Abstract
Genetic relationships among Indian aromatic and quality rice (Oryza sativa) germplasm were assessed using 30 fluorescently labeled rice microsatellite markers. The 69 rice genotypes used in this study included 52 Basmati and other scented/quality rice varieties from different parts of India and 17 indica and japonica varieties that served as controls. A total of 235 alleles were detected at the 30 simple sequence repeat (SSR) loci, 62 (26.4%) of which were present only in Basmati and other scented/quality rice germplasm accessions. The number of alleles per locus ranged from 3 to 22, with an average of 7.8, polymorphism information content (PIC) values ranged from 0.2 to 0.9, with an average of 0.6, and the size range between the smallest and the largest allele for a given microsatellite locus varied between 3 bp and 68 bp. Of the 30 SSR markers, 20 could distinguish traditional Basmati rice varieties, and a single panel of eight markers could be used to differentiate the premium traditional Basmati, cross-bred Basmati, and non-Basmati rice varieties having different commercial value in the marketplace. When estimates of inferred ancestry or similarity coefficients were used to cluster varieties, the high-quality Indian aromatic and quality rice genotypes could be distinguished from both indica and japonica cultivars, and crossbred varieties could be distinguished from traditional Basmati rices. The results indicate that Indian aromatic and quality germplasm is genetically distinct from other groups within O. sativa and is the product of a long, independent pattern of evolution. The data also suggest that there is scope for exploiting the genetic diversity of aromatic/quality rice germplasm available in India for national Basmati rice breeding programs.
Similar content being viewed by others
References
Aggarwal RK, Shenoy VV, Ramadevi J, Rajkumar R, Singh L (2002) Molecular characterization of some Indian Basmati and other elite rice genotypes using fluorescent-AFLP. Theor Appl Genet 105:680–690
Ahuja SC, Panwar DVS, Ahuja U, Gupta KR (1995) Basmati rice—the scented pearl. Directorate of Publications, CCS Haryana Agricultural University, Hisar
Anderson JA, Churchill GA, Autrique JE, Tanksley SD, Sorrells ME (1993) Optimizing parental selection for genetic linkage maps. Genome 36:181–186
Bhasin VK (2000) India and the emerging global rice trade. In: Singh RK, Singh US, Khush GS (eds) Aromatic rices. Oxford & IBH, New Delhi, pp 252–276
Blair MW, Hedetale V, McCouch SR (2002) Fluorescent-labeled microsatellite panels useful for detecting allelic diversity in cultivated rice (Oryza sativa L.). Theor Appl Genet 105:449–457
Chen X, Temnykh S, Xu Y, Cho YG, McCouch SR (1997) Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.). Theor Appl Genet 95:553–567
Cho YG, Ishii T, Temnykh S, Chen X, Lipovich L, McCouch SR, Park WD, Ayres N, Cartinhour S (2000) Diversity of microsatellites derived from genomic libraries and GeneBank sequences in rice (Oryza sativa L.). Theor Appl Genet 100:713–722
Coburn JR, Temnykh SV, Paul EM, McCouch SR (2002) Design and application of microsatellite marker panels for semi-automated genotyping of rice (Oryza sativa L.). Crop Sci 42:2092–2099
Dellaporta SL, Wood T, Hicks TB (1983) A plant DNA mini preparation: version II. Plant Mol Biol Rep 1:19–21
Garris A, McCouch S, Kresovich S (2003) Population structure and its effect on haplotype diversity and linkage disequilibrium surrounding the xa5 locus of rice (Oryza sativa L.). Genetics 165:759–769
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 (1997) Methods for precise sizing, automated binning of alleles, and reduction of error rates in large-scale genotyping using fluorescently labeled dinucleotide markers. Genome Res 7:165–178
Glaszmann JC (1987) Isozymes and classification of Asian rice varieties. Theor Appl Genet 42:233–240
Hamada H, Petrino MG, Kakunaga T (1982) A novel repeated element with Z-DNA-forming potential is widely found in evolutionarily diverse eukaryotic genomes. Proc Natl Acad Sci USA 79:6465–6469
Khush GS (2000) Taxonomy and origin of rice. In: Singh RK, Singh US, Khush GS (eds) Aromatic rices. Oxford & IBH, New Delhi, pp 5–13
Khush GS, de la Cruz N (1998) Developing Basmati rices with high yield potential. Cahiers Options Mediterraneennes, vol 24. Rice quality. A pluridisciplinary approach. (CD-ROM computer file). CIHEAM, Paris
Kumar S, Shobha Rani N, Krishnaiah K (1996) Problems and prospects of food grain aromatic rice in India. In: IRRI (ed) Rep INGER Monitoring Visit Fine Grain Aromatic Rice India, Iran, Pakistan, and Thailand. IRRI, Manila, pp 21–29
Macaulay M, Ramsay L, Powell W, Waugh R (2001) A representative, highly informative genotyping set of barley SSRs. Theor Appl Genet 102:801–809
McCouch S, Teytelman L, Xu Y, Lobos K, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L (2002) Development of 2,240 new SSR markers for rice (Oryza sativa L.). DNA Res 9:199–207
Nagaraju J, Kathirvel M, Kumar RR, Siddiq EA, Hasnain SE (2002) Genetic analysis of traditional and evolved Basmati and non-Basmati rice varieties by using fluorescence-based ISSR-PCR and SSR markers. Proc Natl Acad Sci USA 99:5836–5841
Nene YL (1998) Basmati rice: a distinct variety (cultivar) of the Indian subcontinent. Asian Agric Hist 2:175–188
Ni J, Colowit PM, Oster JJ, Mackill DJ (2001) Evaluation of genetic diversity in rice sub-species using SSLP markers. Crop Sci 42:601–607
Olufowote JO, Xu Y, Chen X, Park WO, Beachell HM, Dilday RH, Goto M, McCouch SR (1997) Comparative evaluation of within-cultivar variation of rice (Oryza sativa L.) using microsatellite and RFLP markers. Genome 40:370–378
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure from multilocus genotype data. Genetics 155:945–959
Reed PW, Davies JL, Copeman JB, Bennett ST, Palmer SM, Pritchard LE, Gough SCL, Kawaguchi Y, Cordell HJ, Balfour KM, Jenkins SC, Powell EE, Vignal A, Todd JA (1994) Chromosome specific microsatellite sets for fluorescence-based, semi-automated genome mapping. Nat Genet 7:390–395
Rohlf FJ (1993) ntsys-pc: numerical taxonomy and multivariate analysis system, version 1.8, Exeter Software, Setauket, N.Y.
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Singh RK, Gautam PL, Saxena S, Singh S (2000a) Scented rice germplasm: conservation, evaluation and utilization. In: Singh RK, Singh US, Khush GS (eds) Aromatic rices. Oxford & IBH, New Delhi, pp 107–133
Singh RK, Singh US, Khush GS, Rohilla R, Singh JP, Singh G, Shekhar KS (2000b) Small and medium grained aromatic rices of India. In: Singh RK, Singh US, Khush GS (eds) Aromatic rices. Oxford & IBH, New Delhi, pp 155–177
Smith S (1998) Cultivar identification and varietal protection. In: Caetano-Anollés G, Gresshoff PM (eds) DNA markers: protocols, applications, and overviews. Wiley-VCH, New York, p 283
Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11:1441–1452
Weber JL, May PE (1989) Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am J Hum Genet 44:388–396
Westman AL, Kresovich S (1997) Use of molecular marker techniques for description f plant genetic variation. In: Callow JA, Ford-Lloyd BV, Newbury HJ (eds) Plant genetic resources. Conservation and use. CAB Int, Wallingford, pp 9–48
Acknowledgements
We gratefully acknowledge financial support from the Rockefeller Foundation (RF 99001#736, RF99001#726 and RF2001FS048). We thank Sharon Mitchell for help with the genotyping, Steve Kresovich for his generosity in providing access to the ABI Sequencer at the Institute of Genomic Diversity, and Navinder Saini for help with DNA extraction. We also thank Marappa Maheswaran, Mande Semon, and Amanda Garris for assistance with the data analysis and Lois Swales for help with formatting.
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by P. Langridge
Electronic Supplementary Material
Rights and permissions
About this article
Cite this article
Jain, S., Jain, R.K. & McCouch, S.R. Genetic analysis of Indian aromatic and quality rice (Oryza sativa L.) germplasm using panels of fluorescently-labeled microsatellite markers. Theor Appl Genet 109, 965–977 (2004). https://doi.org/10.1007/s00122-004-1700-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00122-004-1700-2