DNA fingerprinting and phylogenetic analysis of Indian aromatic high-quality rice germplasm using panels of flourescent-labeled microsatellite markers
2003
Jain, S. | Mitchell, S.E. | Jain, R.K. | Kresovich, S. | McCouch, S.R.
Four multiplex panels composed of 30 flourescent-labeled simple sequence repeat (SSR) markers were used to study the genetic diversity and phylogenetic relationship among the aromatic high-quality rice germplasm collections from different parts of India. A total of 248 alleles were detected at 30 SSR loci: the number of alleles per locus ranged from 3 to 22, with an average of 8.2. Genetic diversity was evaluated by estimating the polymorphism information content (PIC), distribution, frequency, and range of allele sizes for each microsatellite locus. The similarity coefficients were analyzed to study phylogenetic relationships by clustering algorithms. The PIC values, which are a reflection of allelic diversity among the varieties, were quite high for all the microsatellites, averaging 0.565, and ranging from 0.203 to 0.904. The size range between the smallest and largest allele for a given microsatellite varied from 3 to 68 bp. Microsatellite marker-based polymosphism was useful for dissecting fine levels of genetic diversity among basmati rice varieties, and between basmati and nonbasmati varieties. Clustering analyses indicate high levels of genetic diversity among the scented/high-quality rice germplasm of India. Several SSR markers were identified that can be used to differentiate the commercially important basmati rice varieties.
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