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

    Varshney, R K and Beier, U and Khlestkina, K E and Kota, R and Korzun, V and Graner, A and Borner, A (2007) Single nucleotide polymorphisms in rye (Secale cereale L.): discovery, frequency, and applications for genome mapping and diversity studies. TAG Theoretical and Applied Genetics, 114. pp. 1105-1116.

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    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 (p) 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.

    Item Type: Article
    Divisions: UNSPECIFIED
    CRP: UNSPECIFIED
    Subjects: Others > Genetics and Genomics
    Depositing User: Library ICRISAT
    Date Deposited: 20 Oct 2011 10:59
    Last Modified: 08 May 2014 07:54
    URI: http://oar.icrisat.org/id/eprint/3026
    Official URL: http://dx.doi.org/10.1007/s00122-007-0504-6
    Projects: UNSPECIFIED
    Funders: UNSPECIFIED
    Acknowledgement: The authors thank Dr. Nils Stein, IPK, for his constructive suggestions during the course of study.
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