Theoretical and Applied Genetics

, Volume 109, Issue 5, pp 965–977 | Cite as

Genetic analysis of Indian aromatic and quality rice (Oryza sativa L.) germplasm using panels of fluorescently-labeled microsatellite markers

  • Sunita Jain
  • Rajinder K. Jain
  • Susan R. McCouch
Original Paper


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.


Simple Sequence Repeat Marker Rice Variety Polymorphism Information Content Simple Sequence Repeat Locus Rice Genotype 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



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.

Supplementary material

122_2004_1700_esm_table1.xls (24 kb)
sTable 1 (Excel 24 KB)
122_2004_1700_esm_table2.xls (16 kb)
sTable 2 (Excel 15 KB)


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Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • Sunita Jain
    • 2
  • Rajinder K. Jain
    • 2
  • Susan R. McCouch
    • 1
  1. 1.Department of Plant BreedingCornell UniversityIthacaUSA
  2. 2.College of Basic Sciences and HumanitiesCCS Haryana Agricultural UniversityHisarIndia

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