 2007.
The impact of constitutive heterologous expression of a moss
Na+ transporter on the metabolomes of rice and barley.
Metabolomics3(3): 307-317
42 2007 ACPFG ANNUAL REPORT

34. Johnson AAT, Yu SM and Tester M. 2007. Activation tagging
systems in rice. In: Upadhyaya, NM., ed., ‘Rice Functional
Genomics: Challenges, Progress and Prospects’. Springer, pp.
333-353
35. Jones C, Brown A and Baumann U. 2007. Estimating the
annotation error rate of curated GO database sequence
annotations. BMC Bioinformatics. 2007.; 8: 170. Published
online 2007. May 22. doi: 10.1186/1471-2105-8-170. PMCID:
1892569
36. Kuchel H, Williams KJ, Langridge P, Eagles HA and Jefferies
SP. 2007. Genetic dissection of grain yield in bread wheat. I.
QTL analysis. Theor Appl Genet 115:1029-1041
37. Larmande P, Gay C, Lorieux M, Périn C, Bouniol M, Droc G,
Sallaud C, Perez P, Barnola I, Biderre-Petit C, Martin J, Morel
JB, Johnson AAT, Bourgis F, Ghesquière A, Ruiz M, Courtois B
and Guiderdoni E. 2008. Oryza Tag Line, a phenotypic mutant
database for the Genoplante rice insertion line library. Nucleic
Acids Research. In press
38. Lim GAC, Jewell EG, Li X, Erwin TA, Love C, Batley J,
Spangenberg G and Edwards D. 2007. A Comparative Map
Viewer Integrating Genetic Maps for Brassica and Arabidopsis.
BMC Plant Biology, 7: 40
39. Lloyd AH, Milligan AS, Langridge P and Able JA. 2007.
TaMSH7: A cereal mismatch repair gene that affects fertility in
transgenic barley (Hordeum vulgare L.) BMC Plant Biol. 7:67
40. Lopato S, Borisjuk L, Milligan AS, Shirley N, Bazanova N and
Langridge P. 2007. Systematic identification of factors involved
in post-transcriptional processes in wheat grain. Plant Mol Biol.
62; 637-653
41. Love CG and Edwards D. 2007. Accessing integrated Brassica
genetic and genomic data using the BASC server. Plant
Bioinformatics. Ed. Edwards D. Methods in Molecular Biology,
Humana Press (USA) (2007.), pp. 229-244
42. Lunde C, Drew D, Jacobs A and Tester M. 2007. Exclusion of
Na+ via a sodium ATPase (PpENA1) ensures normal growth
of Physcomitrella patens under moderate salt stress. Plant
Physiology 144: 1786-1796
43. Moller I, Sorensen I, Bernal AJ, Blaukopf C, Lee K, Øbro J,
Pettolino F, Roberts A, Mikkelsen JD, Knox JP, Bacic A and
Willats WGT. 2007. High-throughput mapping of cell wall
polymers within and between plants using novel microarrays.
Plant Journal 50, 1118-1128
44. Møller IS and Tester M. 2007. Salinity tolerance of Arabidopsis:
a good model for cereals? Trends in Plant Science 12: 534-540
45. Natera S, Ford K, Cassin A, Patterson J, Newbigin E and Bacic
A. 2008. Analysis of the Oryza sativa plasma membrane
proteome using combined protein and peptide fractionation
approaches in conjunction with mass spectrometry. Journal of
Proteome Research. In press
46. Paltridge N, Langridge P and Fincher GB. 2008. GM Wheat
and Barley 1: Genetics, reproductive biology and agronomic
considerations. Australian Institute of Agricultural Science and
Technology, (ed. Reuter D). In Press
47. Patterson J, Ford K, Cassin A, Natera and Bacic A. 2007.
Increased abundance of proteins involved in phytosiderophore
production in boron tolerant barley. Plant Physiology 144,
1612-1631
48. Périn C, Rebouillat J, Brasileiro AMC, Diévart A, Gantet P,
Breitler JC, Johnson AAT, Courtois B, Ahmadi N, de Raissac M,
Luquet D, Conte M, This D, Pati PK, Le QH, Meynard D, Verdeil
JL and Guiderdoni E. 2007. Novel insights into the genomics of
rice root adaptive development. In Brar DS, Mackill DJ, Hardy B
(Eds.) Rice Genetics V, Proceedings of the Fifth International Rice
Genomics Symposium (pp. 117-141). Los Banos, Philippines:
International Rice Research Institute
49. Reynolds MP, Saint Pierre C, Vargas M and Condon AG. 2008.
Evaluating potential genetic gains in wheat associated with
stress-adaptive trait expression in diverse germplasm under
drought and heat stress. Crop Science 48. In press
50. Roessner U and Pettolino F. 2008. The importance of anatomy
and physiology in plant metabolomics. In “Metabolomics”
of the book series Topics in Current Genetics, Jewett MC and
Nielson J, eds., Springer, Heidelberg, Germany. In press
51. Roessner-Tunali U. 2007. Uncovering the plant metabolome:
current and future challenges. Proceedings of the 3rd congress
on plant metabolomics. Nikolau B, ed, Springer, Dortrecht, The
Netherlands
52. Sanchez DH, Siahpoosh MR, Roessner U, Udvardi M and
Kopka J. 2008. Plant metabolomics reveals conserved and
divergent metabolic responses to salinity. Physiologia Plantarum.
132(2):209–219
53. Schnurbusch T, Huang C, Collins NC, Sutton T, John U, Roy S,
Paltridge N, Tester MA, Langridge P and Fincher GB. 2007.
GM Wheat and Barley II. Prospects for Enhanced Productivity
and Quality. Australian Institute of Agricultural Science and
Technology, (ed. Reuter D), 21; 4-11
54. Schnurbusch, T, Collins N, Eastwood R, Sutton T, Jefferies S
and Langridge P. 2007. Fine mapping and targeted SNP survey
using rice-wheat gene colinearity in the region of the Bo1 boron
toxicity tolerance locus of bread wheat. Theor. Appl. Genet.
115:451-61
55. Schreiber AW and Baumann U. 2007. A framework for gene
expression analysis. Bioinformatics. 2007. Jan 15;23(2):191-197
56. Shi B-J, Collins NC, Miftahudin, Schnurbusch T, Langridge P
and Gustafson JP. 2008. Construction of a rye cv. Blanco BAC
library, and progress towards cloning the rye Alt3 aluminium
(aluminum) tolerance gene. Vorträge für Pflanzenzüchtung. In
press
57. Singh K, Ghai M, Garg M, Chhuneja P, Schnurbusch T, Keller
B and Dhaliwal HS. 2007. An integrated molecular linkage
map of diploid wheat based on a Triticum boeoticum × T.
monococcum RIL population. Theor Appl Genetics 115:
301-312
58. Sutton T, Baumann U, Hayes J, Collins NC, Shi B-J,
Schnurbusch T, Hay A, Mayo G, Pallotta M, Tester M. and
Langridge P. 2007. Boron toxicity in barley arising from efflux
transporter amplification. Science, 318: 1446-1449
59. Tarpley L and Roessner U. 2007. Metabolomics: Enabling
systems-level phenotyping in rice functional genomics. In “Rice
Functional Genomics – Challenges, Progress and Prospects”,
Upadhyaya NM, ed., Springer, Heidelberg, Germany, pp 91-108
60. Tommasini L, Schnurbusch T, Mascher F, Fossati D and Keller
B. 2007. Association mapping and validation of Stagonospora
nodorum blotch resistance in modern European winter wheat.
Theor Appl Genet. 115: 697-708
61. Varshney R, Marcel, T, Ramsay L, Russell J, Roeder M, Stein
N, Waugh R, Langridge P, Niks R and Graner A. 2007. A high
density barley microsatellite consensus map with 775 SSR loci.
Theor. Appl. Genet. 114, 1091-1103
62. Varshney RK, Langridge P and Graner A. 2007. Application of
genomics for molecular breeding of wheat and barley. Advances
in Genetics, 58, 122-155
63. Villas-Boas SG, Roessner U, Hansen M, Smedsgaard J and
Nielsen J. 2007. Metabolome Analysis. An introduction.
Publ. Wiley and Sons, New Jersey, NJ, USA. ISBN:
978-0-471-74344-6, 311 pp
2007 ACPFG ANNUAL REPORT
43

Summary of Contributions
Summary of Contributions – 2007
Australian Research Council $124,724
Grains Research and Development Corporation $2,000,000
South Australian Government $750,000
University of Adelaide $1,250,000
University of Melbourne $100,000
University of Queensland $50,000
Total Grants Received $4,274,724
Other income
In 2007, funds deposited in the University of Adelaide Project Account earned
$141,717.50 and this was paid to Australian Centre for Plant Functional Genomics Pty Ltd.
The company also earned $2,488.56 in interest from funds deposited with the Adelaide Bank.
In-kind contributions received
aCTUal Original
South Australian Government* $500,000 $500,000
University of Adelaide $5,137,263 $2,666,663
University of Melbourne $833,268 $640,901
Victorian DPI $664,036 $916,065
University of Queensland $480,077 $263,671
Total In-kind contributions received $7,614,645 $4,987,299
* Agreed annual value of Plant Genomics Centre funding
44 2007 ACPFG ANNUAL REPORT

Contacts
Adelaide
University of Melbourne
La Trobe
University of Queensland
Plant Genomics Centre
Hartley Grove, Urrbrae SA 5064
Postal address:
PMB 1, Glen Osmond SA 5064
P: +61 8 8303 7423
F: +61 8 8303 7102
E: acpfg@acpfg.com.au
www.acpfg.com.au
Melbourne Node
Tony Bacic
School of Botany
University of Melbourne
Parkville Vic 3052
P: +61 3 8344 5041
F: +61 3 9347 1071
E: abacic@unimelb.edu.au
www.plantcell.unimelb.edu.au
La Trobe Node
German Spangenberg
Research Director, Plant Genetics
and Genomics
Primary Industries Research Victoria
Department of Primary Industries
Plant Biotechnology Centre
La Trobe University
R. L. Reid Building
Bundoora Vic 3086
Queensland Node
Kaye Basford
School of Land Food Sciences
The University of Queensland
Brisbane Qld 4072
P: +61 7 3365 2810
F: +61 7 3365 1177
E: k.e.basford@uq.edu.au
www.uq.edu.au/~agkbasfo
P: +61 3 9479 2995
F: +61 3 9479 3618
E: german.spangenberg@dpi.vic.gov.au
www.acpfg.com.au
Acronyms
ABARE Australian Bureau of Agricultural and Resource Economics
ACPFG Australian Centre for Plant Functional Genomics
AGT Australian Grain Technology
ANU Australian National University
ARC Australian Research Council
CGIAR Consultative Group on International Agricultural Research
CIMMYT International Centre for the Improvement of Wheat and Maize
CRC Cooperative Research Centre
CSIRO Commonwealth Scientific and Industrial Research Organisation
DNA Deoxyribonucleic acid
DREB dehydration responsive element binding
DHs doubled haploid lines
EU European Union
GRDC Grains Research and Development Corporation
GM genetic modification
HD-ZIP homeodomain-leucine zipper
ICARDA International Centre for Agricultural Research in the Dry Areas
IRIPs ice recrystallisation inhibition proteins
IRRI International Rice Research Institute
ITMI International Triticeae Mapping Initiative
LIEF Linkage, Infrastructure, Equipment and Facilities
MPBCRC Molecular Plant Breeding Cooperative Research Centre
mRNA messenger ribonucleic acid
NCRIS National Collaborative Research Infrastructure Strategy
OGTR Office of the Gene Technology Regulator
PCT Patent Cooperation Treaty
QPCR quantitative polymerase chain reaction
QTL quantitative trait loci
RILs recombinant inbred lines
RNA ribonucleic acid
ROS reactive oxygen species
SA South Australia
SARDI South Australian Research and Development Institute
SNP Single nucleotide polymorphism
SSR simple sequence repeat
TFs transcription factors
UA University of Adelaide
UM University of Melbourne
UniSA University of South Australia
UQ University of Queensland
Vic DPI Victorian Department of Primary Industries

A PrOGrAM initiAted By
the commonwealth Government of Australia
And fUnded By
the Australian research council
the Grains research and development corporation
SUPPOrt AlSO PrOvided By
the Government of South Australia
AdditiOnAl finAnciAl SUPPOrt frOM
the University of Adelaide
the University of Melbourne
the University of Queensland
reSeArcH PrOviderS
the University of Adelaide
the University of Melbourne
the University of Queensland
department of Primary industries, victoria
www.acpfg.com.au