Theoretical and Applied Genetics

, Volume 132, Issue 2, pp 515–529 | Cite as

A major QTL and candidate genes for capsaicinoid biosynthesis in the pericarp of Capsicum chinense revealed using QTL-seq and RNA-seq

  • Minjeong Park
  • Joung-Ho Lee
  • Koeun Han
  • Siyoung Jang
  • Jiwoong Han
  • Jung-Hyun Lim
  • Ji-Won Jung
  • Byoung-Cheorl KangEmail author
Original Article


Key message

A major QTL and candidate genes controlling capsaicinoid content in the pericarp were identified by QTL-seq and RNA-seq in Capsicum chinense.


Capsaicinoid biosynthesis was previously thought to be restricted to the placental tissue; however, the recent discovery of their biosynthesis in the pericarp provides new opportunities to increase the capsaicinoid content in pepper fruits. Currently, the genetic mechanisms regulating capsaicinoid biosynthesis in the pericarp remain unknown. Here, we performed quantitative trait loci (QTL) mapping and RNA sequencing (RNA-seq) to reveal the genes controlling capsaicinoid biosynthesis in the pericarp. A whole-genome sequencing-based QTL-seq strategy was employed, identifying a major QTL on chromosome 6. To validate the QTL on chromosome 6, we performed traditional QTL mapping using the same population in QTL-seq with an additional biparental population. A total of 15 QTLs for capsaicinoid content distributed on chromosomes 3, 6, and 11 were newly identified. Among these QTLs, the genetic loci on the lower arm of chromosome 6 were commonly detected in the two mapping populations, corresponding to the location of the major QTL detected using whole-genome sequencing-based QTL-seq. Our RNA-seq analysis identified candidate genes within the common QTL that were differentially expressed in the pungent and non-pungent pericarp tissues. Our results are expected to contribute to the elucidation of the regulation of capsaicinoid biosynthesis. We also demonstrated that a combination of QTL mapping and RNA-seq is helpful for refining the candidate genes of a complicated trait of interest.



This work was supported by the Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, and Forestry (IPET) through the Agriculture, Food, and Rural Affairs Research Center Support Program (Vegetable Breeding Research Center, 710011-03), funded by the Ministry of Agriculture, Food, and Rural Affairs (MAFRA). This work was carried out with the support of the Cooperative Research Program for Agriculture Science & Technology Development (Project No. PJ01327801), Rural Development Administration, Republic of Korea.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standards

The experiments were performed according to the laws of Germany.

Supplementary material

122_2018_3238_MOESM1_ESM.docx (3.5 mb)
Supplementary material 1 (DOCX 3623 kb)
122_2018_3238_MOESM2_ESM.xlsx (125 kb)
Supplementary material 2 (XLSX 124 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Minjeong Park
    • 1
  • Joung-Ho Lee
    • 1
  • Koeun Han
    • 1
  • Siyoung Jang
    • 1
  • Jiwoong Han
    • 1
  • Jung-Hyun Lim
    • 3
  • Ji-Won Jung
    • 3
  • Byoung-Cheorl Kang
    • 1
    • 2
    Email author
  1. 1.Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulRepublic of Korea
  2. 2.Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangRepublic of Korea
  3. 3.Research Institute of BiotechnologyCJ CheilJedang Corp.SuwonRepublic of Korea

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