Divergence in hybrid rice parental lines detected by RAPD and ISSR markers

Authors

  • Ghaffar KIANI Department of Plant Breeding and Biotechnology, Sari Agricultural Sciences and Natural Resources University, P.O. Box: 578, Sari, Iran
  • Camellia KATALANI Department of Plant Breeding and Biotechnology, Sari Agricultural Sciences and Natural Resources University, P.O. Box: 578, Sari, Iran

DOI:

https://doi.org/10.14720/aas.2018.111.2.12

Keywords:

rice, restorer, maintainer, cluster analysis, molecular marker

Abstract

Genetic distance between parental lines used in hybrid rice breeding program was estimated based on information from molecular markers data. Sixteen parents (5 CMS, 5 maintainers and 6 restorers) were analyzed with 15 random amplification polymorphic DNA (RAPD) and 20 inter simple sequence repeat (ISSR) marker. Out of 15 RAPD markers, 9 were polymorphic and 79 bands were generated, of which 28 bands were polymorphic (35 %). By using 10 out of 20 ISSR markers 86 bands were detected, of which 35 bands were polymorphic (41 %). Marker index (RAPD = 1.68; ISSR = 1.88) and percent of polymorphic bands indicated that ISSR markers were relatively more efficient in polymorphism detection. Cluster analysis of the parents based on Jaccard’s genetic similarity and UPGMA method were revealed 3 groups. Restorer lines IR68061 and IR5931 with origin of the Philippines were found in distinct group. Results suggesting the cross between CMS lines Neda and Nemat with restorer lines IR68061 and IR5931, can be used as the best heterotic groups for exploration of heterosis.

References

Dellaporta, S. L., Wood, J. and & Hicks, J. B. (1983). A Plant DNA Mini-preparation: version II. Plant Molecular Biology Reporter, 1, 19-21. doi:10.1007/BF02712670

Godwin, I. D., Aitken, E. A. and & Smith, L. W. (1997). Application of inter simple sequence repeat (ISSR) markers to plant genetics. Electrophoresis, 18, 1524-1528. doi:10.1002/elps.1150180906

Hou, Y. C., Yan, Z. H., Wei, Y. M. and & Zheng, Y. L. (2005). Genetic diversity in barley from west China based on RAPD and ISSR analysis. Barley Genetics Newsletter, 35, 9-22.

Joshi, S., Gupta, V., Aggarwal, R., Ranjekar, P. & Brar, D. (2000). Genetic diversity and phylogenetic relationship as revealed by inter simple sequence repeat (ISSR) polymorphism in the genus Oryza. Theoretical and Applied Genetics, 100, 1311-1320. doi:10.1007/s001220051440

Kumar, A., Mishra, P., Singh, S. C. and & Sundaresan, V. (2014). Efficiency of ISSR and RAPD markers in genetic divergence analysis and conservation management of Justicia adhatoda L., a medicinal plant. Plant Systematics and Evolution, 1-12. doi:10.1007/s00606-013-0970-z

Mansour, A., Teixeira Da Silva, J., Edris, S. and & Younis, R.A. (2010). Comparative assessment of genetic diversity in tomato cultivars using IRAP, ISSR and RAPD molecular markers. Focus on Tree Genetics and Genomics. Genes, Genomes and Genomics, 4, 41-47.

Mantel N. (1967). The detection of disease clustering and a generalized regression approach. Cancer Research, 27 , 209–220.

Muthusamy, S., Kanagarajan, S. and & Ponnusamy, S. (2008). Efficiency of RAPD and ISSR markers system in accessing genetic variation of rice bean (Vigna umbellata) landraces. Electronic Journal of Biotechnology, 11, 32-41. doi:10.2225/vol11-issue3-fulltext-8

Nematzadeh, G., Arefi, H., Amani, R. and & Mani, R. (1997). Introduction of high yield variety “Nemat” with good quality. Agricultural science journal, 28, 79-86 (Persian).

Nematzadeh, G., Arefi, H., Khonacdar, Y. and & Nasiri, Z. 2001. "Neda" a high yielding rice cultivar with suitable physicochemical characteristics. Seed and Plant, 24, 107-115 (Persian).

Nematzadeh, Gh. and & Kiani, G. (2010). Genetic analysis of fertility restoration genes for WA type cytoplasmic male sterility in Iranian restorer rice line DN-33-18. African Journal of Biotechnology, 9, 6273–6277.

Powell, W., Morgante, M., Andre, C., Hanafey, M., Vogel, J., Tingey, S. and & Rafalski, A. (1996). The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Molecular breeding, 2, 225-238. doi:10.1007/BF00564200

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. Theoretical and Applied Genetics, 102, 440-449. doi:10.1007/s001220051665

Rabbani, M. A., Pervaiz, Z. H., and & Masood, M. S. (2008). Genetic diversity analysis of traditional and improved cultivars of Pakistani rice (Oryza sativa L.) using RAPD markers. Electronic Journal of Biotechnology, 11, 52-61. doi:10.2225/vol11-issue3-fulltext-3

Raghunathachari, P., Khanna, V. K., Singh, U. S., & Singh, N. K. (2000). RAPD analysis of genetic variability in Indian scented rice germplasm (Oryza sativa L.). Current Science, 79, 994-998.

Raghunathachari, P.; Khanna, V.K.; Singh, U.S. and Singh, N.K. 2000 RAPD analysis of genetic variability in Indian scented rice germplasm (Oryza sativa L.). Current Science, 7, 994-998.

Rahman, S. N., Islam, M. S., Alam, M. S. and & Nasiruddin, K. M. (2007). Genetic polymorphism in rice (Oryza sativa L.) through RAPD analysis. Indian Journal of Biotechnology, 6, 224.

Rohlf, F.J. (1994). NTSYS-PC: Numerical Taxonomy and Multivariate Analysis System Version 2.2. State University of New York, Stony Brook N.Y.

Subudhi, P., Nandi, S., Casal, C., Virmani, S. and & Huang, N. (1998). Classification of rice germplasm: III. High-resolution fingerprinting of cytoplasmic genetic male-sterile (CMS) lines with AFLP. Theoretical and applied genetics, 96, 941-949. doi:10.1007/s001220050824

Wang, B., Xu, W., Wang, J., Wu, W., Zheng, H., Yang, Z., Ray, J. and & Nguyen, H. (1995). Tagging and mapping the thermo-sensitive genic male-sterile gene in rice (Oryza sativa L.) with molecular markers. Theoretical and Applied Genetics, 91, 1111-1114. doi:10.1007/BF00223928

Wang, S. and & Lu, Z. (2006). Genetic diversity among parental lines of Indica hybrid rice (Oryza sativa L.) in China based on coefficient of parentage. Plant Breeding, 125, 606-612. doi:10.1111/j.1439-0523.2006.01268.x

Wu, C. J., Cheng, Z. Q., Huang, X. Q., Yin, S. H., Cao, K. M. and & Sun, C. R. (2004). Genetic diversity among and within populations of Oryza granulata from Yunnan of China revealed by RAPD and ISSR markers: implications for conservation of the endangered species. Plant Science, 167, 35-42. doi:10.1016/j.plantsci.2004.02.022

Xiao, J., Li, J., Yuan, L., Mc Couch, S. and & Tanksley, S. (1996). Genetic diversity and its relationship to hybrid performance and heterosis in rice as revealed by PCR-based markers. Theoretical and Applied Genetics, 92, 637-643. doi:10.1007/BF00226083

Xu, W., Virmani, S. S., Hernandez, J. E., Sebastian, L. S., Redoña, E. D. and & Li, Z. (2002). Genetic diversity in the parental lines and heterosis of the tropical rice hybrids. Euphytica, 127, 139-148. doi:10.1023/A:1019960625003

Yao, F., Y., Xu, C., G., Yu, S, .B., Li, J, .X., Gao, Y., J., Li, X, .H. and & Zhang, Q, .F. (1997). Mapping and genetic analysis of two fertility restorer loci in the wild-abortive cytoplasmic male sterility system of rice (Oryza sativa L.). Euphytica, 98, 183-187. doi:10.1023/A:1003165116059

Zhang, Q., Liu, K., Yang, G., Maroof, M. S., Xu, C. and & Zhou, Z. (1997). Molecular marker diversity and hybrid sterility in indica-japonica rice crosses. Theoretical and Applied Genetics, 95, 112-118. doi:10.1007/s001220050538

Zhao, M., Li, X., Yang, J., Xu, C., Hu, R., Liu, D. and & Zhang, Q. (1999). Relationship between molecular marker heterozygosity and hybrid performance in intra‐and inter‐subspecific crosses of rice. Plant Breeding, 118, 139-144. doi:10.1046/j.1439-0523.1999.118002139.x

Zietkiewicz, E., Rafalski, A. and & Labuda, D. (1994). Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics, 20, 176-183. doi:10.1006/geno.1994.1151

Downloads

Published

29. 10. 2018

Issue

Section

Agronomy section

How to Cite

KIANI, G., & KATALANI, C. (2018). Divergence in hybrid rice parental lines detected by RAPD and ISSR markers. Acta Agriculturae Slovenica, 111(2), 369–376. https://doi.org/10.14720/aas.2018.111.2.12

Similar Articles

1-10 of 482

You may also start an advanced similarity search for this article.