Genetic Diversity For Submergence Tolerance In Rice  (Oryza Sativa L.) Utilizing Ssr Markers

Nilmani Prakash; Yaswant Kumar Pankaj; Rajesh  Kumar; Pankaj Kumar; Raj Kumar Jat

doi:10.48165/

Authors

Nilmani Prakash Borlaugh Institute of South Asia, Pusa - 848 125, Bihar (India)
Yaswant Kumar Pankaj Department of Agricultural Biotechnology & Molecular Biology, Dr. Rajendra Prasad Central Agricultural University (RPCAU), Pusa, Bihar (India)
Rajesh Kumar Department of Plant Breeding and Genetics, Dr. Rajendra Prasad Central Agricultural University (RPCAU), Pusa, Bihar (India)
Pankaj Kumar Cereal Systems Initiative for South Asia, CIMMYT, Patna -800 025, Bihar (India)
Raj Kumar Jat Borlaugh Institute of South Asia, Pusa - 848 125, Bihar (India)

DOI:

https://doi.org/10.48165/

Keywords:

Allele, divergence, loci, rice, submergence

Abstract

The present study was aimed to analyze molecular diversity of submergence tolerant genotypes of rice. Thirty four SSR primers were used to generate allelic variants (4 alleles in RM 23843 and 27 in RM 23662). Altogether 410 allelic variants were detected at 42 SSR loci with a mean of 9.76 alleles per locus. Analysis of divergence pattern based on SSR markers allowed differentiation and classification of rice varieties into 8 clusters. A large range of similarity coefficient revealed by SSR markers provided greater confidence for the assessment ofgenetic divergence and interrelationship among the submergence tolerant rice genotypes. A perusal of similarity coefficients reflected a very high degree of similarity between rice genotypes ‘Anh Hsung Seln’ (C 11) and ‘Hsung Teing’, whereas ‘FR 13A’ and ‘Swarna Sub-1’ were more diverse for breeding programme to generate more recombinants. Use of SSR markers appeared more efficient in achieving unique and unambiguous characterization and differentiation of varieties used in the present study. The SSR analysis also revealed unique or variety specific allele which could be useful as DNA fingerprints in the identification and preservation of different genotype and to develop highly submergence tolerance varieties.

Downloads

Download data is not yet available.

References

Anderson, J.A., Chhurchill, G.A., Autrique, J.E., Tanksley, S.D. and Sorrells, M.E. 1993. Optimizing parental selection for genetic linkage maps. Genome, 36: 181-186. Biswas, T., Das, A. and Bhattacharyya, S. 2012. Microsatellite marker-based diversity analysis for submergence tolerance in some Bengal landraces of rice (Oryza sativa L.). Journal of Tropical Agriculture, 50: 67-71.

Choudhary, G., Ranjitkumar, N., Surapaneni, M., Deborah, D.A., Vipparla, A. and Anuradha, G. 2013. Molecular genetic diversity of major Indian rice cultivars over decadal period. PLoS One, 8(6): 66197.

Doyle, J.J. and Doyle, J.L. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf material. Phytochemical Bulletin, 119: 11-15.

Iftekharuddaula, K.M. Ahmed, H.U. and Ghosal, S. 2015. Development of new submergence tolerant rice variety for Bangladesh using marker-assisted backcrossing. Rice Science, 22: 16- 26.

Iftekharuddaula, K.M. Ahmed, H.U. and Ghosal, S. 2016. Development of early maturing submergence-tolerant rice varieties for Bangladesh. Field Crops Research, 190: 44-53. Ismail, A.M., Mackill, D.J., Jackson, M., Ford-Lloyed, B. and Parry, M. 203. Response to flooding: Submergence tolerance in rice, pp. 251-269. In: Plant Genetic Resources and Climate Change - A 21st Century Perspective. CAB International, Wallingford, UK.

Joshi, R.K. and Behera, L. 2006. Identification and differentiation of indigenous non-Basmati aromatic rice genotypes of India using microsatellite markers. African Journal of Biotechnology, 6: 348-354.

Kalinowaski, S.T. and Taper, M.L. 2006. Maximum likelihood estimation of the frequency of null alleles at microsatellite loci. Conservation Genetics, 7: 991-995.

Prathyusha, A., Reddy, D.M., Sreenivasulu, Y., Sudhakar, P. and Reddy, K.R. 2009. Molecular characterization and diversity analysis of traditional and elite cultivars of rice simple sequence repeat (SSR) markers. Oryza, 46: 275-278.

Rao, M., Grithlahre, S., Bisen, P., Singh, N.K., Dar, M.H., Singh, U.S. and Singh, P.K. 2016. Genetics of marker assisted backcross progenies of the cross HUR-105 X Swarna - SUB1. International Journal of Agriculture, Environment & Biotechnology, 9: 499-505.

Rathi, S. and Sharma, R.N. 2012. Microsatellite diversity in indigenous glutinous rice landraces of Assam. Indian Journal of Biotechnology, 11: 23-29.

Ray, B.P. 2018. Genetic analysis and development of submergence tolerance rice (Oryza sativa L.) lines through MAS. International Journal of Complementary & Alternative Medicine, 11: 244-249.

Genetic diversity for submergence tolerance in rice 157

Ray, B.P., Iftekharuddaula, K.M. and Ghoshal, S. 2014. Marker-assisted backcross for the development of submergence tolerant rice (Oryza sativa L.). Journal of Biological and Chemical Research, 31: 01-05.

Rohlf, F.J. 2000. NTSYSpc: Numerical Taxonomy and Multivariate Analysis System. Version 2.1. Exeter Publications, New York, USA.

Sarkar, R.K. and Bhattacharjee, B. 2011. Rice genotypes with SUB1 QTL differ in submergence tolerance, elongation ability during submergence and re-generation growth at re-emergence. Springer Rice Journal, 5: 7 [https://doi.org/10.1007/s12284-011-9065-z].

Singh, N., Choudhury, D.R., Tiwari, G., Singh, A.K., Kumar, S., Srinivasan, K. and Singh, R. 2016. Genetic diversity trend in Indian rice varieties: An analysis using SSR markers. BMC Genetics, 17: 127.

Singh, U.S., Dar, M.H., Singh, S., Zaidi, N.W., Bari, M.A., Mackill, D.J., Collard, B.C.Y., Singh, V.N., Singh, J.P., Reddy, J.N., Singh, R.K., Ismail, A.M. 2013. Field performance, dissemination, impact and tracking of submergence tolerant (Sub1) rice varieties in South Asia. SABRAO Journal of Breeding and Genetics, 45: 112-131.

Upadhyay, P., Neeraja, C.N., Kole, C. and Singh, V.K. 2012. Population structure and genetic diversity in popular rice varieties of India as evidenced from SSR analysis. Biochemical Genetics, 50: 770-783.