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    Discovery of single nucleotide polymorphism in Capsicum and SNP markers for cultivar identification

    Access Status
    Fulltext not available
    Authors
    Jung, J.
    Park, S.
    Liu, Wing Yee
    Kang, B.
    Date
    2010
    Type
    Journal Article
    
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    Citation
    Jung, J. and Park, S. and Liu, W.Y. and Kang, B. 2010. Discovery of single nucleotide polymorphism in Capsicum and SNP markers for cultivar identification. Euphytica. 175 (1): pp. 91-107.
    Source Title
    Euphytica
    DOI
    10.1007/s10681-010-0191-2
    ISSN
    0014-2336
    School
    Centre for Crop Disease Management
    URI
    http://hdl.handle.net/20.500.11937/30363
    Collection
    • Curtin Research Publications
    Abstract

    Molecular markers based on single nucleotide polymorphisms (SNPs) are abundant and evenly distributed in a whole genome enough to distinguish individuals in a population. In recent years, sets of SNP markers have been designed and applied for cultivar identification in various crop species. This paper is the first to report the development of a panel of SNP markers for variety identification in peppers. We used conserved ortholog set II (COSII) markers developed from conserved unigenes between tomato and Arabidopsis to identify SNPs in peppers. We tested 438 COSII primer sets amplified as single PCR products out of a total 600 COSII primer sets. Among the 438 COSII primers, 170 primer sets (38.8%) showed polymorphisms between Capsicum annuum 'RNaky (RN)'and C. chinense 'PI 159234 (234)'. In contrast, only 48 primer sets (11.0%) out of 438 primers sets were polymorphic between C. annuum 'Perennial (PER), and 'Dempsey (DEMP)'. The average frequency of SNPs plus InDels between C. annuum and C. chinense was 1/189 bp and between C. annuum spp. was 1/948 bp. Primer sets showing SNP between C. annuum PER and DEMP were re-designed to Allele Specific PCR (AS-PCR) primers and we finally selected a total of 40 SNP markers for cultivar identification. As the result, we were able to discriminate 97.5% of the 81 commercial hot cultivars and 100% of the 17 sweet pepper cultivars. We conclude the paper by discussing the use of the SNP marker set for cultivar identification and other applications. © 2010 Springer Science+Business Media B.V.

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