Abstract
Microsatellite or simple sequence repeat (SSR) marker analysis was carried out to assess allelic diversity and prepare a DNA fingerprint database of 24 rice genotypes including three premium traditional Basmati, 9 cross-bred Basmati, a local scented selection, eight indica and three japonica rice varieties. A total of 229 alleles were detected at the 50 SSR loci and 49 alleles were in fact present in only one of the 24 varieties. The size difference between the smallest and largest allele varied from 1 (RM333) to as high as 82 (RM206). Multiple alleles were observed at 13 loci. Polymorphism information content (PIC) values ranged between 0.0 (RM167) to 0.78 (RM170), with an average of 0.62 per marker. At 15 of the SSR loci, traditional and cross-bred Basmati rice varieties amplified different alleles than those in the indica andlor japonica rice varieties. A number of SSRs have been identified, which can be used to differentiate among the traditional Basmati varieties and between traditional Basmati and other cross-bred Basmati or long grain, non-Basmati rice varieties. Genetic relationships among rice genotypes as determined by UPGMA cluster analysis and three-dimensional scaling basedon Principal Component Analysis showed that the three traditional Basmati rice varieties are closely related and have varying degree of similarity with other cross-bred Basmati rice varieties. Further implications of these results in genotype identification, monitoring purity and adulteration, and plant variety protection are discussed.
Similar content being viewed by others
References
Khush GS and dela Cruz N, In Speciality rices of the world: Breeding, production and marketing, (R Duffy, Editor), Science Pub, Inc, Enfield, USA (2001) pp 15–18.
Singh RK, Singh US & Khush GS & Rohilla R, In Aromatic rices, (RK Singh, US Singh, GS Khush, Editors), Oxford & IBH Pub Co Pvt Ltd, New Delhi, India (2000) pp 47–69.
Singh RK, Khush GS, Singh US, Singh AK & Singh S, In Aromatic rices, (RK Singh, US Singh, GS Khush, Editors), Oxford & IBH Pub Co Pvt Ltd, New Delhi, India (2000) pp 71–105.
Bhasin VK, In Aromatic rices, (RK Singh, US Singh, GS Khush, Editors), Oxford & IBH Pub Co Pvt Ltd, New Delhi, India (2000) pp 252–276.
Khush GS, In Aromatic rices, (RK Singh, US Singh, GS Khush, Editors), Oxford & IBH Pub Co Pvt Ltd, New Delhi, India, (2000) pp 5–13.
Glaszmann JC, Theor Appl Genet, 74 (1987) 21.
Bligh HFJ, Inti J Food Sci Technol, 35 (2000) 257.
Bligh HFJ, Blackhall NW, Edwards KJ & McClung AM, Crop Sci, 39 (1999) 1715.
Jain S, Mitchel S, Jain RK, Kresovich S & McCouch SR, In Rice Genetic IV Supplement, (GS Khush, OSBrar, B Hardy, Editors), IRRI, Los Banos, Laguna, Philippines (2003) (In press).
McCouch SR, Temnykh S, Lukashova A, Coburn J, DeClerck G, Cartinhour S, Harrington S, Thomson M, Septiningsih E, Semon M, Moncada P & Li J, In Rice Genetics IV (GS Khush, OS Brar, B Hardy, Editors), IRRI, Los Banos, Philippines, Science Publishers, Inc, New Delhi, India (2001) pp 117–135.
Blair MW, Hedetale V & McCouch SR, Theor Appl Genet, 105 (2002) 449.
Nagaraju J, Kathirvel M, Kumar RR, Siddiq EA & Hasnain SE, Proc Natl Sci Acad, USA, 99 (2002) 5836.
Chen X, Temnykh S, Xu Y, Cho YG & McCouch SR, Theor Appl Genet, 95 (1997) 553.
Temnykh S, Park WD, Ayres N, Cartinhour S, Hauck N, Lipovich L, Cho YG, Ishii T & McCouch SR, Theor Appl Genet, 100 (2000) 697.
Saghai-Maroof MA, Soliman KM, Jorgensen RA & Allard RW, Proc Natl Acad Sci, USA, 81 (1984) 8014.
Pal S, Jain S, Saini N & Jain RK, Rice Genet Newsleft, 18 (2001) 94.
Ghosh S, Karanjawala ZE, Hauser ER, Ally D, Knapp JI, Rayman JB, Musick A, Tannenbaum J, Te C, Shapiro S, Elrridge W, Musick T, Martin C, Smith JR, Carpten, Brownstein MJ, Powell JI, Whiten R, Chines P, Nylund SJ, Magnuson VL, Boehnke M & Collins FS, Genome Res, 7 (1997)165.
Anderson JA, Churchill GA, Autrique JE, Tanksley SD & Sorrells ME, Genome, 36 (1993) 181.
Rohlf FJ, NTSYS-PC: Numerical Taxonomy and Multivariate Analysis System Version 18, Exeter Software, Setauket, New York (1993)
Olufowote JO, Xu Y, Chen X, Park WO, Beachell HM, Dilday RH, Goto M & McCouch SR, Genome, 40 (1997) 370.
Cho YG, Ishii T, Temnykh S, Chen X, Lipovich L & Mc Couch SR, Theor Appl Genet, 100 (2000) 713.
Panaud 0, Chen X & McCouch SR, Mol Gen Genet, 252 (1996) 597.
Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, & McCouch SR, Genome Res, 11 (2001) 1441.
Wu KS & Tanksley SD, Mol Genet, 241 (1993) 225.
Ni J, Colowit PM & Mackill DJ, Crop Sci, 42 (2002) 601.
Kato S, Kosaka H & Hara S, Bull Sci Fac Agric Kyushu Univ, Fukuoka, Japan, 3 (1928) 132
Matuso T, Bull Natl Institute of Agril Sci, Japan, 3 (1952) 1 (in Japanese).
Ting Y, Acta Agron Sinica, 8 (3) (1957) 243 (in Chinese).
Aggarwal RK, Brar DS, Nandi S, Huang N & Khush GS, Theor Appl Genet, 98 (1999) 1320.
Ishii T, Brar DS, Second G, Tsunewaki K & Khush GS, Jap J Genet, 70 (1995) 643.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Siwach, P., Jain, S., Saini, N. et al. Allelic Diversity Among Basmati and Non-Basmati Long-grain Indica Rice Varieties using Microsatellite Markers. J. Plant Biochem. Biotechnol. 13, 25–32 (2004). https://doi.org/10.1007/BF03263186
Received:
Revised:
Published:
Issue Date:
DOI: https://doi.org/10.1007/BF03263186