Abstract AFLP markers were employed to assess the genetic diversity amongst 21 established natural and nine synthetic varietes and lines of Brassica juncea originating from Asia, Australia, Canada, Eastern Eu- rope and Russia. Six of the synthetics used for diversity studies have been developed recently. Twenty one EcoRI/MseI-based AFLP primer pairs generated a total of 1251 scorable fragments among the 30 genotypes studied, of which 778 bands were polymorphic with an average of 37 polymorphic bands per primer pair. On the basis of the similarity coefficients (F value), cluster analysis was performed using the UPGMA method. The 30 B. juncea lines could be grouped into three distinct clusters. All the Indian, Chinese and previously devel- oped synthetics formed one cluster (cluster A), the re- cently developed synthetics formed a separate cluster (cluster B) and the lines from Australia, Canada, Eastern Europe and Russia formed the third cluster (cluster C). A majority of the lines were uniquely identified by one or more primer pairs due to the presence or absence of variety specific band(s). Four primer pairs were found to be most informative, since these uniquely identified all the genotypes assayed. These four primer pairs, could therefore be used as fingerprinting primers for varietal identification. Keyword AFLP markers · Brassica juncea · Genetic diversity Introduction Evaluation of genetic divergence and relatedness among breeding materials has significant implications for the improvement of crop plants. Besides providing predic- tive estimates of genetic variation within a species these studies also facilitate the planning of new breeding ap- proaches for cultivar development. Diverse parental combinations could be either used to create segregating progenies with maximum genetic variability for selection or for heterosis breeding. Brassica juncea (Indian mustard) is a major oilseed crop of India and is grown in about six million hectares of land, particularly in the rainfed areas of Northern In- dia during the winter growing season. It is also a poten- tial crop in the western prairies of Canada and to some extent is grown in Australia, China and Russia. B. jun- cea is predominantly a self-pollinated crop with 5–15% cross-pollination (Asthana and Singh 1973). Cultivar improvement programmes in B. juncea have generally followed breeding methodologies for self-pollinating grain crops. Over the past two decades, breeding pro- grammes, particularly in India, have endeavoured to make selections from segregating populations of crosses amongst varieties from regional programmes. Crossing within such germplasm, has resulted in only marginal improvements in the productivity of B. juncea. To real- ize further gains in productivity, it would be important to utilize new sources of variation which would lead to broadening the genetic base of the existing varieties. Productivity can also be substantially increased by het- erosis breeding. In Brassica species, it has been shown that F 1 hybrids between genetically diverse genotypes and/or genotypes of different geographical regions are more productive than those involving genotypes which are more regional and have a narrow genetic base (Banga and Labana 1984; Lefert-Buson et al. 1987; Pradhan et al. 1993). DNA markers are increasingly being recognised as useful tools for assessing genetic diversity amongst germplasm since these are least influenced by the envi- ronment (Lee 1995). The marker systems include restric- tion fragment length polymorphism (RFLP), random am- plified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP) and simple sequence re- Communicated by H.F. Linskens A. Srivastava · V. Gupta · D. Pental · A.K. Pradhan ( ✉ ) Centre for Genetic Manipulation of Crop Plants and Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India e-mail: pradhanakshay@hotmail.com Theor Appl Genet (2001) 102:193–199 © Springer-Verlag 2001 ORIGINAL ARTICLE A. Srivastava · V. Gupta · D. Pental · A.K. Pradhan AFLP-based genetic diversity assessment amongst agronomically important natural and some newly synthesized lines of Brassica juncea Received: 1 November 1999 / Accepted: 8 May 2000