A ten year research project undertaken by the CSIRO consortium in conjunction with The Australian Prawn Farmers Association to remove the barriers to domestication of Penaeus monodon (Fabricius) has resulted in major advances in the understanding of the reproductive biology and epidemiology of penaeid prawns (CSIRO, 2010). Eight generations of selective breeding has substantially improved growth and survival rates (Preston et al., 2009). The screening of animals for pathogenic viruses e.g. GAV, MoV and MBV using the molecular techniques , in situ hybridization (ISH) and polymerase chain reaction (PCR) assays has brought the industry to the forefront in obtaining specific pathogen fee (SPF) certification (Coman et al. 2009). The choice of sampling tissue for RT-PCR tests is the pleopod exopodite.
A large number of polymorphic markers are needed to examine genetic variation in cultured penaeid species, trace pedigrees and apply marker assisted selection in breeding programs (Garcia and Alcivar-Warran, 2007). The domestication project is characterized by a robust genetic and biosecurity management regime with vertical and horizontal lineage in family tracking protocols, resulting in gains in growth of approximately 4-5% per generation (Benzie, 2009). The use and development of molecular markers specifically microsatellites and AFLP (amplified fragment length polymorphisms) markers have contributed to the reliable, efficient and reproducible construction of genetic linkage maps (Wilson et al., 2002; Jerry et al., 2006 a and b, Kenway et al., 2006). A linkage map can be used for identification of qualitative and quantitative trait loci (QTLs) controlling economically important characters e.g. growth and disease resistance (Wuthisuthimethavee et al., 2005; Le Francois et al., 2010; You et al., 2010). A substantive molecular marker has been determined with a sex linked association (Macbeth et al., 2007; Staelens et al., 2008). A highlight of the domesticated P.monodon research is the improved reproductive ability in comparison with wild animals (Sellars, 2010).