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Title: SSR marker based genetic diversity analysis of modern rice varieties and coastal landraces in Bangladesh
Authors: Shakil, Shahriar Kabir
Sultana, Shahanaz
Hasan, Md Mehedi
Hossain, Md Musharaf
Ali, Md Shamsher
Prodhan, Shamsul H
Keywords: Genetic diversity;PIC;Rice landraces;Salinity;SSR
Issue Date: 11-May-2015
Abstract: In Bangladesh, large cultivable areas lie in the coastal saline zone where rice cultivation is largely hindered by the salinity. This problem can be effectively addressed by identifying salt-tolerant genotypes using both conventional and modern biotechnological methods. In the present study, the genetic relationship among 24 rice (Oryza sativa L.) genotypes including Pokkali, the salt tolerant benchmark, 5 BRRI released modern varieties and some coastal landraces were assessed using 19 rice SSR markers. A total of 110 reproducible polymorphic alleles were identified from the loci with an average of 5.79 alleles per locus (range from 3-12 alleles). The polymorphism information content (PIC) values enumerated from the data obtained from allelic variation ranged from 0.3694 (RM18) to 0.8711 (RM493) with an average of 0.6533. Based on the discriminatory power value (D-value) calculated from the allelic information revealed RM493 (0.9203) as the best diagnostic PCR marker for varietal identification. The UPGMA cluster revealed six main genetic groups at a cut off value of 32% of similarities comprising of three separate clusters formed by BRRI dhan47 (Cluster III), Lolo (Cluster IV) and Purbachi (Cluster V). The reference salt tolerant cultivar Pokkali and Nonabokra clustered with 4 other tolerant and moderately tolerant rice cultivars in cluster I. The highest genetic dissimilarity was found between Pokkali and Nona (85.29%), Pokkali and Nona kochi (85.29%), and Purbachi and Nona kochi (85.29%), whereas Lona kuchi and Nona kochi (23.69%) showed the lowest genetic dissimilarity between them. DNA fingerprints of these rice cultivars by means of SSR markers provided meaningful data, which can be extended by additional SSR markers, and that information will enable maximized selection of diverse parents and assist in broadening the germplasm based on future rice breeding programmes.
Page(s): 33-41
ISSN: 0975-0967 (Online); 0972-5849 (Print)
Appears in Collections:IJBT Vol.14(1) [January 2015]

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