Indian Journal of Biotechnology Vol 5, April 2006, pp 200-206 Distinguishing Indian commercial wheat varieties using RAPD based DNA fingerprints G Thomas 2 , T Mohapatra 1 , A R Rao 3 and R P Sharma 1* 1 National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi 110 012, India 2 Department of Biotechnology, Allahabad Agricultural Institute-Deemed University, Allahabad 211 007, India 3 Indian Agricultural Statistics Research Institute, New Delhi 110 012, India Received 3 September 2004; revised 10 May 2005; accepted 8 July 2005 Wheat is a major contributor to food self-sufficiency in India. A large number of varieties have been bred over years to sustain higher production levels. These varieties have been described primarily by morphological characteristics, which show stage and tissue specific expression, and interaction with environment. The present study was undertaken to test the efficiency of RAPD in distinguishing and determining the extent of genetic relatedness among 96 varieties belonging to Triticum aestivum, T. durum, T. dicoccum and Triticale, using 50 random decamer primers. Eighty-two per cent of these primers and 78.8% of the amplified fragments were found to be polymorphic. The number of polymorphic fragments per primer ranged from 1-13 with an average of 4.92. The varieties could be unambiguously distinguished from each other by RAPD profiles based on all the 50 as well as 10 most informative primers, which detected more than 5 polymorphic fragments each. The estimated probability of identical match by chance suggested that the RAPD based DNA fingerprints can be used with high degree of confidence for establishing distinctness of the varieties. Average similarity (75%) among the hexaploids was the same as in the tetraploids, although the range was broader in case of the former group of varieties. This suggested a relatively narrow genetic base of the tetraploid varieties as compared to the hexaploids. Cluster and principal component analysis clearly distinguished the tetraploids from the hexaploids. Keywords: commercial varieties, DNA fingerprinting, RAPD, Triticale, Triticum aestivum, T. dicoccum, T. durum. IPC Code: Int. Cl. 8 C12N15/10 Introduction The introduction of Mexican wheat varieties in the early 1960s and their subsequent utilization in wheat improvement programmes were primarily responsible for food sufficiency in India. The semi-dwarfing and high yielding characteristics of introductions, such as Sonora-64 and Lerma Rojo, were combined with other desirable features including disease resistance to breed improved wheat varieties 1 . A large number of varieties have been released in the post-green revolution phase and new ones are continuously being added to the list every year. These varieties possess a great deal of similarity in respect of growth, morphology and yield related characteristics. Combinations of morphological descriptors available to establish uniqueness of wheat varieties being developed are limited. Furthermore, morphology based distinctness is not very accurate because of the influence of environment on expression of these characteristics. For the purposes of registration, protection, maintenance of purity of the nucleus and breeder seeds, and testing the quality of commercial seed lots, it is essential to develop descriptors for an unambiguous identification and differentiation of the varieties. Molecular markers assay variation at the level of nucleotide sequence of DNA. The polymorphism detected by molecular markers, therefore, reveals differences among genotypes, which are not influenced by environment. Availability of many sources of DNA probes and primers enables screening of a large proportion of genome, both coding and non- coding, thereby facilitating differentiation of even closely related genotypes. Random amplified polymorphic DNA (RAPD) analysis, in particular, has been shown to reveal a significant level of DNA polymorphism in different plant species 2,3 . Factors, such as speed, efficiency and amenability to automation, make RAPD a useful method for effective germplasm management with respect to ______________ * Author for correspondence: Tel: 91-011-25848783; Fax: 91-011-25823984 E-mail: rpsnrcpb@yahoo.co.in