Abstract—Durian is the flagship fruit of Mindanao and there is an abundance of several cultivars with many confusing identities/ names. The project was conducted to develop procedure for reliable and rapid detection and sorting of durian planting materials. Moreover, it is also aimed to establish specific genetic or DNA markers for routine testing and authentication of durian cultivars in question. The project developed molecular procedures for routine testing. SSR primers were also screened and identified for their utility in discriminating durian cultivars collected. Results of the study showed the following accomplishments: 1. Twenty (29) SSR primers were selected and identified based on their ability to discriminate durian cultivars, 2. Optimized and established standard procedure for identification and authentication of Durian cultivars 3. Genetic profile of durian is now available at Biotech Unit Our results demonstrate the relevance of using molecular techniques in evaluating and identifying durian clones. The most polymorphic primers tested in this study could be useful tools for detecting variation even at the early stage of the plant especially for commercial purposes. The process developed combines the efficiency of the microsatellites development process with the optimization of non-radioactive detection process resulting in a user-friendly protocol that can be performed in two (2) weeks and easily incorporated into laboratories about to start microsatellite development projects. This can be of great importance to extend microsatellite analyses to other crop species where minimal genetic information is currently available. With this, the University can now be a service laboratory for routine testing and authentication of durian clones. Keywords—DNA, SSR Analysis, genotype, genetic diversity, cultivars. I. INTRODUCTION URIAN, (Durio zibethinus) is tagged and revered in Southeastern Asia as the king of fruit [1] and is the flagship fruit in Mindanao. Moreover, among durian eaters it is known as a fruit that “smells like hell but tastes like heaven” due to its unusual odor. It is distinctive for its large size, unique odor and formidable thorn-covered hush. Southern Mindanao is considered the durian republic where several collection and cultivars are widely grown. Moreover, it grows almost exclusive in Mindanao and very few in other parts of the country. This fruit is becoming more important and the demand had increased from year to year [1]. In the past, durian fruit is priced by piece but recently it is sold by the kilogram. This is E.K. Sales is with the Genetics Molecular Biology Laboratory, University of Southern Mindanao, 9407 Kabacan, Cotabato Philippines She is the Director of USM CHED Higher Education Regional Research Center (Telefax: 064-248-2610; e-mail: eperezkalaw@gmail.com). due to the increasing demand as fresh fruit as well as other uses such as flavor base of sweet edibles e.g. ice cream, candy, jam, preserve, etc. Interestingly, previous non durian eaters had acquired the taste for this fruit such that the demand spread from Mindanao to other parts of the country. Meanwhile, overseas consumers prefer durians that do not smell, taste sweet, slightly bitter, thick fruit meat and yellow fruit meat [2]. There are numerous varieties of durian. Some are considered with superior quality. Different market segments showed various consumer preferences and its distinction for superior quality depends on the consumer preferences like flavor, odor and meat/flesh content. In view of the numerous cultivars available, preferences for recommended varieties fetch higher price as planting materials or as fresh produce. This therefore results to a greater demand for quality planting materials of specified variety. However, many cultivar names are thought to be synonyms for the same cultivars which in turn cause confusion among breeders and farmers. So far, no critical method for cultivar identification currently exist thus one of the constraints and gap is the lack of a proper and reliable identification of clones and varieties in the nursery. Identification is mostly done through evaluation of fruit and leaf traits. Varieties or clones should be properly identified as true to type before they are disposed to the farmers for planting. Any simple mistake or mislabeling will seriously jeopardize the economic profitability of the plantation. Mother plants/seedlings and other propagates used as source of planting materials should be checked, verified or confirmed to be the best variety (variety of interest) for multiplication. With the advent of DNA technology, this gap can be bridged. Molecular marker techniques have proved useful in population and improvement studies, clone/genotype identification, certification of controlled species and hybrids, paternity determination, marker assisted early selection and development of strategies for improvement and suitable management of genetic resources. Moreover, genetic diversity of durian cultivars in the Philippines has been successfully assessed [3]. At present USM has an existing collection of 23 varieties of fruit bearing durian at the USM clonal garden. So far, characterization even at the morphological level has not been done. Identification is only through the difference in fruit appearance which is quite arbitrary. Likewise, the university is also endowed with an established genetics and molecular biology laboratory equipped with the required facilities (thru the DA-BAR IDG Emma K. Sales Durian Marker Kit for Durian (Durio zibethinus Murr.) Identity D World Academy of Science, Engineering and Technology International Journal of Biological, Food, Veterinary and Agricultural Engineering Vol:9, No:5, 2015 497 International Scholarly and Scientific Research & Innovation 9(5) 2015 International Science Index Vol:9, No:5, 2015 waset.org/Publication/10001505