An experiment was carried out at BAU-GPC and laboratory of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh to study morphological characteristics of Wax Jambu (Syzygium samarangense), genetic variability, characters association, correlation and path coefficient analysis of 5 accessions of Wax Jambu collected from BAU-GPC and from Indonesia during the period from February, 2012 to March, 2013. Random amplified polymorphic DNA (RAPD) was used to characterize these accessions at molecular level. In spite of having close resemblance, the morphotypes of 5 accessions of Wax Jambu were different from each other in respect of fruit color, shape and TSS percentage with different leaf characteristics. In respect of path analysis, fruit breadth, dry matter and percent moisture contributed towards maximum phenotypic and genotypic direct effect on fruit weight indicating its importance as a selection parameter. Molecular characterization was conducted to investigate the variability of 5 Wax Jambu accessions using random amplified polymorphic DNA (RAPD) markers. Out of 4 primers screened, 2 primers were selected which gave 23 clear and bright fragments. Between the two primers used, CCAACGTCGG showed the highest level of polymorphism (83.33%). Of the 23 bands, 19 (82.7%) were polymorphic. The estimation of Nei’s (1972) genetic diversity for entire accessions of Wax Jambu was 0.3339 and Shannon’s information index was 0.4952. The highest genetic distance (0.9861) was observed between the accessions BAU Jamrul 3 and Indonesian Jamrul. On the other hand, the lowest distance (0.1911) was found between the accessions BAU Jamrul 1 and BAU Jamrul 2 which revealed that there is a great genetic difference among the accessions. The present lend an adequate support to the potentiality of using molecular markers as supplementary to morphological descriptors in the identification process of different morphotypes and accessions of Syzygium samarangense
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