Genetic analysis of castor (Ricinus communis L.) using ISSR markers

Document Type : Original research paper


1 Department of Horticulture, Urmia University, Urmia, Iran.

2 Department of Plant Breeding and Biotechnology, Urmia University, Urmia, Iran. Institute of Biotechnology, Urmia University, Urmia, Iran.


Castor (Ricinus communis L.) is one of the most ancient medicinal oil crops in the world. It has been vastly distributed in different parts of Iran. In the present study, the inter simple sequence repeat (ISSR) markers were used to evaluate the molecular genetic diversity among and within 12 castor accessions collected from 7 regions of Iran. Totally, 16 ISSR primers amplified 166 loci, of which 116 loci (69.89 %) were polymorph, indicating high genetic variability in castor germplasm. An accession-specific ISSR band was detected in ‘80-29’accession. Genetic distance among accessions ranged from 0.2 to 0.056. Analysis of molecular variance revealed a higher level of genetic variation within (80%) than between (20%) accessions. A model-based Bayesian approach subdivided 60 genotypes from 12 accessions into 6 subgroups. UPGMA dendrogram based on Nei’s genetic distance classified 12 accessions into 4 groups. The result indicates that there was no association between geographical origin and ISSR patterns. The results suggest that ISSR technique is a useful tool for studying genetic diversity in castor germplasm.


- References
[1]        Aghaei, M., Darvishzadeh, R. and Hassani, A. 2012. Molecular Characterization and similarity relationships among Iranian basil (Ocimum basilicum L.) accessions using inter simple sequence repeat markers. Rev Ciênc Agron,43: 312-320.
[2         Allan, G., Williams, A., Rabinowicz, P.D., Chan, A., Ravel, P. and Keim, J.P. 2008. World-wide genotyping of castor bean germplasm (Ricinus communis L.) using ALFP and SSRs. Genet Resour Crop Evol, 55: 365–378.
[3]        Anjani, K. 2012. Castor genetic resources: A primary gene pool for exploitation. Ind Crop Prod, 35: 1–14.
[4]        Audi, J., Belson, M., Patel, M., Shier, J. and Osterloh, J. 2005. Ricin poisoning—a comprehensive review. J Am Med Assoc, 294: 2342–51.
[5]        Bajay, M.M. 2010. Development of microsatellite markers and characterization of germplasm of castor (Ricinus communis L.). Dissertation, Universidade de Sao Paulo-USP, Brazil.
[6]        Chan, A.P., Crabtree, J., Zhao, Q., Lorenzi, H., Orvis, J., Puiu, D., Melake-Berhan, A., Jones, K.M., Redman, J., Chen, G., Cahoon, E.B., Gedil, M., Stanke, M., Haas, B.J., Wortman, J.R., Fraser-Liggett, C.M., Ravel, J. and Rabinowicz, P.D. 2010. Draft genome sequence of the oilseeds species Ricinus communis. Nat Biotechnol, 28(9): 951-956.
[7]        Carter, S. and Smith, A.R. 1987. Euphorbiaceous Flora of Tropical East Africa. A.A., Balkema Publishers, Rotterdam, Netherlands.
[8]        Chen, Y., Zhou, R., Lin, X., Wu, K., Qian, X. and Huang, S. 2008. ISSR analysis of genetic diversity in sacred lotus cultivars. Aquat Bot, 89: 311–316.
[9]        Courtois, B., Audebert, A., Dardou, A., Roques, S., Ghneim- Herrera, T., Droc G., Frouin, J., Rouan, L., Gozé, E., Kilian, A., Ahmadi, N. and Dingkuhn, M. 2013. Genome-wide association mapping of root traits in a Japonica rice panel. PLoS ONE, 8(11): e78037. doi: 10.1371/journal. pone.0078037.
[10]      Dashchi, S., Abdollahi Mandoulakani, B., Darvishzadeh, R. and Bernoosi I. 2012. Molecular similarity relationships among iranian bread wheat cultivars and breeding lines using ISSR markers.Not Bot Horti Agrobo, 40(2): 254-260.
[11]      Duke, J.A. 1998. Ricinus communis. from Purdue University New Crop Resource Online Program. http: //www.hort.purdue .edu/newcrop/duke_energy/Ricinus_communis.html.
[12]      Endo, Y.K., Mitsui, K., Motizuki, M. and Tsurugi, K. 1987. The mechanism of action of ricin and related toxic lectins on eukaryotic ribosomes: the site and the characteristics the modification in 28S ribosomal RNA caused by the toxins. J Biol Chem, 262: 5908–5917.
[13]      Evanno, G., Regnaut, S. and Goudet, J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol, 14: 2611–2620.
[14]      Excoffier, L., Smouse, P.E. and Quattro, J.M. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data. Genet, 131: 479-491.
[15]      Foster, J., Allan, T., Chan, G.J., Rabinowicz, A.P., Ravel, P.D., Jackson, J. and Keim, P.J.P. 2010. Single nucleotide polymorphism for assessing genetic diversity in castor (Ricinus communis L.). BMC Plant Biol, 10: 13.
[16]      Gajera, B.B., Kumar, N., Singh, A.S. and Punvar, B.S. 2010. Assessment of genetic diversity in castor (Ricinus communis L.) using RAPD and ISSR markers. Ind Crop Prod, 32: 491-498.
[17]      Godwin, L.A., Aitken, E.A. and Smith L.A. 1997. Application of inter simple sequence repeat (ISSR) markers to plant genetics. Electrophor, 18: 1524-1528.
[18]      Gupta, M., Chyi, Y.S., Romero-Severson, J. and Owen, J.L. 1994. Amplification of DNA markers from evolutionarily diverse genomes using single primers of simple-sequence repeats. Theor Appl Genet, 89: 998–1006.
[19]      Govaerts, R., Frodin, D.G. and Radcliffe-Smith, A. 2000. World checklist and bibliography of Euphorbiaceae (with Pandaceae). Redwood Books Limited, Trowbridge, Wiltshire.
[20]      Hamrick, J.L. and Godt, M.J.W. 1989. Allozyme diversity in plants species. In Plant Population Genetics, Breeding and Genetic Resources, pp. 43– 63. Eds A.H.D. Brown, M.T. Clegg, A.L. Kahler and B.S. Weir. Sunderland, MA ,USA: Sinauer Associates.
[21]      Hamrick, J.L. and Godt, M.J.W. 1996. Effects of life history traits on genetic diversity in plant species. Philos Trans R Soc Lond B,351: 1291-1298.
[22]      He, F., Kang, D., Ren, Y., Qu, L-J., Zhen, Y., and Gu, H. 2007. Genetic diversity of the natural populations of Arabidopsis thaliana in China. Hered, 99: 423-431.
[23]      Hu, Y., Wang, L., Xie, X., Yang, J., Li Y. and Zhang, H. 2010. Genetic diversity of wild populatio ns of Rheum tanguticum endemic to China as revealed by ISSR analysis. Biochem Sys Ecol, 38: 264–274.
[24]      Isshiki, S., Iwata, N. and Mizanur Rahim Khan, M.D. 2008. ISSR variations in eggplant (Solanum melongena L.) and related Solanum species. Sci Hort, 117: 186–190.
[25]      Jabbarzadeh, Z., Khosh-Khui, M., Salehi, H. and Saberivand, A. 2010. Inter simple sequence repeat (ISSR) markers as reproducible and specific tools for genetic diversity analysis of rose species. Afr J Biotechnol, 9: 6091- 6095.
[26]      Joshi, K., Chavan, P., Warude, D. and Patwardhan, B. 2004. Molecular markers in herbal drug technology. Curr Sci, 87(2): 159-165.
[27]      Kholghi, M., Darvishzadeh, R., Bernousi I., Pirzad, A. and Laurentin H. 2012. Assessment of genomic diversity among and within Iranian confectionery sunflower (Helianthus annuus L.) populations by using simple sequence repeat markers.Acta Agri Scand Sect B Soil Plant Sci, 62: 488-498.
[28]      Khush, G.S. 2002. Molecular genetics-plant breeder’s perspective. In: Jain, S.M., Brar, D.S., Ahloowalia, B.S. (Eds.), Molecular Techniques in Crop Improvement. Kluwer Academic.
[29]      Kovach, W. 1999.MVSP-A Multivariate Statistical Package for Windows, ver. 3.1. Kovach Computing Services, Pentraeth, Wales, UK.
[30]      Lobb, K. 1992. Fatty acid classification and nomenclature. In: Chow, C.K. (Ed.), Fatty Acids in Foods and their Health Implications. Marcel Dekker, New York, pp. 1–15.
[31]      Lu, Z., Wang, Y., Peng, Y., Korpelainen, H. and Li, C. 2006. Genetic diversity of populus cathayana Rehd populations in southwestern china revealed by ISSR markers. Plant Sci, 170: 407–412.
[32]      Lynch, M. and Milligan B. 1994. Analysis of population-genetic structure using RAPD markers. Mol Ecol, 3: 91-99.
[33]      Marak, C.K. and Laskar, M.A. 2010. Analysis of phenetic relationship between Citrus indica Tanaka and a few commercially important citrus species by ISSR markers. Sci Hort, 124: 345–348.
[34]      Modareskia, M., Darvishzadeh, R., Hassani, A. and Kholghi M. 2012. Molecular diversity within and between Ajowan (Carum copticum L.) populations based on inter simple sequence repeat (ISSR) markers.J Plant MB, 1: 51-62.
[35]      Moshkin, V.A. 1986. Castor. Amerind Publishing Co. PVT Ltd, New Delh.
[36]      Muirhead, J. R., Gray, D. K., Kelly, D. W., Ellis, S. M., Heath, D. D., and Macisaac, H. J. 2008. Identifying the source of species invasions: sampling intensity vs. Genet Divers Mol Ecol, 17: 1020-1035.
[37]      Murray, M.G. and Thompson, W.F. 1980. Rapid isolation of high molecular-weight plant DNA. Nucleic Acids Res, 8: 4321-4325.
[38]      Muthusamy, S., S. Kanagarajan and S. Ponnusamy, 2008. Efficiency of RAPD and ISSR marker system in accessing variation of rice bean (Vigna umbellate) landrace. Electron J Biotechnol, Vol. 11.
[39]      Nagaoka, T. and Ogihara, Y. 1997. Applicabilty of inter-simple sequence repeat polymorphisms in wheat for use as DNA markers in comparison to RFLP and RAPD markers. Theor Appl Genet, 94: 597–602.
[40]      Nei, M. 1973. Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA, 70: 3321-3323.
[41]      Nei, N. M. and Li, W. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA,76: 5269-5273.
[42]      Nybom, H. 1994. DNA fingerprinting – a useful tool in fruit breeding. Euphytica, 77: 59-64.
[[43]     Ogunniyi, D.S. 2006. Castor oil: a vital industrial raw material. Bioresour Technol, 97: 1086–1091.
[44]      Peakall, R. and Smouse, P.E. 2006. GENALEX 6: genetic analysis in Excel. Population genetic sof tware for teaching and research. Mol Ecol Notes, 6: 288-295.
[45]      Piazza, G.J. and Farrell, H.M. 1991. Generation of ricinoleic acid from castor oil using the lipase from ground oat (Avena sativa L.) seeds as a catalyst. Biotechnol Lett, 13:179–184.
[46]      Pritchard, J.K., Stephanes, M., Rosenberg, N.A. and Donnelly, P. 2000. Association mapping in structured populations. Am J Hum Genet, 67:170–181.
[47]      Qian, W., Ge S. and Hong, D.Y. 2001. Genetic variation within and among populations of a wild rice Oryza granulata from China detected by RAPD and ISSR markers. Theor Appl Genet, 102: 440–449.
[48]      Ratnaparkhe, M.B., Tekeoglu, M. and Muehlbauer, F.J. 1998. Inter-simple-sequence-repeat (ISSR) polymorphisms are useful for finding markers associated with disease resistance gene clusters. Theor Appl Genet, 97: 515–519.
[49]      Reif, J.C., Gumpert, F., Fischer, S. and Melchiger, A.E. 2007. Impact of genetic divergence on additive and dominance variance in hybrid populations. Genet, 176: 1931-1934.
[50]      Rohlf, F.J. 1998. NTSYS-pc: Numerical Taxonomy and Multivariate Analysis System. version 2.02. Exter Software, Setauket, New York, NY, USA.
[51]      Roldan-Ruiz, I., Dendauw, J., VanBockstaele, E., Depicker, A., and De Loose, M. 2000. AFLP markers reveal high polymorphic rates in ryegrasses (Lolium spp.). Mol Breed,6: 125-134.
[52]      Rosenberg, N.A., Pritchard, J.K., Weber, J.L., Cann, H.M., Kidd, K.K., Zhivotovsky, L.A. and Feldman, M.W. 2002. The genetic structure of human populations. Sci, 298: 2381-2385.
[53]      Rossetto, M., Weaver, P.K. and Dixon, K.W. 1995. Use of RAPD analysis in devising conservation strategies for the rare and endangered Grevillea scapigera (Proteaceae). Mol Ecol, 4: 321–329.
[54]      Savy Filho, A. 2005. Castor bean breeding. In: Borém A. (Ed.) Improvement of Cultivated Species. Viçosa: Federal University of Viçosa.
[55]      Schall, B.A., Hayworth, D.A., Olsen, K.M., Rauscher, J.T. and Smith, W.A. 1998. Phylogeographic studies in plants: problems and prospects. Mol Ecol, 7: 465– 474.
[56]      Shannon, C.E. and Weaver, W. 1949. The Mathematical theory of communication, Urbana (Illinois), University of Illinois Press.
[57]      Sica, M., Gamba, G., Montieri, S., Gaudio, L. and Aceto, S. 2005. ISSR markers show differentiation among Italian populations of Asparagus acutifolius L. BMC Genet, 6: 17.
[58]      Shi, W., Yang, C.-F., Chen, J.-M. and Guo, Y.-H. 2007. Genetic variation among wild and cultivated populations of the Chinese medicinal plant Coptis chinensis (Ranunculaceae). Plant Biol, 10: 485-491.
[59]      Slatkin, M., and Barton, N. H. 1889. A comparison of three methods for estimating average levels of gene flow. Evol, 43: 1349-1 368.
[60]      Solomon, K.F., Labuschagne, M.T. and Viljoen, C.D. 2007. Estimates of heterosis and association of genetic distance with heterosis in durum wheat under different moisture regimes. J Agric Sci, 145: 239-248.
[61]      Tachida, H. and Yoshimaru, H. 1996. Genetic diversity in partially selfing populations with the stepping-stone structure. Heredity, 77(5): 469–475.
[62]      Tomar Rukam, S., Parakhia, M.V., Kavani, R.H., Dobariya, K.L., Thakkar, J.R., Rathod, V.M., Dhingani, R.M. and Golakiya B.A. 2014. Characterization of castor (Ricinus communis L.) genotypes using different markers. Res J Biotech, 9(2): 6-13.
[63]      Velasco, L., Rojas-Barros, P. and Fernández-Martínez, J.M. 2005. Fatty acid and tocopherol accumulation in the seeds of a high oleic acid castor mutant. Ind Crop Prod, 22: 201–206.
[64       Verma, S. and Rana, T.S. 2011. Genetic diversity within and amon g the wild populations of Murraya koenigii (L.) Spreng., as revealed by ISSR analysis. Biochem Syst Ecol, 39: 139–144.
[65]      Wang, H.Z., Feng, S.G., Lu J.J., Shi, N.N. and Liu, J.J. 2009. Phylogenetic study and molecular identification of 31 DendrObium species using inter-simple sequence repeat (ISSR) markers. Sci Hort, 122: 440–447.
[66]      Weising, K., Nybom, H., Wolff, K. and Meyer, W. 1995. DNA fingerprinting in plants and fungi. CRC Press, Inc Boca Raton, FL. 322 pp.
[67]      Yao, M.Z., Chen, L. and Liang, Y.R. 2008. Genetic diversity among tea cultivars from China, Japan and Kenya revealed by ISSR markers and its implication for parental selection in tea breeding programmes. Plant Breed, 127: 166 -172.
[68]      Yeh, F.C., Yang, R.C., Boyle, T.J., Ye, Z.H. and Mao, J.X. 1999. Popgene ver. 1.32, the user-friendly shareware for population genetic analysis. Edmonton, Canada: Molecular Biology and Biotechnology Centre, University of Alberta.
[69]      Yip, P.Y., Chau, C.F., Mak, C.Y. and Kwan, H.S. 2007. DNA methods for identification of Chinese medicinal materials. Chin Med,2(9): 1-19.
[70]      Zhao K.G., Zhou M.Q., Chen L.Q. 2007. Genetic diversity and discrimination of Chimonanthus praecox (L.) Link germplasm using ISSR and RAPD markers. Hortscience, 42(5): 1144–1148.
[71]      Zheng L., Qi J., Fang P., Su J., Xu J., Tao A. 2010. Genetic diversity and phylogenetic relationship of castor germplasm as revealed by SRAP analysis. Plant Sci J, 28(1): 1-6.
[72]      Zietkiewicz, E., Rafalski, A. and Labuda, D. 1994. Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics, 20: 176–183.
Volume 3, Issue 1
June 2015
Pages 18-34
  • Receive Date: 26 April 2015
  • Revise Date: 26 August 2015
  • Accept Date: 26 August 2015
  • First Publish Date: 26 August 2015