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      A large-scale collection of phenotypic data describing an insertional mutant population to facilitate functional analysis of rice genes

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          Abstract

          In order to facilitate the functional analysis of rice genes, we produced about 50,000 insertion lines with the endogenous retrotransposon Tos17. Phenotypes of these lines in the M 2 generation were observed in the field and characterized based on 53 phenotype descriptors. Nearly half of the lines showed more than one mutant phenotype. The most frequently observed phenotype was low fertility, followed by dwarfism. Phenotype data with photographs of each line are stored in the Tos17 mutant panel web-based database with a dataset of sequences flanking Tos17 insertion points in the rice genome (http://tos.nias.affrc.go.jp/). This combination of phenotypic and flanking sequence data will stimulate the functional analysis of rice genes.

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          Most cited references 27

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          Genome-wide insertional mutagenesis of Arabidopsis thaliana.

           J Alonso (2003)
          Over 225,000 independent Agrobacterium transferred DNA (T-DNA) insertion events in the genome of the reference plant Arabidopsis thaliana have been created that represent near saturation of the gene space. The precise locations were determined for more than 88,000 T-DNA insertions, which resulted in the identification of mutations in more than 21,700 of the approximately 29,454 predicted Arabidopsis genes. Genome-wide analysis of the distribution of integration events revealed the existence of a large integration site bias at both the chromosome and gene levels. Insertion mutations were identified in genes that are regulated in response to the plant hormone ethylene.
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            Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS.

            A major quantitative trait locus (QTL) controlling response to photoperiod, Hd1, was identified by means of a map-based cloning strategy. High-resolution mapping using 1505 segregants enabled us to define a genomic region of approximately 12 kb as a candidate for Hd1. Further analysis revealed that the Hd1 QTL corresponds to a gene that is a homolog of CONSTANS in Arabidopsis. Sequencing analysis revealed a 43-bp deletion in the first exon of the photoperiod sensitivity 1 (se1) mutant HS66 and a 433-bp insertion in the intron in mutant HS110. Se1 is allelic to the Hd1 QTL, as determined by analysis of two se1 mutants, HS66 and HS110. Genetic complementation analysis proved the function of the candidate gene. The amount of Hd1 mRNA was not greatly affected by a change in length of the photoperiod. We suggest that Hd1 functions in the promotion of heading under short-day conditions and in inhibition under long-day conditions.
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              GIBBERELLIN INSENSITIVE DWARF1 encodes a soluble receptor for gibberellin.

              Gibberellins (GAs) are phytohormones that are essential for many developmental processes in plants. It has been postulated that plants have both membrane-bound and soluble GA receptors; however, no GA receptors have yet been identified. Here we report the isolation and characterization of a new GA-insensitive dwarf mutant of rice, gid1. The GID1 gene encodes an unknown protein with similarity to the hormone-sensitive lipases, and we observed preferential localization of a GID1-green fluorescent protein (GFP) signal in nuclei. Recombinant glutathione S-transferase (GST)-GID1 had a high affinity only for biologically active GAs, whereas mutated GST-GID1 corresponding to three gid1 alleles had no GA-binding affinity. The dissociation constant for GA4 was estimated to be around 10(-7) M, enough to account for the GA dependency of shoot elongation. Moreover, GID1 bound to SLR1, a rice DELLA protein, in a GA-dependent manner in yeast cells. GID1 overexpression resulted in a GA-hypersensitive phenotype. Together, our results indicate that GID1 is a soluble receptor mediating GA signalling in rice.
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                Author and article information

                Contributors
                miyao@affrc.go.jp
                iwasaki@fpu.ac.jp
                hdkitano@nuagr1.agr.nagoya-u.ac.jp
                ajunito@mail.ecc.u-tokyo.ac.jp
                mmaekawa@rib.okayama-u.ac.jp
                kmurata@agri.pref.toyama.jp
                yatou@affrc.go.jp
                anagato@mail.ecc.u-tokyo.ac.jp
                hirohiko@affrc.go.jp
                Journal
                Plant Mol Biol
                Plant Molecular Biology
                Kluwer Academic Publishers (Dordrecht )
                0167-4412
                1573-5028
                19 December 2006
                March 2007
                : 63
                : 5
                : 625-635
                Affiliations
                [1 ]Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, 2-1-2, Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
                [2 ]Faculty of Bioscience, Fukui Prefectural University, 4-1-1, Kenjyojima, Matsuoka, Eiheiji-cho, Yoshida-gun, Fukui, 910-1195 Japan
                [3 ]Bioscience and Biotechnology Center, Nagoya University, Furocho, Chikusa, Nagoya, 464-8601 Japan
                [4 ]Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, 113-8657 Japan
                [5 ]Research Institute for Bioresources, Okayama University, Kurashiki, 710-0046 Japan
                [6 ]Agricultural Experiment Station, Toyama Agricultural Research Center, 1124-1 Yoshioka, Toyama, 939-8153 Japan
                [7 ]Rice Biotechnology Research Subteam, Hokuriku Research Center, National Agricultural Research Center (NARC), 1-2-1 Inada, Joetsu, Niigata, 943-0193 Japan
                Article
                9118
                10.1007/s11103-006-9118-7
                1805041
                17180734
                © Springer Science+Business Media B.V. 2006
                Categories
                Article
                Custom metadata
                © Springer Science+Business Media B.V. 2007

                Plant science & Botany

                retrotransposon, database, oryza sativa, insertion mutagenesis, phenotyping

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