Genetic analysis of Indian aromatic and quality rice (Oryza sativa L.) germplasm using panels of fluorescently-labeled microsatellite markers
Open Access
- 7 August 2004
- journal article
- research article
- Published by Springer Science and Business Media LLC in Theoretical and Applied Genetics
- Vol. 109 (5), 965-977
- https://doi.org/10.1007/s00122-004-1700-2
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.Keywords
This publication has 19 references indexed in Scilit:
- Design and Application of Microsatellite Marker Panels for Semiautomated Genotyping of Rice (Oryza sativa L.)Crop Science, 2002
- Fluorescent-labeled microsatellite panels useful for detecting allelic diversity in cultivated rice (Oryza sativa L.)Theoretical and Applied Genetics, 2002
- Evaluation of Genetic Diversity in Rice Subspecies Using Microsatellite MarkersCrop Science, 2002
- Computational and Experimental Analysis of Microsatellites in Rice (Oryza sativa L.): Frequency, Length Variation, Transposon Associations, and Genetic Marker PotentialGenome Research, 2001
- Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.)Theoretical and Applied Genetics, 1997
- Methods for precise sizing, automated binning of alleles, and reduction of error rates in large-scale genotyping using fluorescently labeled dinucleotide markers. FUSION (Finland-U.S. Investigation of NIDDM Genetics) Study Group.Genome Research, 1997
- Chromosome–specific microsatellite sets for fluorescence–based, semi–automated genome mappingNature Genetics, 1994
- Optimizing parental selection for genetic linkage mapsGenome, 1993
- Isozymes and classification of Asian rice varietiesTheoretical and Applied Genetics, 1987
- A plant DNA minipreparation: Version IIPlant Molecular Biology Reporter, 1983