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Morphological traits and randomly amplified polymorphic DNA (RAPD) markers are used to identify their relationship of 49 pepper(Capsicum annuum L.) cultivars from Know You and Evergrow Seed Companies. Twenty five horticultural traits based on the classification system of National Plant Genetic Resource Center showed that the morphological traits of seed, leaf, flower, and fruit can be used to distinguish 49 Capsicum annuum L. cultivars. By utilization of the differences of 14 fruit characteristics to test these 49 cultivars that they could not be fully distinguished by the morphological traits along.A total of 10 DNA primers are selected from 110 random primers which has shown the polymorphic patterns among 7 pepper cultivars from Know You Seed Company. Ten of the 110 primers, i. e. UBC-327, UBC-484, UBC-002, UBC-005, UBC-019, UBC-020, UBC-042, UBC-043, UBC-066, UBC-084, showed polymorphism and could distinguish all 49 Capsicum annuum L. cultivars. The least similarity of cluster analysis is about 81% among cultivars by 10 primers.Pepper cultivars with UBC-019m(1330bp) or UBC-020j(1800bp) band belong to group of hot pepper cultivars with UBC-043e(1300bp) band had strong pungency, narrower fruit shape, and smooth fruit surface. Hot pepper only showed cultivars with UBC-020j(1800bp) band but without UBC-043e(1300bp) band are slight pungency , wider fruit shape, and groove fruit surface, such as ‵Peace Star′ and ‵ Group Stars′ cultivars of Know You Seed Company. The dendrograms displayed sweet pepper and hot pepper can be distinguished through the cluster analysis of using RAPD markers. Cultivar ‵Uranus′ showed proximate genetic relationship with ‵Big Star′ of Know You Seed Company. And Know You cultivars of ‵Peace Star′ and ‵Group Stars′ were clustered in the same group with Evergrow Seed Company cultivars of ‵Lady Square′ and ‵Summer Bell′. The same as ‵Vega′ and ‵Beauty Bell′ cultivars of Know You Seed Company and ‵Square Lamuyo′, ‵Rich Square′, and ‵Blocky Red′ cultivars of Evergrow Seed Company. The result of genetic relationship among 49 Capsicum annuum L. cultivars based on RAPD markers are similarity with cluster analysis of morphological traits.
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