Divergent phenotypes are often detected in domesticated plants despite the existence of invariant phenotypes in their wild forms. One such example in rice is the occurrence of varying degrees of apiculus coloration due to anthocyanin pigmentation, which was previously reported to be caused by a series of alleles at the C locus. The present study reveals, on the basis of comparison of its maps, that the C gene appears to be the rice homolog (OsC1) of maize C1, which belongs to the group of R2R3-Myb factors. Two different types of deletions causing a frameshift were detected in the third exon, and both of the deleted nucleotides corresponded to the positions of putative base-contacting residues, suggesting that the Indica and Japonica types carry loss-of-function mutations with independent origins. In addition, replacement substitutions were frequently detected in OsC1 of strains carrying the previously defined C alleles. Molecular population analysis revealed that 17 haplotypes were found in 39 wild and cultivated rices, and the haplotypes of most cultivated forms could be classified into one of three distinct groups, with few shared haplotypes among taxa, including Indica and Japonica types. The genealogy of the OsC1 gene suggests that allelic diversification causing phenotypic change might have resulted from mutations in the coding region rather than from recombination between preexisting alleles. The McDonald and Kreitman test revealed that the changes in amino acids might be associated with selective forces acting on the lineage of group A whose haplotypes were carried by most Asian cultivated forms. The results regarding a significant implication for genetic diversity in landraces of rice are also discussed.

Genetic engineering and functional analysis of genes in horticultural plants, including crops and floricultural plants have been a great challenge. Among strategies that aim to improve plant traits and analyze gene functions, there have been several successful applications to confer useful traits to plants by employing exogenous genes, such as genes encoding herbicide resistance (Comai and Shen 1983), pest resistance (Bates et al. 2005), and increased production of nutrients (Ye et al. 2000). Geneknockout or knockdown technology is major strategies for functional analysis of genes, and can confer new traits on plants. However, these techniques have various difficulties mainly due to genetic redundancy, polyploidy, and limited information of genomic or transcriptomic information. Although RNA interference (RNAi) effectively knocks down the expression of the targeted genes in model plants such as Arabidopsis thaliana and rice, it is difficult to apply this technology to horticultural plants because sequence information of the target gene is required. Furthermore, even if the technique is successfully applied, genetic redundancy of genes often compensates for the specific gene that has been knocked- Abstract Manipulation of horticultural plants' traits using genetic engineering has been a challenge because of gene redundancy and limited information concerning genome or other factors necessary for successful engineering. Recently we have developed a powerful tool with potential to overcome these difficulties, a novel gene silencing technology targeting transcription factor, which is designated Chimeric REpressor gene-Silencing Technology (CRES-T). Using this system, we are now analyzing biological functions of transcription factors in Arabidopsis and trying to manipulate morphological traits of various floricultural plants. To provide these information for genetic engineering of horticultural plants, we have developed the 'FioreDB' database in a web-based interface (http://www.cres-t.org/fiore/public_db/), which stores phenotypic information induced by various chimeric repressors in Arabidopsis and six floricultural plants, namely torenia, chrysanthemum, gentian, cyclamen, eustoma, morning glory. Users can find gene constructs that induce their preferred phenotype in Arabidopsis using simple searches, and can browse induced phenotypes in floricultural plants. Most phenotypic information has photo data. FioreDB is continually updated by addition of new data derived from the CRES-T analyses. FioreDB will help to improve traits of horticultural plants using the CRES-T system. FioreDB: a database of phenotypic information induced by the chimeric repressor silencing technology (CRES-T) in

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