K. EXPERIMENTAL FARM

RESEARCH ACTIVITIES

--Experimaental Farm is responsible for preparation of all kinds of rice strains necessary for the studies of genetic resources and of functional genomics. All works in the Experimental Farm have been carried out as collaborative works with the Plant Genetics Lab. For details, see the reports of plant genetics lab.

(1) Examination of genetic and phenotypic nature of newly prepared core collections for wild rice comparative genomics

Toshie Miyabayashi, Mitsugu Eiguchi, Ken-Ichi Nonomura and Nori Kurata

--For making rice genetic stocks good resources, we developed core collection of wild rice. Out of 2,000 accessions composed of twenty-one wild rice species in nine genomes, several accessions from each species were selected to prepare core collection. About 300 selected lines had already sub-grouped to Rank1, Rank2 and Rank3 categories, and a part of them were characterized for their phenotypes to record them in the Oryzabase, a rice comprehensive database.
--Comparative genomics among nine rice genomes will reveal important aspects on evolution and genetic diversity in rice. For finding out genome specific genes or far-related genes different from AA, comparison of BB and CC genome species with the cultivated AA species have been started. Searches for structural and functional diversity between genes of different genomes are performed by cDNA clone sequencing and by microarray expression profile analysis. Some details obtained in 2004 were presented in the report of Plant Genet. Lab.
--In addition, to estimate genome sizes of each genome and species, strains in the core collection were examined for their DNA content by the simple flow-cytometric analysis. Differences of DNA content among genomes and among species would give some relationships to the molecular nature of genetic diversity.

PUBLICATIONS

Papers
1. Miyoshi, K., Ahn, B-O., Kawakatsu, T., Ito, Y., Itoh, J-I., Nagato, Y. and Kurata, N. (2004). PLASTOCHRON1, a timekeeper of leaf initiation in rice, encodes cytochrome P450. Proc. Natl. Acad. Sci. USA 101, 875-880.
2. Ito, Y., Chujo, A., Eiguchi, M. and Kurata, N. (2004). Radial axis differentiation in a globular embryo is marked by HAZ, a PHD-finger homeobox gene of rice. Gene 331, 9-15.
3. Nonomura, K.I., Nakano, M., Murata, K., Miyoshi, K., Eiguchi, M., Miyao, A., Hirochika, H. and Kurata, N. (2004). The insertional mutation of rice PAIR2 gene, the ortholog of Arabidopsis ASY1, caused a defect in homologous chromosome pairing in meiosis. Mol. Genet. Genomics 271, 121-129.
4. Nonomura, K.I., Nakano, M., Fukuda, T., Eiguchi, M., Miyao, A., Hirochika, H. and Kurata, N. (2004). The novel gene HOMOLOGOUS PAIRING ABERRATION IN RICE MEIOSIS 1 of rice encodes a putative coiled-coil protein required for homologous chromosome pairing in meiosis. Plant Cell 16, 1008-1020.
5. Salina, E.A., Adonina, I., Vatolina, T. and Kurata, N. (2004). A comparative analysis of the composition and organization of two subtelomeric repeat families of Aegilops speltoides Tausch.and related species. Genetica 122, 227-237.
6. Moriguchi, K., Suzuki, T., Ito, Y., Yamazaki, Y., Niwa, Y. and Kurata, N. (2005). Functional isolation of novel nuclear proteins showing a variety of sub-nuclear localizations. Plant Cell, 17, 389-403.

Reviews
7. Itoh, J.I., Nonomura, K.I., Ikeda, K., Yamaki, S., Inukai, Y., Yamagishi, H., Kitano, H. and Nagato, Y. (2005). Rice plant development: from zygote to spikelet. Plant Cell Physiol. 46, 23-47.
8. Kurata, N., Miyoshi, K., Nonomura, K.I., Yamazaki, Y. and Ito Y. (2005). Rice mutants and genes related to organ development, morphogenesis and physiological traits. Plant Cell Physiol. 46, 48-62.