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      YGL138(t), encoding a putative signal recognition particle 54 kDa protein, is involved in chloroplast development of rice

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          Abstract

          Background

          Normal development of chloroplast is vitally important to plants, but its biological mechanism is still far from fully being understood, especially in rice.

          Results

          In this study, a novel yellow-green leaf mutant, ygl138, derived from Nipponbare ( Oryza sativa L. ssp. japonica) treated by ethyl methanesulfonate (EMS), was isolated. The mutant exhibited a distinct yellow-green leaf phenotype throughout development, reduced chlorophyll level, and arrested chloroplast development. The phenotype of the ygl138 mutant was caused by a single nuclear gene, which was tentatively designed as YGL138( t). The YGL138( t) locus was mapped to chromosome 11 and isolated into a confined region of 91.8 kb by map-based cloning. Sequencing analysis revealed that, Os11g05552, which was predicted to encode a signal recognition particle 54 kDa (SRP54) protein and act as a chloroplast precursor, had 18 bp nucleotides deletion in the coding region of ygl138 and led to a frameshift. Furthermore, the identity of Os11g05552 was verified by transgenic complementation.

          Conclusions

          These results are very valuable for further study on YGL138( t) gene and illuminating the mechanism of SRP54 protein involving in chloroplast development of rice.

          Electronic supplementary material

          The online version of this article (doi:10.1186/1939-8433-6-7) contains supplementary material, which is available to authorized users.

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          Most cited references 53

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          MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations.

          With the advent of RFLPs, genetic linkage maps are now being assembled for a number of organisms including both inbred experimental populations such as maize and outbred natural populations such as humans. Accurate construction of such genetic maps requires multipoint linkage analysis of particular types of pedigrees. We describe here a computer package, called MAPMAKER, designed specifically for this purpose. The program uses an efficient algorithm that allows simultaneous multipoint analysis of any number of loci. MAPMAKER also includes an interactive command language that makes it easy for a geneticist to explore linkage data. MAPMAKER has been applied to the construction of linkage maps in a number of organisms, including the human and several plants, and we outline the mapping strategies that have been used.
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            CDD: a Conserved Domain Database for the functional annotation of proteins

            NCBI’s Conserved Domain Database (CDD) is a resource for the annotation of protein sequences with the location of conserved domain footprints, and functional sites inferred from these footprints. CDD includes manually curated domain models that make use of protein 3D structure to refine domain models and provide insights into sequence/structure/function relationships. Manually curated models are organized hierarchically if they describe domain families that are clearly related by common descent. As CDD also imports domain family models from a variety of external sources, it is a partially redundant collection. To simplify protein annotation, redundant models and models describing homologous families are clustered into superfamilies. By default, domain footprints are annotated with the corresponding superfamily designation, on top of which specific annotation may indicate high-confidence assignment of family membership. Pre-computed domain annotation is available for proteins in the Entrez/Protein dataset, and a novel interface, Batch CD-Search, allows the computation and download of annotation for large sets of protein queries. CDD can be accessed via http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml.
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              Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.).

              A total of 2414 new di-, tri- and tetra-nucleotide non-redundant SSR primer pairs, representing 2240 unique marker loci, have been developed and experimentally validated for rice (Oryza sativa L.). Duplicate primer pairs are reported for 7% (174) of the loci. The majority (92%) of primer pairs were developed in regions flanking perfect repeats > or = 24 bp in length. Using electronic PCR (e-PCR) to align primer pairs against 3284 publicly sequenced rice BAC and PAC clones (representing about 83% of the total rice genome), 65% of the SSR markers hit a BAC or PAC clone containing at least one genetically mapped marker and could be mapped by proxy. Additional information based on genetic mapping and "nearest marker" information provided the basis for locating a total of 1825 (81%) of the newly designed markers along rice chromosomes. Fifty-six SSR markers (2.8%) hit BAC clones on two or more different chromosomes and appeared to be multiple copy. The largest proportion of SSRs in this data set correspond to poly(GA) motifs (36%), followed by poly(AT) (15%) and poly(CCG) (8%) motifs. AT-rich microsatellites had the longest average repeat tracts, while GC-rich motifs were the shortest. In combination with the pool of 500 previously mapped SSR markers, this release makes available a total of 2740 experimentally confirmed SSR markers for rice, or approximately one SSR every 157 kb.
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                Author and article information

                Affiliations
                [ ]College of Life Sciences, Jiangxi Normal University, Nanchang, 330022 China
                [ ]Biotechnology Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200 China
                Contributors
                zhang84004@yahoo.com.cn
                xdluolf@163.com
                hubiaolin992@yahoo.com.cn
                Wanyong025@163.com
                jiankunxie@yahoo.com.cn
                Journal
                Rice (N Y)
                Rice (N Y)
                Rice
                Springer New York (New York )
                1939-8425
                1939-8433
                27 March 2013
                27 March 2013
                2013
                : 6
                43
                10.1186/1939-8433-6-7
                4883693
                24280537
                © Zhang et al.; licensee Springer. 2013

                This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                Categories
                Research
                Custom metadata
                © The Author(s) 2013

                Agriculture

                srp54 protein, oryza sativa l, yellow-green leaf mutant, chloroplast development

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