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

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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.

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Acknowledgements

This work was supported by by a grant (GC1132-1) from the Crop Functional Genomics Center of the 21st Century Frontier Research Program and was also supported by the Technology Development Program (607004-05) for Agriculture and Forestry, Ministry for Agriculture, Forestry and Fisheries, Republic of Korea.

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  1. Department of Plant Science, Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences, Seoul National University, 599 Gwanak-ro, Gwank-gu, Seoul, 151-921, Korea

    Jin-kee Jung, Soung-Woo Park, Wing Yee Liu & Byoung-Cheorl Kang

  2. Research Institute and Experiment, National Agricultural Products Quality Management Service, Seoul, 150-043, Korea

    Jin-kee Jung

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  1. Jin-kee Jung
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Correspondence to Byoung-Cheorl Kang.

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Jin-Kee Jung and Soung-Woo Park equally contributed to this work.

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Jung, Jk., Park, SW., Liu, W.Y. et al. Discovery of single nucleotide polymorphism in Capsicum and SNP markers for cultivar identification. Euphytica 175, 91–107 (2010). https://doi.org/10.1007/s10681-010-0191-2

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