Annual Report 2006

seems 300-350 and the increases of the genes
are strongly limited by selection pressures.
Especially the numbers of the pump system
genes are 70-170. This indicates that, the active
transport systems (= the system that operates
structure material concentration against a
physicochemical situations ) are strongly
controlled its working situations. Many of the
newly diverged genes of higher animals and
plants are channels and secondary transporters
works by adapting already existing
concentration gradients.
Phenotype catalog of
insertion mutants
Functional identification of rice genes is an
important target after whole genome sequencing
of rice. Gene disruption is one of the most
powerful methods for this purpose. The
endogenous retrotransposon in rice, ,is
only active in cultured cell, and is transposed
with copy and past manner. This
characteristic is suitable for gene disruption
system. Because the copy number of original
in japonica rice Nipponbare is two,
detection of newly transposed by
hybridization and isolation of flanking region of
are relatively easier than other highcopy
number of transposons. Furthermore,
because is an endogenous retrotransposon,
gene disruption line with is same as
spontaneous mutation lines for handling mutant
plants and is not under regulation of the
genetically modified organism (GMO). This
enables large scale phenotyping in the field.
Currently, more than 50,000 insertion lines have
been produced and stocked.
In the project of MAFF Isolation and
Functional Analysis of Useful Rice Genes and
Development of Techniques for Their Utilization,
large scale phenotyping proceeded with
collaboration of 7 laboratories for 3 years
project. From 1000 to 3000 lines were observed
in each laboratory for a year. It was difficult to
keep the quality of data without standard. We
chose standardized vocabularies for phenotyping.
Their consist 12 categories, germination,
growth, leaf color, leaf shape, culm shape, mimic
response, tillering, heading date, flower, panicle,
sterility, and seed. The categories were divided
into 53 sub category with phenotype ID
numbers for description more detailed
phenotypes. The phenotype ID system enables
to input phenotype data into barcode handy
terminal in the field. Even using the
standardized phenotyping system, personal
bias for observation is still remaining,
determination between dwarf and semi-dwarf
phenotypes, yellow green and pale green
phenotypes. To solve the personal bias
problem, photo images were also obtained in
the field. All phenotype data with phenotype ID
and photo images have been stored into webbased
relational database with PostgreSQL and
CGI script written in perl language.
Descriptions of special phenotypes were saved
into free style comment box. Phenotyping of
50,000 insertion lines is almost finished. Nearly
half of insertion lines showed at lease one
phenotype. Most frequently appeared
phenotype was dwarf and sterile (including
partial sterile). Pigmentation mutant also
relatively frequently appeared. For the low
frequency but characteristic phenotype,
narrow leaf, brittle culm, viviparous, abnormal
shoot, abnormal tillering, abnormal flower,
were observed. Isolation and characterization
of the responsible gene of these phenotypes will
be helpful to design new shape of rice for
improvement of photosynthesis, yield, resistance
of plant pathogens, etc.. Currently, more than
172,000 phenotype descriptions and 58,000
photo images are maintained with the relational
database and stored data is still growing. We
are also constructing the database for
disruption site by on the rice genome.
Mutant lines can be searched by BLAST
search (http://tos.nias.affrc.go.jp). When the
candidate of the knock-out line is detected,
phenotype description with photo images will
be listed. Seed of mutant lines is distributed by
rice genome resource center.
A major QTL,
for shattering habit in rice
Loss of seed shattering habit is one of the
critical events during domestication of rice
plant, because the easy-to-shatter trait in wild