Theoretical and Applied Genetics

, Volume 114, Issue 6, pp 1105–1116 | Cite as

Single nucleotide polymorphisms in rye (Secale cereale L.): discovery, frequency, and applications for genome mapping and diversity studies

  • R. K. Varshney
  • U. Beier
  • E. K. Khlestkina
  • R. Kota
  • V. Korzun
  • A. Graner
  • A. Börner
Original Paper


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.



The authors thank Dr. Nils Stein, IPK, for his constructive suggestions during the course of study.

Supplementary material

122_2007_504_MOESM1_ESM.doc (172 kb)
Table ESM 1: Details on genomic (gSSR) and EST-derived SSR (eSSR) marker loci used with the SNP markers for comparative assessment of diversity in rye (DOC 172 kb)


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Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  • R. K. Varshney
    • 1
    • 4
  • U. Beier
    • 1
  • E. K. Khlestkina
    • 2
  • R. Kota
    • 1
    • 5
  • V. Korzun
    • 3
  • A. Graner
    • 1
  • A. Börner
    • 1
  1. 1.Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
  2. 2.Institute of Cytology and GeneticsSiberian Branch of the Russian Academy of SciencesNovosibirskRussia
  3. 3.Lochow-Petkus GmbHEinbeckGermany
  4. 4.International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)PatancheruIndia
  5. 5.Plant Disease Resistance GroupCSIRO, Plant IndustryCanberraAustralia

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