Article | 02. 2016 Vol. 34, Issue. 1
A Database of Simple Sequence Repeat (SSR) Marker-Based DNA Profiles of Citrus and Related Cultivars and Germplasm



Experiment Research Institute, National Agricultural Products Quality Management Service, Ministry for Agriculture, Food & Rural Affairs1
Jeju Office, Korea Seed & Variety Service, Ministry for Agriculture, Food & Rural Affairs2
Vegetable Research Center, National Institute of Horticultural & Herbal Science3
Department of Genetic Engineering, College of Natural Resources and Life Science, Dong-A University4




2016.02. 142:153


PDF XML




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-1st sub-cluster and 23 mandarin cultivars in the II-1st 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.



1. Ahmad, R., D. Struss, and S. Southwick. 2003. Development and characterization of microsatellite markers in . J. Am. Soc. Hortic. Sci. 128:584-590.  

2. Al-Mouei, R. and W. Choumance. 2014. Assessment of genetic variability within the genus in Syria using SSR markers. Am. J. Exp. Agric. 4:939-950.  

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 germplasm collection. Sci. Hortic. 128:220-227.  

4. Barkley, N.A., M.L. Roose, R.R. Krueger, and C.T. Federici. 2006. Assessing genetic diversity and population structure in a germplasm collection utilizing simple sequence repeat markers (SSRs). Theor. Appl. Genet. 112:1519-1531.  

5. Chen, C., P. Zhou, Y.A. Choi, S. Huang, F.G. Gmitter Jr. 2006. Mining and characterizing microsatellites from ESTs. Theor. Appl. Genet. 112:1248-1257.  

6. Federici, C.T., D.Q. Fang, R.W. Scora, and M.L. Roose. 1998. Phylogenetic relationships within the genus (Rutaceae) and related genera as revealed by RFLP and RAPD analysis. Theor. Appl. Genet. 96:812-822.  

7. Hazarika, T.K., B.N. Hazarika, and A.C. Shukla. 2014. Genetic variability and phylogenetic relationships studies of genus L. with the application of molecular markers. Genet. Resour. Crop Evol. 61:1441-1454.  

8. Jannati, M., R. Fotouhi, A.P. Abad, and Z. Salehi. 2009. Genetic diversity analysis of Iranian 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 . Theor. Appl. Genet. 94:701-706.  

10. Kim, Y.H., S.Y. Kawabata, and R.Z. Sakiyama. 1996. Classification of 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.  

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 ( sinensis L. Osbeck). Genet. Mol. Biol. 29:90-96.  

13. Ollitrault, F., J. Terol, J.A. Pina, L.Navarro, M. Talon, and P. Ollitrault. 2010. Development of SSR markers from clementina (Rutaceae) BAC end sequences and interspecific transferability in . Am. J. Bot. e124-e129.  

14. Palmieri, D.A., V.M. Novelli, M. Bastianel, M. Cristofani-Yaly, G. Astúa-Monge, E.F. Carlos, A.C. de Oliveira and M. A. Machado. 2007. Frequency and distribution of microsatellites from ESTs of . Genet. Mol. Biol. 30:1009-1018.  

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 and its wild relative, p. 190-430. In: W. Reuther, H.J. Webber, and L.D. Batchelor (eds.). The Industry, Vol 1. University of California Press, Berkeley, USA  

18. Tanaka, T. 1977. Fundamental discussion of 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.