DOI QR코드

DOI QR Code

Development of Chloroplast Genome-based Insertion/Deletion Markers in the Genus Broussonetia

닥나무 속 식물의 엽록체 유전체 기반 InDel 마커의 개발

  • Eun Jee Lee (Department of Industrial Plant Science & Technology, Chungbuk National University) ;
  • Yoon A Kim (Department of Industrial Plant Science & Technology, Chungbuk National University) ;
  • Mi Sun Lee (Department of Industrial Plant Science & Technology, Chungbuk National University) ;
  • Ju Hyeok Kim (Department of Industrial Plant Science & Technology, Chungbuk National University) ;
  • Young Kyu Choi (Department of Forest Science, Chungbuk National University) ;
  • Jung Sung Kim (Department of Forest Science, Chungbuk National University) ;
  • Chang Seob Sin (Department of Forest Science, Chungbuk National University) ;
  • Yi Lee (Department of Industrial Plant Science & Technology, Chungbuk National University)
  • 이은지 (충북대학교 특용식물학과) ;
  • 김윤아 (충북대학교 특용식물학과) ;
  • 이미선 (충북대학교 특용식물학과) ;
  • 김주혁 (충북대학교 특용식물학과) ;
  • 최용규 (충북대학교 산림학과) ;
  • 김정성 (충북대학교 산림학과) ;
  • 신창섭 (충북대학교 산림학과) ;
  • 이이 (충북대학교 특용식물학과)
  • Received : 2022.11.01
  • Accepted : 2023.04.28
  • Published : 2023.08.01

Abstract

Several members of the genus Broussonetia are woody plants with high-quality cellulose fibers and are used to make a traditional type of Korean paper known as Hanji. Three of these species, Broussonetia kazinoki, Broussonetia monoica, and Broussonetia papyrifera, are found in the Korean Peninsula. Because it is challenging to distinguish different Broussonetia species based on morphology alone, we have developed a set of insertion/deletion (InDel) markers for genetic identification of these species. From twenty-two Broussonetia samples collected throughout Korea, we selected six for next-generation sequencing analysis. InDel marker candidates were identified by comparing this sequence information with the B. kazinoki chloroplast genome sequence. The marker candidates were used to screen the genomes of the twenty-two Broussonetia plants, and five useful chloroplast-based InDel markers were identified. Detailed genotyping using these five markers showed that the twenty-two plants of the genus Broussonetia could be clustered into five groups, verifying that the markers developed here can be used for breeding, identification, and analysis of species in the genus Broussonetia.

본 연구에서는 닥나무 속 식물에 대한 InDel 마커를 개발하였다. 전국의 닥나무 속 식물 22개체를 수집하였고, 수집한 닥나무 속 식물 중 6개체를 차세대염기서열 분석(NGS)을 실시하였다. NGS를 통하여 얻은 염기서열 정보를 기존에 발표되었던 닥나무 엽록체 서열과 비교하여 InDel 마커 후보를 선발하였다. 선발한 마커 후보를 수집된 닥나무 속 식물에 적용하여 마커의 특성 검정을 통해 총5개의 엽록체 기반 마커를 개발하였다. 개발된 InDel 마커를 22개의 유전자원에 적용한 후 군집 분석을 실시한 결과, 총5개의 그룹으로 나뉘었다. 본 연구에서 개발된 마커들은 닥나무 속의 육종이나 종 판별에 활용할 수 있을 것이라 판단된다.

Keywords

Acknowledgement

본 논문은 2022년도 교육부의 재원으로 한국연구재단의 지원을 받아 수행된 지자체-대학 협력기반 지역혁신 사업의 결과입니다.(2021RIS-001)

References

  1. Chang, C.S., H.L. Liu, X. Moncada, A. Seelenfreund, D. Seelenfreund and K.F. Chung. 2015. A holistic picture of Austronesian migrations revealed by phylogeography of Pacific paper mulberry. PNASU. 112(44):13537-13542. https://doi.org/10.1073/pnas.1503205112
  2. Chen, R., L. Chang, X. Cai, J. Wu, J. Liang, R. Lin, Y. Song and X. Wang. 2021. Development of InDel markers for Brassica rapa based on a high-resolution melting curve. Hortic. Plant J. 7(1):31-37. https://doi.org/10.1016/j.hpj.2020.05.003
  3. Chun, J.B., M.A. Jin, N.H. Jeong, C.O. Cho, M.S. Seo, M.S. Choi, D.Y. Kim, H.B. Sohn and Y.H. Kim. 2019. Genetic identification and phylogenic analysis of new varieties and 149 Korean cultivars using 27 InDel markers selected from dense variation blocks in soybean (Glycine max (L.) Merrill). Korean J. Plant Res. 32(5):519-542 (in Korean).
  4. Chung, K.F., W.H. Kuo, Y.H. Hsu, Y.H. Li, R.R. Rubite and W.B. Xu. 2017. Molecular recircumscription of Broussonetia (Moraceae) and the identity and taxonomic status of B. kaempferi var. australis. Bot. Stud. 58(1):11.
  5. Doyle, J.J. and J.L. Doyle. 1990. Isolation of plant DNA from fresh tissue. Focus 12:13-15.
  6. Go, I.H. and S.H. Jeong. 2018. Anatomical, morphological, and chemical characteristics of paper-mulberry wood and bast fiber for raw material of Korean paper (hanji). Journal of Conservation Science 34(6):517-524 (in Korean). https://doi.org/10.12654/JCS.2018.34.6.07
  7. Go, I.H., A.H. Jo, K.J. Jang, K.T. Park, S.M. Park, S.J. Park and S.H. Jeong. 2019. Molecular phylogenetic and dendrological study of paper-mulberry (B. kazinoki) in Gyeongsang-do region. Proceedings of the Plant Resources Society of Korea Conference 2019, The Plant Resources Society of Korea. p. 68 (in Korean).
  8. Jeong, H.J., J.B. Lee, J.S. Gil, C.P. Hong, S.H. Kang, S.J. Kwon, H.J. Kim, C.K. Kim, J.H. Lee and Y. Lee. 2021. Development of chloroplast-based InDel markers for the discrimination of Schisandraceae plant species. Korean Journal of Medicinal Crop Science 29(1):11-16 (in Korean). https://doi.org/10.7783/KJMCS.2021.29.1.11
  9. Kim, G.M., J.M. Chung, J.Y. Jung, H.J. Choi and S.Y. Lee. 2022a. Germination characteristics in seeds of Broussonetia kazinoki Siebold ex Siebold & Zucc (Moraceae) native to East Asia. Korean J. Plant Res. 35(1):36-43 (in Korean).
  10. Kim, J.H., D.W. Lee, M.K. Kim, M.S. Lee, N.S. Jo and Y. Lee. 2022b. Development of InDel markers to distinguish between Prunus mume, Prunus armeniaca var. ansu, and their interspecific hybrids. Korean Journal of Medicinal Crop Science 30(3):210-216 (in Korean). https://doi.org/10.7783/KJMCS.2022.30.3.210
  11. Kim, M.K., J.H. Kim, M.S. Lee, N.S. Jo, S.I. Park, J.S. Gil, E. Yeruult, H.K. Oh, K.H. Lee, H.B. Kim, M.S. Lee and Y. Lee. 2021. Development of insertion or deletion markers to distinguish Korean jujube cultivars. Korean Journal of Medicinal Crop Science 29(4):282-292 (in Korean). https://doi.org/10.7783/KJMCS.2021.29.4.282
  12. Kim, M.Y., T.J. Kim and S.T. Lee. 1992. A taxonomic study of the Korean Broussonetia (Moraceae) by multivariate analysis. Korean J. Plant Taxon. 22(4):241-254 (in Korean). https://doi.org/10.11110/kjpt.1992.22.4.241
  13. Kwon, Y.H. 2020. Paper and forest culture. Forest Culture Series No. 14. Society for Forests & Culture Publishing Co., Seoul, Korea. pp. 189-198 (in Korean).
  14. Liu, K. and S.V. Muse. 2005. PowerMarker: An integrated analysis environment for genetic marker analysis. Bioinformatics 21(9):2128-2129. https://doi.org/10.1093/bioinformatics/bti282
  15. Ohba, H. and S. Akiyama. 2014. Broussonetia (Moraceae) in Japan. Journal of Japanese Botany 89(3):123-128 (in Japanese).
  16. Pan, I.C., D.C. Liao, F.H. Wu, H. Daniell, N.D. Singh, C. Chang, M.C. Shih, M.T. Chan and C.S. Lin. 2012. Complete chloroplast genome sequence of an orchid model plant candidate: Erycina pusilla apply in tropical Oncidium breeding. PloS One 7(4):e34738.
  17. Park, S.I. 2021. Rooting characteristics of Broussonetia kazinoki according to auxin concentration and cuttings length by cutting time. Department of Forest Science, MS Thesis, Chungbuk National Univ., Korea. pp. 1-49 (in Korean).
  18. Park, S.I., K. Hwangbo, J.S. Gil, H. Chung, H.B. Kim, O.T. Kim, S.C. Kim, S.C. Koo, Y.R. U m and Y. Lee. 2017. Determination of the origin of angelica roots using Angelica gigas chloroplast based SSR markers. Korean Journal of Medicinal Crop Science 25(6):361-366 (in Korean). https://doi.org/10.7783/KJMCS.2017.25.6.361
  19. Penailillo, J., G. Olivares, X. Moncada, C. Payacan, C.S. Chang, K.F. Chung, P.J. Matthews, A. Seelenfreund and D. Seelenfreund. 2016. Sex distribution of paper mulberry (Broussonetia papyrifera) in the Pacific. PloS One 11(8):e0161148.
  20. Penailillo, J., W. Kuo, G. Olivares, G. Silva-Poblete, B. Pena-Ahumada, S. Munoz, X. Moncada, K.F. Chung, D. Seelenfreund and A. Seelenfreund. 2017. Characterization of microsatellite markers for Broussonetia papyrifera (Moraceae). Appl Plant Sci. 5(8):1700044.
  21. Pratiwi, I.R., Syamsuardi and Nurainas. 2021. Genetic relationships of mulberry (Morus L.) using internal transcribed spacer (ITS) markers. The International Journal of Social Sciences World 3(2):55-63.
  22. Wolfe, K.H., W.H. Li and P.M. Sharp. 1987. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. PNASU. 84(24):9054-9058. https://doi.org/10.1073/pnas.84.24.9054
  23. Won, H.S. 2019. Test of the hybrid origin of Broussonetia × kazinoki (Moraceae) in Korea using molecular markers. Korean J. Plant Taxon. 49(4):282-293. https://doi.org/10.11110/kjpt.2019.49.4.282
  24. Yun, K.W. and M. Kim. 2009. Taxonomic study of Broussonetia (Moraceae) in Korea. Korean J. Plant Taxon. 39(2):80-85. https://doi.org/10.11110/kjpt.2009.39.2.080