Pak. J. Bot., 41(1): 167-176, 2009. MOLECULAR ANALYSIS OF GENETIC DIVERSITY IN BRASSICA SPECIES S. J. ABBAS 1 , FARHATULLAH 2 , KHAN BAHADAR MARWAT 3 , I. A. KHAN 1 AND IQBAL MUNIR 1 1 Institute of Biotechnology and Genetic Engineering, NWFP Agricultural University, Peshawar, Pakistan, 2 Department of Plant Breeding and Genetics, NWFP Agricultural University, Peshawar, Pakistan. 3 Department of Weed Science, NWFP Agricultural University, Peshawar, Pakistan. Abstract Brassica species are the most important source of vegetable oil and the second most important oilseed crop in the international oilseed market after soybean. Genetic improvement of the seed quality made Brassica a source for high quality edible oil for human consumption and high quality protein meal for feeding animals. To improve yield and quality of oil content of Brassica, presence of sufficient genetic diversity in the germplasm is an important prerequisite. On an average, 45.8 and 25.8 alleles were amplified using RAPD and Brassica specific SSR primer sets, respectively. Mean genetic distance estimates ranged from 26-89% and 5-61%, respectively. Size of scorable fragments ranged from approximately 250 to >2000 bp. A high level of genetic dissimilarity (GD= up to 100%) was estimated among the 14 genotypes. Entries were grouped in clusters using cluster analysis. On the basis of dendrogram, most diverse genotypes were identified, that can be used in future brassica breeding program. Introduction The family Brassicaceae, containing about 350 genera and 3500 species, is one of the ten most economically important plant families with a wide range of agronomic traits (Rich, 1991; Christopher et al., 2005). In Pakistan, rapeseed and mustard is the second most important source of oil after cotton. It is sown from mid September to mid November throughout the country. In the season of 2006-07, total area under rapeseed and mustard cultivation was 265.8 thousand hectares with a total production of 221.0 thousand tonnes and an average yield of 831 Kg per hectare. In North West Frontier Province (NWFP), total area under rapeseed and mustard cultivation was 119.6 thousand hectares with a total production of 9.4 thousand tonnes with an average yield of 480 kg per hectare (Anon., 2006-2007). The basic chromosome number for Brassica (and the tribe itself) is controversial, with number for X ranging from 7-11. Molecular studies do not provide support for the ancestral status of X = 7, as it has been found to have multiple origins in separate lineages (Warwick & Black, 1993). The evolution and relationship between members of the plant genus Brassica. (Anon., 1935) showed that there were three different ancestral genomes Brassica rapa or Brassica campestris AA - 2n=2x=20 (Turnip, Chinese cabbage), Brassica nigra BB - 2n=2x=16 (Black mustard) and Brassica oleracea CC - 2n=2x=18 (Cabbage, kale, broccoli, cauliflower). These three species exist as separate species but they are closely related. The interspecific breeding allowed the creation of 3 new species of tetraploid, Brassica juncea AABB - 2n=4x=36 (Indian mustard), Brassica napus AACC - 2n=4x=38 (rapeseed, rutabaga) and Brassica carinata BBCC - 2n=4x=34 (Ethiopian mustard). Because they are derived from the genomes of 2 different species, these hybrid plants are said to be allotetraploid (contain four genomes, derived from two