Genetic diversity of rapeseed (Brassica napus L.) using SSR and ISJ molecular markers

Document Type : Research Paper

Authors

1 Former MSc Student, Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Zabol.

2 Associate Professor of Plant Breeding, Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Zabol.

3 Assistant Professor of Plant Breeding, Department of Agronomy, Faculty of Agriculture, University of Lorestan.

4 Associate Professor of Plant Disease, Department of Plant Protection, Faculty of Agriculture, University of Zabol

Abstract

To investigate the genetic diversity of 21 rapeseeds (Brassica napus L.), 20 semi-random ISJ and SSR primers were used. Primers produced a total number of 158 (81.5%) polymorphic bands (51 SSR and 107 ISJ bands). Average numbers of polymorphic bands for ISJ, SSR and combined of them were 10.7, 5.1 and 7.9, respectively. PIC values ranged from 0.0150 for specific primer O110D08 to 0.3420 for semi-random primer ET15-33. No significant differences were found between IT and ET primers with regard to polymorphic bands. According to UPGMA cluster analysis and Dice similarity matrix, rapeseed cultivars were divided in 3, 6 and 4 groups for ISJ, SSR primers and combine of them, respectively. Genetic variations don’t agreed with geographic pattern and Iranian and foreign cultivars were not grouped in separate clusters, indicating presumably the proximity and kinship of Iranian and foreign genotypes. SLM096 and Licord with same origin produced separate groups and had high genetic distance with other genotypes; therefore, they can be used in the future breeding programs.

Keywords


  1.  

    1. Dellaporta, S. C., Wood, F. & Hicks, J. B. (1983). A Plant DNA minipreparation. Version II. Plant Mol. Biol. Rep., 1(4), 19- 21.
    2. Devos, K. M. & Gale, M. D. (1992). The use of random amplified polymorphic DNA markers in wheat. Theor Appl Genet, 84, 567-572.
    3. Dongre, A. B., Bhandarkar, M. & Banerjee, Sh. (2007). Genetic diversity in tetraploid and diploid cotton (Gossypium spp.) using ISSR and microsatellite DNA markers. Indian J. Biotechnol., 6, 349-353.
    4. Erlich, H. A. (1989). PCR Technology: Principle and Applications for DNA Amplification. Stockton Press, New York, USA.
    5. Gawel, M., Wisniewska, I. & Rafalski, A. (2002). Semi-specific PCR for evaluation of diversity among cultivars of Wheat and Triticale. Cell. Mol. Biol. Lett., 7, 577- 582.
    6. Food and Agriculture Organization (FAO). (2007). Available at http://www.faostat.fao.org /site/567/efault.aspx.Last access on 01.12.2008.
    7. Hasan, M., Seyis, F., Badani, A. G., Pons-Kuhnemann, J., Friedt, W., Luhs, W. & Snowdon, R. J. )2006). Analysis of genetic diversity in the Brassica napus L. gene pool using SSR markers. Genet. Resour. Crop Evol., 53, 793- 802.
    8. Junjian, N., Colowit, P. M. & Mackill, D. (2002). Evaluation of genetic diversity in rice subspecies by microsatellite markers. Crop Sci., 42, 601-607.
    9. Kashi, Y., King, D. & Soller, M. (1997). Simple sequence repeats as a source of a quantitative genetic variation. J. Trends Genet., 13(1), 74-78.
    10. Kimber, D. S. and McGregor D. I. (1995). Brassica Oilseed: Production and Utilization. CAB Intl., UK.
    11. Kumar, L. S. (1999). DNA marker in plant improvement. Biot. Adv., 17(2-3), 143-182.
    12. Lit, M. & Luty, J. A. (1989). A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the caradiac muscle actine gene. American J. Human Genet., 44(3), 397- 401.
    13. Manifesto, M. M., Schlatter, A. S., Hopp, H. E., Suarez, E. Y. & Dubcovky, J. (2001). Quantitative evaluation of genetic diversity germplasm using molecular markers. Crop Sci., 41, 682-690.
    14. Moghaddam, M., Mohammadi, S. A., Mohebalipour, N., Toorchi, M., Aharizad, S. & Javidfar, F. (2009). Assessment of genetic diversity in rapeseed cultivars as revealed by RAPD and microsatellite markers. African J. Biotech., 8 (14), 3160-3167.
    15. Moghaieb, R. E. A., Mohammed, E. H. K. & Youssief, S. S. (2014). Genetic diversity among some canola cultivars as revealed by RAPD, SSR and AFLP analyses. 3 Biot., 4, 403–410.
    16. Mohammadi, S. A. & Prasanna, B. M. (2003). Analysis of genetic diversity in crop plants: Salient statistical tools and consideration. Crop Sci., 43, 1235-1248.
    17. Nowoseielski, J., Podyma, W. & Sielska, D. N. W. (2002). Molecular research on the genetic diversity of Polish varieties and landraces of Phaseoluscocclineus L. and Phaseolus vulgaris L. using the RAPD and AFLP methods. Cell. Mol. Biol. Lett., 7, 753- 762.
    18. Odonougue, L. S., Souza, E., Tanksley, S. D. & Sorrell, M. E. (1999). Relationships among North American oat cultivars based on restriction fragment length polymorphism. Crop Sci., 34, 1251- 1258.
    19. Pejic, I., Ajmone-Marsan, P., Morgante, M., Kozumplick, V., Castiglioni, P., Taramino, G. & Motto, M. (1998). Comparative analysis of genetic similarity among maize inbred lines detected by RFLPs, RAPDs, SSRs and AFLPs. Theor. Appl. Genet., 97, 1248-1255.
    20. Plieske, J. & Struss, D. (2001). Microsatellite markers for genome analysis in Brassica. I. Development in Brassica napus and abundance in  Brassicaceae species. Theor. Appl.Genet., 102, 689- 694.
    21. Qu, C., Hasan, M., Lu, K., Liu, L., Liu, X., Xie, J., Wang, M., Lu, J., Odat, N., Wang, R., Chen, L., Tang, Z. & Li, J. (2012). Genetic diversity and relationship analysis of the Brassica napus germplasm using simple sequence repeat (SSR) markers. Afr J Biotechnol., 11(27), 6923–6933.
    22. Rafalski, A., Gidzinska, M. & Wisniewska, I. (1997). PCR-based system for evolution of relationships among Maize inbreebs. P: 106-111. Tsaftaries, A. S. (ed). Genetics and Biotechnology of Maize and Sorghom. Societyof Chemistry, Cambridge. UK.
    23. Rafalski, A., Madej, L., Wisniewska, I. & Gawelo, M. )2002). The genetic diversity of components of rye hybrids. Cell. Mol. Biol. Lett., 7, 471- 475.
    24. Rohlf, F. J. (1998). ntsys-pc. Numerical taxonomy and multivariate analysis system, version 2.5. Exeter Software, Setauket, NY.
    25. Saal, B., Plieske, J., Hu, J., Quiros, C. F. & Struss, D. (2001). Microsatellite markers for genome analysis in Brassica. II. Assignment of rapeseed microsatellites to the A and C genomes and genetic mapping in Brassica oleracea L. Theor. Appl.Genet., 102, 695- 699.
    26. Salahvarzi, E., Salahvarzi, A., and & Drikvand, R. (2013). Assessment of genetic diversity in (Lens culinaris M.) using ISJ marker. Ann. Biol. Res., 4 (7), 157-160.
    27. Senior, M. L. & Heun, M. (1993). Mapping maize microsatellites and polymerase chain reaction confirmation of the targeted repeats using a CT primer. Genome, 36, 884-889.
    28. Sharma, K. K., Crouch, J. H. & Hash, C. T. (2002). Application of Biotechnology for crop improvement prospect and constraints. J. Plant Sci., 163(3), 381-395.
    29. Siahsar, B. A., Allahdoo, M. & hahsavand Hasani, H. (2010). Evaluation of Genetic Diversity of Tritipyrum, Triticale and Wheat Lines through RAPD and ISJ Markers. Iran. J. Ffield Crop Sci., 41(3), 555-568.
    30. Soengas, P., Velasco, P., Padilla, G. & Ordás, A. (2006). Genetic relationships among Brassica napus crops based on SSR markers. Hort Sci., 41(5), 1195-1199.
    31. Thiyam-Holländer, U., Eskin, N. A. M. & Matthäus, B. (2012). Canola and Rapeseed: Production, Processing, Food Quality, and Nutrition. CRC Press. 374 P.
    32. Uzunova, M. I. & Ecke, W. (1999). Abundance, polymorphism and genetic mapping of microsatellite in oilseed rape (Brassica napus L.). Plant Breed., 118, 323-326.
    33. Weining, S. & Langridge, P. (1991). Identification and mapping of polymorphism in cereals based on polymerase chain reaction. Theor. Appl.Genet., 82, 209-216.
    34. Westman A, Kresovich, S. 1999. Simple sequence repeat (SSR)-based marker variation in Brassica nigra genebank accessions and weed populations. Euphytica, 109, 85-92.
    35. Yang, Y. X., Wu, W., Zheng, Y. L., Chen, L., Liu, R. J. & Huang, C. Y. (2007). Genetic diversity and relationship among safflower (Carthamus tinctorius L.): Analysis by intersimple sequence repeats (ISSR). Genet. Resour. Crop Evol., 54, 1043- 1051.