Genetic diversity of rice germplasm (Oryza sativa L.) of java island, Indonesia


The role of genetic diversity in crop germplasm is an important concept within genetic conservation. In this research, 43 accessions were analyzed at the agro-morphological and genetic levels. Clustering based on the agro-morphological resulted in four sub-groups. Analysis at the genetic level was conducted using 22 microsatellites, which revealed a total number of alleles to be 203, with a range per allele between 2 and 17 and an average of 9.2 alleles per locus. The highest and lowest Polymorphic Information Content (PIC) values were found in RM431 and RM11, which were 0.95 and 0.67, respectively. The genetic diversity value ranged from 0.71 to 0.95. The genetic similarity among accessions ranged from 0.00 to 0.90. Clustering based on the genetic relatedness divided the Java rice samples into two major groups. The classification created through this research many inform future breeding programs aimed at improving the quality and quantity of yield production.

This is a preview of subscription content, log in to check access.

Fig. 1
Fig. 2 
Fig. 3
Fig. 4 


  1. Ahnert SE (2017) Structural properties of genotype–phenotype maps. J R Soc Interface 14:20170275.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  2. Aljumaili SJ, Rafii MY, Latif MA, Sakimin SZ, Arolu IW, Miah G (2018) Genetic diversity of aromatic rice germplasm revealed By SSR markers. Biomed Res Int 2018:1–11.

    CAS  Article  Google Scholar 

  3. Allhgolipour M, Farshdfar E, Rabiei B, Faculty of Agricultural Sciences, D. of A., and P.B. (2014) Molecular characterization and genetic diversity analysis of different rice cultivars by microsatellite markers. Genetika 46(1):187–198.

    Article  Google Scholar 

  4. Becerra V, Paredes M, Ferreira ME, Gutiérrez E, Díaz LM (2017) Assessment of the genetic diversity and population structure in temperate japonica rice germplasm used in breeding in Chile, with SSR markers. Chil J Agric Res 77(1):15–26.

    Article  Google Scholar 

  5. BPS (Badan Pusat Statistik) (2013) Harvested area of rice field in Java.

  6. BPS (Badan Pusat Statistik) (2015) Geographical area of Java Island.

  7. Dellaporta SL, Wood J, Hicks JB (1983) A plant DNA minipreparation: version II. Plant Mol Biol Rep 1(4):19–21

    CAS  Article  Google Scholar 

  8. Gasim S, Abuanja I, Abdalla AW (2019) Genetic diversity of rice (Oryza sativa L) accessions collected from Sudan and IRRI using SSR markers. African J Agric Res 14:143–150.

    CAS  Article  Google Scholar 

  9. Glaszmann JC (1987) Isozymes and classification of Asian rice varieties. Theor Appl Genet 74(1):21–30.

    CAS  Article  PubMed  Google Scholar 

  10. Hammer Ø, Harper DAT, Ryan PD (2001) Past: paleontological statistics software package for education and data analysis. Palaeontol Electron 4:1–9

    Google Scholar 

  11. Hue HT, Nghia LT, Minh HT, Anh LH, Trang LTT, Khanh TD (2018) Evaluation of genetic diversity of local-colored rice landraces using SSR markers. Int Lett Nat Sci 67:24–34.

    Article  Google Scholar 

  12. Kanawapee N, Sanitchon J, Srihaban P, Theerakulpisut P (2011) Genetic diversity analysis of rice cultivars (Oryza sativa L) differing in salinity tolerance based on RAPD and SSR markers. Electron J Biotechnol 14:6.

    CAS  Article  Google Scholar 

  13. Khush GS, Brar DS, Virk PS, Tang SX, Malik SS, Busto GA, Lee YT, McNally R, Trinh LN, Jiang YY, Shata MAM (2003) Classifying rice germplasm by isozyme polymorphism and origin of cultivated rice In: IRRI (ed) Discussion Paper, No. 46. International Rice Research Institute, Los Banos. pp 1–13

  14. Krupa KN, Shashidhar HE, Dalawai N, Reddy M, Swamy HVV (2017) Molecular marker based genetic diversity analysis in rice genotypes (Oryza sativa L) using SSR markers. Int J Pure App Biosci 5(2):668–674.

    Article  Google Scholar 

  15. Liu K, Muse SV (2005) PowerMaker: an integrated analysis environment for genetic maker analysis. Bioinformatics 21:2128–2129.

    CAS  Article  PubMed  Google Scholar 

  16. Ming H, Fang-min X, Li-yun C, Xiang-qian Z, Jojee L, Madonna D (2010) Comparative analysis of genetic diversity and structure in rice using ILP and SSR markers. Rice Sci 17(4):257–268.

    Article  Google Scholar 

  17. Nachimuthu VV, Raveendran M, Duraialaguraja S, Sivakami R, Pandian BA, Ponniah G, Gunasekaran K, Swaminathan M, Suji KK, Sabariappan R (2015) Analysis of population structure and genetic diversity in rice germplasm using SSR markers: an initiative towards association mapping of agronomic traits in Oryza sativa. Rice 8(6):30.

    Article  PubMed  PubMed Central  Google Scholar 

  18. Pachauri V, Taneja N, Vikram P, Singh NK, Singh S (2013) Molecular and morphological characterization of Indian farmers rice varieties (Oryza sativa L.). Aust J Crop Sci 7(7):923–932

    CAS  Google Scholar 

  19. Rajamoorthy Y, Rahim KA, Munusamy S (2015) Rice Industry in Malaysia: challenges, policies and implications. Procedia Econ Financ 31:861–867

    Article  Google Scholar 

  20. Roy S, Marndi BC, Mawkhlieng B, Banerjee A, Yadav RM, Misra AK, Bansal KC (2016) Genetic diversity and structure in hill rice (Oryza sativa L.) landraces from the North-Eastern Himalayas of India. BMC Genet 17(1):1–15.

    Article  Google Scholar 

  21. Sajib AM, Musharaf Hossain M, Mosnaz A, Hossain H, Monirul Islam M, Shamsher Ali M, Prodhan SH, Haque Prodhan S (2012) SSR marker-based molecular characterization and genetic diversity analysis of aromatic landraces of rice (Oryza sativa L.). J BioSci Biotech 1(2):107–116

    Google Scholar 

  22. Saini N, Jain N, Jain S, Jain RK (2004) Assessment of genetic diversity within and among Basmati and non-Basmati rice varieties using AFLP, ISSR and SSR markers. Euphytica 140(3):133–146.

    CAS  Article  Google Scholar 

  23. Singh N, Choudhury DR, Tiwari G, Singh AK, Kumar S, Srinivasan K, Tyagi RK, Sharma AD, Singh NK, Singh R (2016) Genetic diversity trend in Indian rice varieties: an analysis using SSR markers. BMC Genetics 17(1):1–13.

    Article  Google Scholar 

  24. Thomson MJ, Septiningsih EM, Suwardjo F, Santoso TJ, Silitonga TS, McCouch SR (2007) Genetic diversity analysis of traditional and improved Indonesian rice (Oryza sativa L.) germplasm using microsatellite markers. Theor Appl Genet 114(3):559–568.

    CAS  Article  PubMed  Google Scholar 

  25. Thomson MJ, Polato NR, Prasetiyono J, Trijatmiko KR, Silitonga TS, McCouch SR (2009) Genetic diversity of isolated populations of Indonesian landraces of rice (Oryza sativa L.) collected in East Kalimantan on the Island of Borneo. Rice 2(1):80–92.

    Article  Google Scholar 

  26. Wang C-H, Zheng X-M, Xu Q, Yuan X-P, Huang L, Zhou H-F, Wei X-H, Ge S (2014) Genetic diversity and classification of Oryza sativa with emphasis on Chinese rice germplasm. Heredity 112(5):489–496.

    CAS  Article  PubMed  Google Scholar 

  27. Wong SC, Yiu PH, Bong STW, Lee HH, Neoh PNP, Rajan A (2009) Analysis of Sarawak Bario rice diversity using microsatellite markers. Am J Agric Biol Sci 4:298–304.

    Article  Google Scholar 

  28. Wright S (1943) Isolation by distance. Genetics 28(2):114–138

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Yadav S, Singh A, Singh MR, Goel N, Vinod KK, Mohapatra T, Singh AK (2013) Assessment of genetic diversity in Indian rice germplasm (Oryza sativa L.): use of random versus trait-linked microsatellite markers. J Genet 92(3):545–557.

    CAS  Article  PubMed  Google Scholar 

Download references


This work was supported by IsDB (Islamic Development Bank) Project and University of Jember, Indonesia.


This research did not receive any specific Grant from funding agencies in the public, commercial, or not-for-profit sectors.

Author information



Corresponding author

Correspondence to Mohammad Ubaidillah.

Ethics declarations

Conflict of interest

The authors declare that there are no conflicts of interest regarding the publication of the paper.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Karimah, A.Z., Siswoyo, T.A., Kim, K.M. et al. Genetic diversity of rice germplasm (Oryza sativa L.) of java island, Indonesia. J. Crop Sci. Biotechnol. (2020).

Download citation


  • Diversity
  • Agro-morphological
  • SSR
  • Rice
  • Germplasm