Genetic diversity studies of coarse and fine rice using RAPD markers

Abstract

The availability of a genetically diverse gene pool is vitally important in varietal development. Molecular markers are being extensively utilized to explore the genetic diversity among native and exotic germplasm. This study was designed to reveal the genetic diversity and patterns of relationships among the 20 accessions/genotypes representative of basmati and non-basmati rice from the existing rice gene pool using RAPD markers. Employing RAPD, 17 decamer oligonucleotide primers directed the amplification of 116 fragments, out of which 101 were polymorphic (87.06%) while 15 fragments were monomorphic (12.93%). Similarity coefficients had ranged from 0.47 to 0.90. The average genetic similarity was calculated 0.68 (68%). In this study, the coarse rice genotypes showed more polymorphism (85.84%) than the fine rice genotypes (61.76%). Genotypes were clustered into 8 distinct groups: A, B, C, D, E, F, G, and H but two genotypes, i.e., Shadab and Kangni-27 showed divergence from all the genotypes of the groups. Therefore, these diverse genotypes may be included in future breeding programmes.

Keywords

RAPD / diversity studies / genetic markers / fine rice / coarse rice

References

[1] Ahmadikhah A (2009). A rapid mini-prep DNA extraction method in rice (Oryza sativa). Afr J Biotechnol, 8(2): 323-327

[2] Anonymous (2007). Pakistan Economic Survey 2007-2008. Finance Division, Economic Advisor’s Wing, Islamabad, Pakistan

[3] Anonymous (2008). Pakistan Economic Survey, 2008-2009. Ministry of Food, Agriculture, and Livestock. Federal Bureau of Statistics, Economic Advisor’s Wing, Finance Division, Islamabad, Pakistan

[4] Hadrys H, Balick M, Schierwater B (1992). Applications of random amplified polymorphic DNA (RAPD) in molecular ecology. Mol Ecol, 1(1): 55-63

[5] Iqbal M J, Aziz N, Saeed N A, Zafar Y, Malik K A (1997). Genetic diversity evaluation of some elite cotton varieties by RAPD analysis. Theor Appl Genet, 94(1): 139-144

[6] Moser H, Lee M (1994). RFLP variation and genealogical distance, multivariate distance, heterosis and genetic variation in oats. Theor Appl Genet, 87(8): 947-956

[7] Muhammad A, Samina K, Muhammad A B, Anjuman A, Yusuf Z (2005). Genetic diversity among rice genotypes of Pakistan through random amplified polymorphic DNA (RAPD) analysis. Pak J Bot, 37(3): 585-592

[8] Nei M (1987). Unweighted Paired Group of Arithmetic Means Averages (UPGMA) to Estimate Genetic Distances and Relatedness. Molecular Evolutionary Genetics.New York: Columbia Univ Press, 106-107

[9] Ranade S A, Farooqui N, Bhattacharya E, Verma A (2001). Gene tagging with random amplified polymorphic DNA (RAPD) markers for molecular breeding in plants. Crit Rev Plant Sci, 20(3): 251-275

[10] Yeh F C, Yang Y, Boyle T J, Ye Z, Xiyan J M (2000). Popgene32, Microsoft Windows Based Freeware for Population Genetic Analysis. Molecular Biology and Biotechnology Centre, University of Alberta, Edmontrn, Canada

[11] Yu G Q, Bao Y, Shi C H, Dong C Q, Ge S (2005). Genetic diversity and population differentiation of Liaoning weedy rice detected by RAPD and SSR markers. Biochem Genet, 43(5-6): 261-270

RIGHTS & PERMISSIONS

2014 Higher Education Press and Springer-Verlag Berlin Heidelberg