Horticultural Science & Technology (원예과학기술지)

Korean Society of Horticultural Science (한국원예학회)
권호 표지
DOI QR코드

DOI QR Code

A Database of Simple Sequence Repeat (SSR) Marker-Based DNA Profiles of Citrus and Related Cultivars and Germplasm

SSR Marker를 이용한 감귤속 품종 및 유전자원에 대한 DNA Profile Data Base 구축

  • Hong, Jee-Hwa (Experiment Research Institute, National Agricultural Products Quality Management Service, Ministry for Agriculture, Food & Rural Affairs) ;
  • Chae, Chi-Won (Jeju Office, Korea Seed & Variety Service, Ministry for Agriculture, Food & Rural Affairs) ;
  • Choi, Keun-Jin (Vegetable Research Center, National Institute of Horticultural & Herbal Science) ;
  • Kwon, Yong-Sham (Department of Genetic Engineering, College of Natural Resources and Life Science, Dong-A University)
  • 홍지화 (농림축산식품부 국립농산물품질관리원 시험연구소) ;
  • 채치원 (농림축산식품부 국립종자원 제주지원) ;
  • 최근진 (국립원예특작과학원 채소과) ;
  • 권용삼 (동아대학교 생명자원과학대학 유전공학과)
  • Received : 2015.08.31
  • Accepted : 2016.01.25
  • Published : 2016.02.29
Download PDF
⟨ Previous Next ⟩

Abstract

The present study investigated identification of cultivars through phylogenetic analysis of 108 Citrus varieties and related cultivars using simple sequence repeat (SSR) markers. Two hundred three SSR primer pairs were used to detect polymorphic markers among 8 Citrus cultivars consisting of 4 mandarins, 1 orange, 1 tangor, 1 tangelo, and 1 pumelo. Eighteen SSR primer pairs were reproducible and showed highly polymorphic alleles. These markers were applied to assess genetic variations of the 108 varieties. Each marker detected 5-14 alleles, with an average of 9.28. The polymorphism information content varied from 0.417 to 0.791 with an average of 0.706. Cluster analysis with SSR markers resulted in 13 major groups reflecting cultivar types and pedigree information. Twelve orange cultivars in the $I-1^{st}$ sub-cluster and 23 mandarin cultivars in the $II-1^{st}$ sub-cluster, respectively, were not discriminated using the SSR markers. This could be due to narrow genetic backgrounds originated through bud mutation or nucellars seedlings. The SSR profile database of Citrus cultivars will be useful as a tool for protection of plant breeders' intellectual property rights in addition to assessing genetic diversity in Citrus cultivars and germplasms.

국내외에서 재배되고 있는 감귤속 식물 108 품종 및 유전자원과 SSR 마커를 활용하여 유전적 유사도 분석을 통한 품종식별력 검정 등에 대한 연구를 수행하였다. 감귤 8품종을 203개의 SSR 마커로 검정하여 반복 재현성이 높은 뿐만 아니라 다형성 정도가 높은 18개를 선정하였다. 이들 마커와 국내외에서 재배되고 있는 감귤 108품종을 검정하였을 때 마커당 평균 대립유전자수는 9.28개로 나타났고, 5-14개까지 다양한 분포를 나타내었다. PIC 값은 분자표지에 따라 0.417-0.791 범위에 속하였으며 평균값은 0.606으로 나타났다. 감귤류 108품종에 대하여 계통도를 작성하였을 때 감귤류 식물의 분류학적 특성 및 품종 육성의 계보도에 따라 13개의 그룹으로 크게 나누어졌다. 감귤류 식물 품종중 오렌지나 온주 밀감의 경우 대부분의 품종이 SSR 마커의 유전자형에 의해 구분이 되지 않은 것으로 나타났다. 본 연구에서 개발된 감귤속 식물의 품종별 SSR DNA 프로파일 데이터베이스는 감귤속 식물의 유전자원 특성평가와 육종가의 지식재산권 보호의 수단으로 유용하게 활용될 수 있을 것이다.

Keywords

References

  1. Ahmad, R., D. Struss, and S. Southwick. 2003. Development and characterization of microsatellite markers in Citrus. J. Am. Soc. Hortic. Sci. 128:584-590.
  2. Al-Mouei, R. and W. Choumance. 2014. Assessment of genetic variability within the genus Citrus in Syria using SSR markers. Am. J. Exp. Agric. 4:939-950. https://doi.org/10.9734/AJEA/2014/8682
  3. Amar, M.H., M.K. Biswas, Z. Zhang, and W.W. Guo. 2011. Exploitation of SSR, SRAP and CAPS-SNP markers for genetic diversity of Citrus germplasm collection. Sci. Hortic. 128:220-227. https://doi.org/10.1016/j.scienta.2011.01.021
  4. Barkley, N.A., M.L. Roose, R.R. Krueger, and C.T. Federici. 2006. Assessing genetic diversity and population structure in a citrus germplasm collection utilizing simple sequence repeat markers (SSRs). Theor. Appl. Genet. 112:1519-1531. https://doi.org/10.1007/s00122-006-0255-9
  5. Chen, C., P. Zhou, Y.A. Choi, S. Huang, F.G. Gmitter Jr. 2006. Mining and characterizing microsatellites from citrus ESTs. Theor. Appl. Genet. 112:1248-1257. https://doi.org/10.1007/s00122-006-0226-1
  6. Federici, C.T., D.Q. Fang, R.W. Scora, and M.L. Roose. 1998. Phylogenetic relationships within the genus Citrus (Rutaceae) and related genera as revealed by RFLP and RAPD analysis. Theor. Appl. Genet. 96:812-822. https://doi.org/10.1007/s001220050807
  7. Hazarika, T.K., B.N. Hazarika, and A.C. Shukla. 2014. Genetic variability and phylogenetic relationships studies of genus Citrus L. with the application of molecular markers. Genet. Resour. Crop Evol. 61:1441-1454. https://doi.org/10.1007/s10722-014-0188-0
  8. Jannati, M., R. Fotouhi, A.P. Abad, and Z. Salehi. 2009. Genetic diversity analysis of Iranian citrus varieties using microsatellite (SSR) based markers. J. Hortic. For. 1:120-125.
  9. Kijas, J.M.H., M.R. Thomas, J.C.S. Fowler, and M.L. Roose. 1997. Integration of trinucleotide microsatellites into a linkage map of Citrus. Theor. Appl. Genet. 94:701-706. https://doi.org/10.1007/s001220050468
  10. Kim, Y.H., S.Y. Kawabata, and R.Z. Sakiyama. 1996. Classification of Citrus cultivars by using random amplified polymorphic DNA analysis. Korean J. Int. Agric. 8:155-159.
  11. Liu K. and S.M. Muse. 2005. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21: 2128-2129. https://doi.org/10.1093/bioinformatics/bti282
  12. Novelli, V.M., M. Cristofani, A.A. Souza, and M.A. Machado. 2006. Development and characterization of polymorphic microsatellite markers for the sweet orange (Citrus sinensis L. Osbeck). Genet. Mol. Biol. 29:90-96. https://doi.org/10.1590/S1415-47572006000100018
  13. Ollitrault, F., J. Terol, J.A. Pina, L.Navarro, M. Talon, and P. Ollitrault. 2010. Development of SSR markers from Citrus clementina (Rutaceae) BAC end sequences and interspecific transferability in Citrus. Am. J. Bot. e124-e129.
  14. Palmieri, D.A., V.M. Novelli, M. Bastianel, M. Cristofani-Yaly, G. Astua-Monge, E.F. Carlos, A.C. de Oliveira and M. A. Machado. 2007. Frequency and distribution of microsatellites from ESTs of citrus. Genet. Mol. Biol. 30:1009-1018. https://doi.org/10.1590/S1415-47572007000500029
  15. Rohlf, F.J. 2000. NTSYSpc: Numerical taxonomy and multivariate analysis system, ver. 2.10b. Applied Biostatistics Inc., New York.
  16. Sneath, P.H.A. and R.R. Sokal. 1973. Numerical taxonomy: The principles and practice of numerical classification, Freeman W.H., San Francisco.
  17. Swingle, W.T. and P.C. Reece. 1967. The botany of Citrus and its wild relative, p. 190-430. In: W. Reuther, H.J. Webber, and L.D. Batchelor (eds.). The Citrus Industry, Vol 1. University of California Press, Berkeley, USA.
  18. Tanaka, T. 1977. Fundamental discussion of Citrus classification. Stud. Citrologia 14:1-6.
  19. UPOV. 2010. UPOV/INF/17/1 Guideline for DNA-Profiling: Molecular Marker Selection and Database Construction ("BMT Guideline"), Geneva.

Cited by

  1. Identification of the ‘Haryejosaeng’ mandarin cultivar by multiplex PCR-based SNP genotyping vol.47, pp.11, 2016, https://doi.org/10.1007/s11033-020-05850-4
  2. Comparative Genetic Analysis between the Jeju ‘Inchangkyool’ and Chinese ‘Ichangensis’ (Citrus ichangensis) using Internal Chloroplast trnL-trnF Intergenic Spacers and Transcri vol.53, pp.1, 2016, https://doi.org/10.9787/kjbs.2021.53.1.16