The use of high resolution melting (HRM) to map single nucleotide polymorphism markers linked to a covered smut resistance gene in barley

• Published in: Theoretical and applied genetics 2008-09, Vol.117 (5), p.721-728
• Main Authors: Lehmensiek, Anke, Sutherland, Mark W., McNamara, Raymond B.
• Format: Article
• Language: English
• Subjects: Agriculture; Barley; Biochemistry; Biological and medical sciences; Biomedical and Life Sciences; Biotechnology; Chromosome Mapping - methods; Chromosomes, Plant; Classical genetics, quantitative genetics, hybrids; Expressed Sequence Tags; Fundamental and applied biological sciences. Psychology; Fungi; Genes, Plant; Genetic Linkage; Genetic Markers; Genetics of eukaryotes. Biological and molecular evolution; Genomes; Hordeum - genetics; Hordeum - microbiology; Immunity, Innate - genetics; Life Sciences; Methods, theories and miscellaneous; Original Paper; Phenotype; Plant Biochemistry; Plant Breeding/Biotechnology; Plant Diseases - genetics; Plant Diseases - microbiology; Plant Genetics and Genomics; Polymorphism; Polymorphism, Single Nucleotide; Pteridophyta, spermatophyta; Seeds; Ustilago; Vegetals
• ISSN: 0040-5752; 1432-2242
• DOI: 10.1007/s00122-008-0813-4

Using an established genetic map, a single gene conditioning covered smut resistance, Ruh.7H , was mapped to the telomere region of chromosome 7HS in an Alexis/Sloop doubled haploid barley population. The closest marker to Ruh.7H , abg704 was 7.5 cM away. Thirteen loci on the distal end of 7HS with potential to contain single nucleotide polymorphisms (SNPs) were identified by applying a comparative genomics approach using rice sequence data. Of these, one locus produced polymorphic co-dominant bands of different size while two further loci contained SNPs that were identified using the recently developed high resolution melting (HRM) technique. Two of these markers flanked Ruh.7H with the proximal marker located 3.8 cM and the distal marker 2.7 cM away. This is the first report on the application of the HRM technique to SNP detection and to rapid scoring of known cleaved amplified polymorphic sequence (CAPS) markers in plants. This simple, precise post-PCR technique should find widespread use in the fine-mapping of genetic regions of interest in complex cereal and other plant genomes.