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Genetic analysis of pungency deficiency in Japanese chili pepper ‘Shishito’ (Capsicum annuum) revealed its unique heredity and brought the discovery of two genetic loci involved with the reduction of pungency

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Abstract

The sensation of pungency generated by capsaicinoids is a characteristic trait of chili peppers (Capsicum spp.), and the presence or absence of pungency is central in determining its usage as a spice or a vegetable. In the present study, we aimed to clarify the heredity and genetic factors involved in the deficiency of pungency (quite low pungency) that is uniquely observed in the Japanese chili pepper ‘Shishito’ (Capsicum annuum). First, the F2 population (‘Shishito’ × pungent variety ‘Takanotsume’) was used for segregation analysis, and pungency level was investigated using capsaicinoid quantification with high-performance liquid chromatography. Also, restriction site associated DNA sequencing of the F2 population was performed, and genetic map construction and quantitative trait locus (QTL) mapping were implemented. The results indicated that the F2 population showed varying capsaicinoid content and two major QTLs were detected, Shql3 and Shql7, which explained 39.8 and 19.7% of the genetic variance, respectively. According to these results, the quite low pungency of ‘Shishito’ was a quantitative trait that involved at least the two loci. Further, this trait was completely separate from general non-pungent traits controlled by individual recessive genes, as described in previous studies. The present study is the first report to investigate the genetic mechanism of pungency deficiency in Japanese chili peppers, and our results provide new insights into the genetic regulation of pungency in chili pepper.

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Acknowledgements

This research was financially supported by Yawataya Isogoro Inc. and the Shinshu Foundation for Promotion of Agricultural and Forest Science. Computations were partially performed on the NIG supercomputer at ROIS National Institute of Genetics.

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Authors and Affiliations

  1. Department of Science and Technology, Graduate School of Medicine, Science and Technology, Shinshu University, Minamiminowa, Nagano, 399-4598, Japan

    Fumiya Kondo & Sathya Prabandaka Sudasinghe

  2. Japan Society for the Promotion of Science (JSPS), Kojimachi Business Center Building, 5-3-1 Kojimachi, Chiyoda-Ku, Tokyo, 102-0083, Japan

    Fumiya Kondo

  3. Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minamiminowa, Nagano, 399-4598, Japan

    Koyuki Umeda, Moe Yamaguchi, Shintaro Aratani & Yui Kumanomido

  4. Institute of Agriculture, Academic Assembly Faculty, Shinshu University, 8304 Minamiminowa, Nagano, 399-4598, Japan

    Kazuhiro Nemoto & Kenichi Matsushima

  5. Faculty of Agriculture, Ryukoku University, Yokotani 1-5, Seta, Ohe-Cho, Otsu, Shiga, 520-2194, Japan

    Atsushi J. Nagano

  6. Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Daihouji, Tsuruoka, Yamagata, 997-0017, Japan

    Atsushi J. Nagano

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  1. Fumiya Kondo
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  2. Koyuki Umeda
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  3. Sathya Prabandaka Sudasinghe
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  9. Kenichi Matsushima
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Correspondence to Kenichi Matsushima.

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Kondo, F., Umeda, K., Sudasinghe, S.P. et al. Genetic analysis of pungency deficiency in Japanese chili pepper ‘Shishito’ (Capsicum annuum) revealed its unique heredity and brought the discovery of two genetic loci involved with the reduction of pungency. Mol Genet Genomics 298, 201–212 (2023). https://doi.org/10.1007/s00438-022-01975-2

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