Identification of RAPD-SCAR marker linked to white spot syndrome virus resistance in populations of giant black tiger shrimp, Penaeus monodon Fabricius S Dutta, S Biswas, K Mukherjee, U Chakrabarty, A Mallik and N Mandal Division of Molecular Medicine, Bose Institute, Kolkata, India Abstract White spot disease (WSD) caused by white spot syndrome virus (WSSV) creates severe epizootics in shrimp aquaculture industry worldwide. Despite several efforts, no such permanent remedy was yet developed. Selective breeding using DNA markers would be a cost-effective strategy for long-term solution of this problem. In the present investigation, out of 30 random primers, only one primer produced a statistically significant (P < 0.01) randomly amplified polymorphic DNA (RAPD) marker of 502 bp, which provided a good discrimination between disease resistant and disease susceptible populations of Penaeus monodon from three geographical locations along the East coast of India. Because RAPD markers are dominant, a sequence characterized amplified region (SCAR) marker was developed by cloning and sequencing of 502 bp RAPD fragment, which generates a single 457 bp DNA fragment after PCR amplification only in the disease resistant shrimps. Challenge experiment was also conducted to validate this 457 bp SCAR marker, and the results suggested that the WSSV loads were 2.25 9 10 3 fold higher in disease susceptible than that in disease resistant shrimps using real-time PCR. Therefore, this 457 bp DNA SCAR marker will be very valuable towards the development of disease-free shrimp aquaculture industry. Keywords: disease resistant, disease susceptible, Penaeus monodon, RAPD, SCAR, shrimp. Introduction Giant black tiger shrimp, Penaeus monodon Fabri- cius, a captured and cultured marine crustacean species, has a global economic impact on employ- ment generation and hard currency earnings (Lucien-Brun 1997; Funge-Smith & Briggs 2003). It is one of most lucrative native shrimp species in India owing to its high growth rate, palatability and nutritional value. Over the last few decades, shrimp farming has suffered relentless destruction due to pandemic diseases caused by diverse viral pathogens across the globe (Lightner 1988, 1993; Brock 1991; Flegel, Fegan & Sriurairatana 1995; Flegel 1997). Among almost 20 viral pathogens known to infect marine shrimps, white spot syndrome virus (WSSV) causative agent of white spot disease (WSD) creates severe destruction in captured and cultured shrimp production (Takahashi et al. 1994). WSSV is an ellipsoidal, enveloped, dsDNA virus of 305 107 bp length, having a bacilliform nucleocapsid belongs to the genus Whispovirus of the family Nimaviridae (Wang et al. 1995; Durand et al. 1997; Yang et al. 2001). WSSV infects post- larval to adult shrimps with transmission ability by both vertically and horizontally (Chang et al. 1996; Zhan et al. 1998). On the other hand, a handful of efforts as prospective protective measures against WSSV infection has been mostly unsuccessful in developing any permanent remedy (Witteveldt et al. 2004; Kim et al. 2007; Rameshthangam & Ramasamy 2007). As an alternative approach, enrichment of disease resistant broodstock and maintenance of their genetic sustainability through selective breeding using DNA markers hold high potential in several species of fish and shellfish (Houston, Haley & Hamilton 2008). In this Correspondence N Mandal, Division of Molecular Medicine, Bose Institute, P-1/12 CIT Scheme VII-M, Kolkata 700054, India (e-mail: mandaln@rediffmail.com) 1 Ó 2013 John Wiley & Sons Ltd Journal of Fish Diseases 2013 doi:10.1111/jfd.12128