Fine mapping and syntenic integration of the semi-dwarfing gene sdw3 of barley

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dc.contributor.author Chandler, Peter M.
dc.contributor.author Graner, Andreas
dc.contributor.author Buchmann, Jan P.
dc.contributor.author Wicker, Thomas
dc.contributor.author Stein, Nils
dc.contributor.author Matsumoto, Takashi
dc.contributor.author Vu, Giang T. H.
dc.date.accessioned 2011-06-01T07:48:32Z
dc.date.available 2011-06-01T07:48:32Z
dc.date.issued 2010-11
dc.identifier.citation Chandler , P M , Graner , A , Buchmann , J P , Wicker , T , Stein , N , Matsumoto , T & Vu , G T H 2010 , ' Fine mapping and syntenic integration of the semi-dwarfing gene sdw3 of barley ' Functional and Integrative Genomics , vol 10 , no. 4 , pp. 509-521 . en
dc.identifier.issn 1438-7948
dc.identifier.other PURE: 162699
dc.identifier.other dspace: 2160/6849
dc.identifier.uri http://hdl.handle.net/2160/6849
dc.description Vu, G.T.H., Wicker, T., Buchmann, J.P., Chandler, P.M., Matsumoto, T., Graner, A., Stein, N. (2010). Fine mapping and syntenic integration of the semi-dwarfing gene sdw3 of barley.   Functional and Integrative Genomics, 10,(4), 509-521. IMPF: 03.39 Sponsorship: Wellcome Trust (WT084273; WT078317); Sandler Center for Basic Research in Parasitic Diseases; WAG Academic Expertise for Business (A4B) en
dc.description.abstract The barley mutant allele sdw3 confers a gibberellin-insensitive, semi-dwarf phenotype with potential for breeding of new semi-dwarfed barley cultivars. Towards map-based cloning, sdw3 was delimited by high-resolution genetic mapping to a 0.04 cM interval in a “cold spot” of recombination of the proximal region of the short arm of barley chromosome 2H. Extensive synteny between the barley Sdw3 locus (Hvu_sdw3) and the orthologous regions (Osa_sdw3, Sbi_sdw3, Bsy_sdw3) of three other grass species (Oryza sativa, Sorghum bicolor, Brachypodium sylvaticum) allowed for efficient synteny-based marker saturation in the target interval. Comparative sequence analysis revealed colinearity for 23 out of the 38, 35, and 29 genes identified in Brachypodium, rice, and Sorghum, respectively. Markers co-segregating with Hvu_sdw3 were generated from two of these genes. Initial attempts at chromosome walking in barley were performed with seven orthologous gene probes which were delimiting physical distances of 223, 123, and 127 kb in Brachypodium, rice, and Sorghum, respectively. Six non-overlapping small bacterial artificial chromosome (BAC) clone contigs (cumulative length of 670 kb) were obtained, which indicated a considerably larger physical size of Hvu_sdw3. Low-pass sequencing of selected BAC clones from these barley contigs exhibited a substantially lower gene frequency per physical distance and the presence of additional non-colinear genes. Four candidate genes for sdw3 were identified within barley BAC sequences that either co-segregated with the gene sdw3 or were located adjacent to these co-segregating genes. Identification of genic sequences in the sdw3 context provides tools for marker-assisted selection. Eventual identification of the actual gene will contribute new information for a basic understanding of the mechanisms underlying growth regulation in barley. en
dc.format.extent 13 en
dc.language.iso eng
dc.relation.ispartof Functional and Integrative Genomics en
dc.title Fine mapping and syntenic integration of the semi-dwarfing gene sdw3 of barley en
dc.type Text en
dc.type.publicationtype Article (Journal) en
dc.identifier.doi http://dx.doi.org/10.1007/s10142-010-0173-4
dc.contributor.institution Aberystwyth University en
dc.contributor.institution Institute of Biological, Environmental and Rural Sciences en
dc.description.status Peer reviewed en


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