Middle-East Journal of Scientific Research 23 (5): 856-860, 2015 ISSN 1990-9233 © IDOSI Publications, 2015 DOI: 10.5829/idosi.mejsr.2015.23.05.9375 Corresponding Author: Sohail Ahmad Jan, Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan. 856 Agro-Morphological and Molecular Characterization of Local Tomato Cultivars Grown in Pakhal Region of Pakistan Using RAPD Markers Samia Nawaz, Zubeda Chaudry, Ayesha Bibi, Sohail Ahmad Jan and Khatiba Bibi 1 1 2 3 2 Department of Botany, Hazara University DhodialMansehra, Pakistan 1 Department of Genetics, Hazara University DhodialMansehra, Pakistan 2 Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan 3 Abstract: Tomato is a very important dietary vegetable crop. Like any other crop species, improvement in tomato for quality and quantity of fruit has always been on the top of scientific breeding programs. Pakhal is an important region in Pakistan for tomato production but problem lies with the proper available cultivars for the area as farmers use different sources to get seed which result in variable per acre production. The studies were carried out to select the best genotype for this area. For this purpose different varieties from the local farmer’s field were collected. Genomic DNA was extracted from 3 weeks old plants and PCR study was performed for Randomly Amplified Polymorphic DNA(RAPD) analysis from 13 genotypes (from Pakhal region) were used for morphological and DNA based fingerprinting. The fruit shape showed largest variation with three types (round, ovate and pear-shaped) among all tested genotypes. A total of 10 different RAPD primers were used for screening of diverse tomato genotypes. Six out of eleven morphological traits showed maximum diversity. A total of thirty-five reproducible and scorable amplification products were generated out of which 23 (65.7%) fragments were polymorphic with 10 RAPD primers. With an average of 5 bands per primer the highest level of polymorphism was detected with primer OPA-18 (83%) whereas primer OPA-05 detected the least polymorphism (25%). It was found that F1 Hybrid and Rio USA accessions were much related to each other. The present study is useful for the selection of improved tomato genotypes for maximum yield production. Key words: Genetic Variation Randomly Amplified Polymorphic DNA Tomato INTRODUCTION produces about 0.3 million tons of tomato annually. Tomato (Solanumlycopersicum L.), originated from production. Parachanar, Pakhal and Battal valley are major South America is nowadays one of the significant tomato growing areas of KP. Tomato crop has a vegetable crops of special economic importance and tremendous export potential due to its demand in the widely grown plant in Solanaceaefamily. Botanically, it is international market [3]. Bulging population demands a fruit and horticulturally it is a vegetable [1]. Tomato increase in the production of tomatoes, which can be met plays an important role in human nutrition by providing by increasing per unit production. Tomato cultivars are essential amino acids, vitamins and minerals. Its vitamin much sensitive to hot climate, is one of the limitations in C content is particularly high. It also contains carotenes optimum production of summer tomato crop in plains of andlycopene, a very potent antioxidant that may be an Naz et al. [4]. Like any other crop species, improvement in important contributor to prevention of cell cancers [2]. tomato for quality and quantity of fruit has always been Other than fresh fruit consumption, processed forms as on the top of scientific breeding programs. The processes canned tomatoes, ketchup and variety of sauces, juice, of domestication and artificial selection contributed to the soups, paste and powder are equally popular. Pakistan depletion of genetic diversity in tomato. A chance of Khyber Pakhtunkhwa (KP) produces 30% of tomato