Journal article
Single nucleotide polymorphisms in rye (Secale cereale L.): discovery, frequency, and applications for genome mapping and diversity studies
Theoretical and Applied Genetics, Vol.114(6), pp.1105-1116
2007
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 (π) 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.
Details
- Title
- Single nucleotide polymorphisms in rye (Secale cereale L.): discovery, frequency, and applications for genome mapping and diversity studies
- Authors/Creators
- R.K. Varshney (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsU. Beier (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)E.K. Khlestkina (Author/Creator) - Siberian Branch of the Russian Academy of SciencesR. Kota (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)V. Korzun (Author/Creator) - Petkus (Germany)A. Graner (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)A. Börner (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)
- Publication Details
- Theoretical and Applied Genetics, Vol.114(6), pp.1105-1116
- Publisher
- Springer Verlag
- Identifiers
- 991005544715407891
- Murdoch Affiliation
- Murdoch University
- Language
- English
- Resource Type
- Journal article
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- Domestic collaboration
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- Citation topics
- 3 Agriculture, Environment & Ecology
- 3.4 Crop Science
- 3.4.96 QTL
- Web Of Science research areas
- Agronomy
- Genetics & Heredity
- Horticulture
- Plant Sciences
- ESI research areas
- Agricultural Sciences