The current level of genome coverage provided by microsatellite markers in rice is sufficient for DNA fingerprinting, providing Information on diversity and population structure which is expected to assist plant breeders by providing a more rational basis for expanding the gene pool and for identifying material that harbours alleles of value for plant improvement. Allelic data from the species studied revealed that rice interspecific hybrids (NERICA) were more closely related to Oryza sativa than to Oryza glaberrimawhich was closely associated to Oryza barthii than to O sativa. Comparative polymorphism between species showed that O. sativa, Nerica, Oryza barthii and O. glaberrima produced 51, 45, 40 and 36 alleles with 1461, 238, 305 and 445 polymorphic bands respectively with 17 SSR markers. Alleles ranged from 2 to 4 in O. sativa and nerica; from 2 to 3 in O. glaberrima and 1 to 4 in O. barthii. The average polymorphic information content and resolving power was highest in O. sativa (0.53, 0.63), followed by nerica (0.52, 0.62), next was O. barthi (0.29, 0.30) and least in O. glaberrima (0.22, 0.22). Alleles at RM508 were most reliable in profiling O. barthii genotypes. Definitive markers (RM240, RM488) for O. glaberrima and O. sativa (RM587) were obtained. Cluster analysis grouped the rice genotypes into ten clusters at a similar coefficient of 68% with genotypes of the same genetic similarity clustering together. Based on this study therefore, molecular fingerprinting and crop improvement could be advanced for breeding programmes.
Key words: Nerica, Oryza barthii, Oryza glaberrima, Oryza Sativa, rare allele.
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