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

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 prox...

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Bibliographic Details
Published in:	Functional & integrative genomics 2010-11, Vol.10 (4), p.509-521
Main Authors:	Vu, Giang T. H, Wicker, Thomas, Buchmann, Jan P, Chandler, Peter M, Matsumoto, Takashi, Graner, Andreas, Stein, Nils
Format:	Article
Language:	eng
Subjects:	Animal Genetics and Genomics Barley Base Sequence Biochemistry Bioinformatics Biological and medical sciences Biomedical and Life Sciences Brachypodium Brachypodium - genetics Brachypodium sylvaticum CAPS markers Cell Biology Chromosome Mapping chromosome walking Chromosomes Chromosomes, Artificial, Bacterial Chromosomes, Plant Comparative mapping Fundamental and applied biological sciences. Psychology General aspects Genes, Plant Genetic Markers Genome synteny Genome, Plant Genomics Genotype Gibberellic acid (GA₃) Gibberellin (GA) insensitivity Gibberellins - pharmacology Hordeum - genetics Hordeum vulgare Life Sciences Map-based cloning Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Microbial Genetics and Genomics Molecular Sequence Data Original Paper Oryza - genetics Oryza sativa Plant Genetics and Genomics Plant growth Plant Growth Regulators - pharmacology Polymorphism, Genetic Seedlings - drug effects Seedlings - physiology Sorghum Sorghum - genetics Sorghum bicolor Synteny
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Summary:	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.
ISSN:	1438-793X 1438-7948