Annual Report 2006

One of the main problems involving
expression profiling is the high level of
variability in microarray data. Although some
of this variability is relevant because it
corresponds to the differential expression of
genes, a large portion of variability usually
results from undesirable biases introduced
during the many technical steps of the
experimental procedure. The so-called
experimental noise has been addressed to
normalize data according to the related effects.
Color swaps are now routinely included in
microarray experimental designs to correct for
labeling biases. The amount of samples for
successful hybridization has also been
investigated. Although it is normally suggested
that about 400 ng of total RNA should be used
for labelling, the amount of sample could be
reduced to 10 ng of total RNA with almost
similar expression intensity for highly and
medium expressed genes. Reducing the amount
of samples to 2 ng also gave a clear expression
pattern. This indicates that the microarray
could be used for analysis of small samples of
RNA derived from tissues or organs, specific
tissues isolated by laser dissection or transient
assay in cell culture (Fig. 5).
The microarray open laboratory has been
used by almost 247 research groups from
different institutes and universities all over
Japan since it became operational in August 1,
2003. Currently, an average of two users/
groups per week use the facilities. In addition to
the rice microarray, the RGRC open laboratory
also supports microarray analysis in ,
silkworm and cow.
G enome Diversity Department
The objectives of the Genetic Diversity
Department are to conduct basic research into
plant, animal and microorganism diversity from
the molecular to the population level. Such
research contributes to the development of
new and improved methods for classification,
characterization and preservation of germplasm
and discovery of new biological resources for
use in agriculture and other industries.
Current plant research includes molecular
and biological characterization and evaluation
of the genera Hordeum,
and Mechanisms in
plants that confer cold hardiness are also being
investigated. Microbiological research includes
functional genomics, biosystematics and
proteomics of such organisms as fungi, yeasts
and bacteria. In particular, plant pathogens
have been focused on. Animal research includes
the development of the methods to utilize
various types of germplasm and to improve the
genetic performance of domestic animals.
Major research outputs of the department
except for Topics of Research during fiscal
2005 are described below.
Very close relationship of the
chloroplast genomes among
species
We recently determined the complete
sequence of the sugarcane chloroplast genome.
Here, we have used the information for a
comprehensive phylogenetic analysis of the
genus using all six species (13
accessions). The polymorphisms between
sugarcane and maize in 26 chloroplast genome
regions were used for the analysis. In 18 of the
26 regions (a total of 5,381 bp), we found 41
mutations involving 17 substitutions, three
inversions, six insertion/deletion mutations, and
15 simple sequence repeat length polymorphisms.
Based on these results, we calculated a
phylogenetic tree of the genus Saccharum, in
which all six species are clearly separated (Fig.
1). By the analysis, (1) and
which have identical sequences, belong to the
same clade, whereas the other four species,