RAPD markers as predictors of infectious hypodermal and hematopoietic necrosis virus (IHHNV) resistance in shrimp (Litopenaeus stylirostris)

Random amplified polymorphic DNA (RAPD) fingerprints of two shrimp populations (Litopenaeus stylirostris) were compared to find genetic marker(s) that may be associated with infectious hypodermal and hematopoietic necrosis virus (IHHNV) resistance or susceptibility. Of the 100 10-mer random primers and 100 intersimple-sequence repeat (ISSR) primers screened, five provided markers specific to the Super Shrimp population and three provided markers specific to the wild caught population. The two populations were further characterized for relative viral load (reported as cycle threshold, C_T) using real-time quantitative PCR with primers specific to the IHHNV genome. The Β-actin gene was amplified to serve as a control for normalization of the IHHNV viral load. The mean viral load was significantly lower (C_T = 34.58; equivalent to 3.3 × 10¹ copies of IHHNV genome/ng DNA) in Super Shrimp than in the wild caught population (C_T = 23.49; equivalent to 4.2 × 10⁴ copies/ng DNA; P < 0.001; C_T values are inversely related to viral load). A preliminary prediction model was created with Classification and Regression Tree (CART) software (Salford Systems, San Diego, Calif.), where the resultant decision tree uses the presence or absence of seven RAPD markers as predictors of the relative viral load.