title: Single nucleotide polymorphisms in rye (Secale cereale L.): discovery, frequency, and applications for genome mapping and diversity studies.
abstract: To elucidate the potential of single nucleotide polymorphism (SNP) markers in rye, a set of 48 barley EST (expressed sequence tag) primer pairs was employed to amplify from DNA prepared from five rye inbred lines. A total of 96 SNPs and 26 indels (insertion-deletions) were defined from the sequences of 14 of the resulting amplicons, giving an estimated frequency of 1 SNP per 58 bp and 1 indel per 214 bp in the rye transcriptome. A mean of 3.4 haplotypes per marker with a mean expected heterozygosity of 0.66 were observed. The nucleotide diversity index (pi) was estimated to be in the range 0.0059-0.0530. To improve assay cost-effectiveness, 12 of the 14 SNPs were converted to a cleaved amplified polymorphic sequence (CAPS) format. The resulting 12 SNP loci mapped to chromosomes 1R, 3R, 4R, 5R, 6R, and 7R, at locations consistent with their known map positions in barley. SNP genotypic data were compared with genomic simple sequence repeat (SSR) and EST-derived SSR genotypic data collected from the same templates. This showed a broad equivalence with respect to genetic diversity between these different data types.
authors.affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany. r.k.varshney@cgiar.org
authors.forename: R K
authors.initials: RK
authors.lastname: Varshney
authors.forename: U
authors.initials: U
authors.lastname: Beier
authors.forename: E K
authors.initials: EK
authors.lastname: Khlestkina
authors.forename: R
authors.initials: R
authors.lastname: Kota
authors.forename: V
authors.initials: V
authors.lastname: Korzun
authors.forename: A
authors.initials: A
authors.lastname: Graner
authors.forename: A
authors.initials: A
authors.lastname: Börner
mesh_terms: D001483:Base Sequence / Q000235:genetics; D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D004262:DNA Restriction Enzymes / Q000378:metabolism; D018744:DNA, Plant; D020224:Expressed Sequence Tags; D005819:Genetic Markers; D014644:Genetic Variation; D018745:Genome, Plant; D006239:Haplotypes; D006579:Heterozygote; D008969:Molecular Sequence Data; D021141:Nucleic Acid Amplification Techniques; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D012434:Secale / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid; D013698:Templates, Genetic
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers; D010940:Plant Proteins; D004262:DNA Restriction Enzymes