Journal of Ginseng Research

The Korean Society of Ginseng (고려인삼학회)
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Molecular discrimination of Panax ginseng cultivar K-1 using pathogenesis-related protein 5 gene

  • Wang, Hongtao (School of Life Sciences, Yantai University) ;
  • Xu, Fengjiao (School of Life Sciences, Yantai University) ;
  • Wang, Xinqi (School of Life Sciences, Yantai University) ;
  • Kwon, Woo-Saeng (Graduate School of Biotechnology and Ginseng Bank, College of Life Sciences, Kyung Hee University) ;
  • Yang, Deok-Chun (Graduate School of Biotechnology and Ginseng Bank, College of Life Sciences, Kyung Hee University)
  • Received : 2018.04.20
  • Accepted : 2018.07.04
  • Published : 2019.07.15
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Abstract

Background: The mixed-cultivation of different Panax ginseng cultivars can cause adverse effects on stability of yield and quality. K-1 is a superior cultivar with good root shape and stronger disease resistance. DNA markers mined from functional genes are clearly desirable for K-1, as they may associate with major traits and can be used for marker-assisted selection to maintain the high quality of Korean ginseng. Methods: Five genes encoding pathogenesis-related (PR) proteins of P. ginseng were amplified and compared for polymorphism mining. Primary, secondary, and tertiary structures of PR5 protein were analyzed by ExPASy-ProtParam, PSSpred, and I-TASSER methods, respectively. A coding single nucleotide polymorphism (SNP)-based specific primer was designed for K-1 by introducing a destabilizing mismatch within the 3' end. Allele-specific polymerase chain reaction (PCR) and real-time allele-specific PCR assays were conducted for molecular discrimination of K-1 from other cultivars and landraces. Results: A coding SNP leading to the modification of amino acid residue from aspartic acid to asparagine was exploited in PR5 gene of K-1 cultivar. Bioinformatics analysis showed that the modification of amino acid residue changed the secondary and tertiary structures of the PR5 protein. Primer KSR was designed for specific discrimination of K-1 from other ginseng cultivars and landraces. The developed real-time allele-specific PCR assay enabled easier automation and accurate genotyping of K-1 from a large number of ginseng samples. Conclusion: The SNP marker and the developed real-time allele-specific PCR assay will be useful not only for marker-assisted selection of K-1 cultivar but also for quality control in breeding and seed programs of P. ginseng.

Keywords

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  1. Characteristics of Panax ginseng Cultivars in Korea and China vol.25, pp.11, 2019, https://doi.org/10.3390/molecules25112635