RAPD markers as predictors of Infectious Hypodermal and Hematopoietic Necrosis Virus (IHHNV) in shrimp (Penaeus stylirostris)

RAPD fingerprints of two shrimp populations (Penaeus stylirostris) were compared to find genetic marker(s) that may be associated with Infectious Hypodermal and Hematopoietic Necrosis Virus (lHHNV) resistance or susceptibility. Of the one hundred 10-mer random primers and one hundred inter-simple sequence repeat (ISSR) primers screened, five primers provided markers specific to the Super Shrimp population and three primers provided markers specific to the wild caught population. The two populations were further characterized for relative viral load (reported as cycle threshold, CT) using real-time quantitative PCR with primers specific to the lHHNV genome. The 13-actin gene was amplified to serve as a control for normalization of the IHHNV viral load. The mean viral load was significantly lower (CT = 34.58; equivalent to 3.3 x 101 copies of IHHNV genome/ng of DNA) in Super Shrimp than in the wild caught population (CT = 23.49; equivalent to 4.2 x 104 copies/ng of DNA; p0.001; CTvalues are inversely related to viral load). A prediction model was created with Classification and Regression Tree (CART) software where the resultant decision tree uses the presence or absence of three RAPD markers as predictors of the relative viral load. Therefore, an assessment of IHHNV resistance or susceptibility in P. stylirostris is based on the RAPD data only.