Background. The aquaculture industry is driven by the need to develop novel interspecific hybrids with improved culture characteristics, however currently no molecular markers are available for the validation of F1 hybrids in the case of groupers. The presently reported study was directed toward the development of molecular markers for F1 hybrids obtained by artificial spawning of eggs derived from orange-spotted grouper, Epinephelus coioides (Hamilton, 1822), with sperm from giant grouper, E. lanceolatus (Bloch, 1790). Materials and methods. DNA was extracted and purified from the fin clip of a single F1 hybrid of E. coioides × E. lanceolatus. Small insert shotgun genomics libraries were constructed, 40 positive transformants were sequenced, and the sequences deposited at the GenBank. Thirty locus-specific primer pairs were designed and tested across 64 F1 hybrid specimens as well as DNA samples extracted from coral grouper, Epinephelus corallicola (Valenciennes, 1828), and brown-marbled grouper, E. fuscoguttatus (Forsskål, 1775). Results. A panel of thirty molecular markers was developed to verify parentage, of these eleven and six of the markers were inherited from the sire and dam respectively. Two markers were specific to the F1 hybrid and none of the markers could be assigned to the closely related groupers E. corallicola and E. fuscoguttatus. Conclusion. The markers developed can be applied to assign parentage and determine the degree of introgression in interspecific grouper hybrids developed from E. coioides and E. lanceolatus. The methods developed in this study can be extended to characterize Quantitative Trait Loci (QTLs) and to identify interspecific F1 hybrids in the wild.

Mendelian inheritance, heterosis, Dobzhansky–Muller incompatibility, single locus DNA markers, genomic library