Fingerprinting and genetic diversity evaluation of rice cultivars using Inter Simple Sequence Repeat marker

Document Type: Research Paper

Authors

1 Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari Agricultural Sciences and Natural Resources University, Sari, Iran.

2 Department of Agronomy and Plant Breeding, Sari Agricultural Sciences and Natural Resources University, P.O. Box 578, Sari, Iran.

3 Department of Biology, University of Mazandaran, Babolsar, Iran.

Abstract

Rice as one of the most important agricultural crops has a putative potential for ensuring food security and addressing poverty in the world. In the present study, in order to provide basic information to improve rice through breeding programs, Inter Simple Sequence Repeat marker (ISSR) was used For DNA fingerprinting and finding genetic relationships among 32 different cultivars. In this study, 12 out of 17 used primers amplified 184 distinct and reproducible fragments with high value of polymorphism (88%). also, for fingerprinting the cultivars 29 loci were used that generated high polymorphic bands among the cultivars. Results indicated that similarity index varied between 39% and 88.4 %, furthermore, PIC value with an average of 23% ranged between 0.1 (for primer #3) to 0.34 (for primer #2). Clustering based on Jaccard coefficient similarity index and UPGMA algorithm divided the cultivars into 6 main sub-clusters in cut-off point of 64% similarity index. The two Italian rice cultivars ‘Ribe’ and ‘Roma’ were the closest cultivars in addition, ‘Vialone nano’ and ‘Anbarbu’ showed the highest dissimilarity. In total, high genetic divergence was observed among the cultivars also, poly (GA)-containing 3-anchored primers amplified the highest number of bands. According to similarity and cluster analysis, it could be inferred that crosses involving Anbarbu cultivar are the most promising ones to improve rice through breeding programs. In fact, results of this study would be promising as a genetic marker for the identification of rice cultivars and an important source of knowledge for subsequent rice researches.    

Keywords

Main Subjects


- References

[1]        Babaei, A., Nematzadeh, G.A. and Hashemi, H. 2011. An evaluation of genetic differentiation in rice mutants using semi-random markers and morphological characteristics. Aust J Crop Sci, 5: 1715-1722.

[2]        Cruz, C.D. and Regazzi, A.J. 1997. Modelos biométricos aplicados ao melhoramento genético Vol. 2. Ed. UFV.

[3]        Cruz, C.D., Regazzi, A.J. and Carneiro, P.C.S. 2003. Biometric models applied to genetic improvement. Editora UFV, Viçosa, MG, Brazil.

[4]        Debnath, S.C. 2007. Inter simple sequence repeat (ISSR) to assess genetic diversity within a collection of wild lingonberry (Vaccinium vitis-idaea L.) clones. Can J Plant Sci, 87: 337-344.

[5]        Debnath, S.C. 2009. Development of ISSR markers for genetic diversity studies in Vaccinium angustifolium. Nord J Bot, 27: 141–148.

[6]        Dellaporta, S.L., Wood, J. and Hicks, J.B. 1983. A plant DNA minipreparation: version II. Plant Mol Biol Rep, 1: 19-21.

[7]        FAO (2008) Food Consumption: Pattern of main food items-share in total dietary energy consumption. FAO Statistic Division. Bulletin.

[8         Ferreira, D.E., Oliveira, A.C., Santos, M.X. and Ramalho, M.A.P. 1995. Métodos de avaliação da divergência genética em milho e suas relações com os cruzamentos dialélicos. Pesq Agropec Bras, 30: 1189-1194.

[9]        Girma, G., Tesfaye, K., and Bekele, E. 2013. Inter Simple Sequence Repeat (ISSR) analysis of wild and cultivated rice species from Ethiopia. Afr J Biotechnol, 9: 5048-5059.

[10]      Ichii, M., Hong, D.L., Ohara, Y., Zhao C.M. and Taketa, S. 2003. Characterization of CMS and maintainer lines in indica rice (Oryza sativa L.) based on RAPD marker analysis. Euphytica, 129: 249-252.

[11]      Khadivi-Khub, A. and Soorni, A. 2014. Comprehensive genetic discrimination of Leonurus cardiaca populations by AFLP, ISSR, RAPD and IRAP molecular markers. Mol Biol Rep, 41: 4007-4016.

[12]      Kwon, Y.S., Lee, J.M., Yi, G.B., Yi, S.I., Kim, K.M., Soh, E.H., Bae, K.M., Park, E.K., Song, I.H. and Kim, B.D. 2005. Use of SSR markers to complement tests of distinctiveness, uniformity and stability (DUS) of pepper (Capsicum annuum L.) varieties. Mol Cell, 19: 428-435.

[13]      Liu, B. and Wendel, JF. 2001. Inter simple sequence repeat (ISSR) polymorphisms as a genetic marker system in cotton. Mol Ecol Notes, 1: 205-208.

[14]      Manonmani, S., Senthlivel, S., Fazlullahkhan, A.K. and Maheswaran, M. 2004. RAPD and Isozyme markers for genetic diversity and their correlation with heterosis in Rice (Oryza sativa L). In Proceedings of the 4th International Crop Science Congress Brisbane, Australia. www. cropscience. org. au.

[15]      McGregor, C.E., Lambert, C.A., Greyling, M.M., Louw, J.H. and Warnich, L. 2000. A comparative assessment of DNA fingerprinting techniques (RAPD, ISSR, AFLP and SSR) in tetraploid potato (Solanum tuberosum L.) germplasm. Euphytica, 113: 135-144.

[16]      Matsumoto, T., Wu, J., Namiki, N., Kanamori, H., Fujisawa, M. and Sasaki, T. 2006. Completion of rice genome sequencing -a paradigm shift of rice biology. J Agric Res, 40: 99-105.

[17]      Orlovskaya, O.A., Koren, L.V. and Khotyleva, L.V. 2012. The impact of parental Genetic Divergence on the Heterosis of F1-Hybrids of Spring Triticales. Russ J Genet, 3: 405-411.

[18]      Pradeep Reddy, M., Sarla, N. and Siddiq, E.A. 2002. Inter simple sequence repeat (ISSR) polymorphism and its application in plant breeding. Euphytica, 128: 9–17.

[19]      Prevost, A. and Wilkinson, MJ. 1999. A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars. Theor Appl Genet, 98: 107-112.

[20]      Wang, Y., Xue, Y., Li, J. 2005. Towards molecular breeding and improvement of rice in China. Trends Plant Sci, 10: 610-614.

[21]      Wu, Y.G., Guo, Q.S., He, J.C., Lin, Y.F., Luo, L.J. and Liu, G.D. 2010. Genetic diversity analysis among and within populations of Pogostemon cablin from China with ISSR and SRAP markers. Biochem. Syst Ecol, 38: 63-72.

[22]      Wünsch, A. and Hormaza, J.I. 2002. Cultivar identification and genetic fingerprinting of temperate fruit tree species using DNA markers. Euphytica, 125: 59-67.

[23]      Yoshida, S., Forno, D.A. and Cock, J.H. 1971. Laboratory manual for physiological studies of rice. Laboratory manual for physiological studies of rice.

[24]      Żebrowska, J.I. and Tyrka, M. 2003. The use of RAPD markers for strawberry identification and genetic diversity studies. Food Agr Environ, 1: 115-117.

[25]      Zhang, D., Shen, F., Liu, J. and Falandysz, J. 2014. Studies on germplasm resources of Auricularia polytricha by Inter-Simple Sequence Repeat (ISSR). Med Engin Bioin, 19: 1.

[26]      Zhou, Y., Zhou, C., Yao, H., Liu, Y. and Tu, R. 2008. Application of ISSR markers in detection of genetic variation among Chinese yam (Dioscorea oppositaThunb) cultivars. Life Sci J, 5: 6-12.