ACPFG Annual Report

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