Genetic variation in the Asian seabass (Lates calcarifer Bloch, 1790) from Wallacea Region estimated using random amplified polymorphic DNA (RAPD) markers

Abstract

The Asian seabass (Lates calcarifer) is an important marine food fish in Southeast Asia. To facilitate a selective breeding program conducted in Indonesia, we genotyped 29 Asian seabass specimens collected from four wild populations in the Wallacea Region originating from coastal waters in two seaways: the Makassar Strait (Bulungan in North Kalimantan and Maros in South Sulawesi) and the Gulf of Bone (Siwa and Bone in South Sulawesi). We used four polymorphic markers with a random amplified polymorphic DNA (RAPD) method. A total of 43 alleles were detected at four loci across the four populations, four of which were shared by all the accessions while 39 were polymorphic. Of these 43 alleles, 34.88% were unique, with 46.67% in the Gulf of Bone and 53.33% in the Makassar Strait. Asian seabass within-population genetic distance was greater in Bone Bay than the Makassar Strait, and an ongoing speciation phenomenon is suspected. The greatest genetic distance (0.291) was between the Asian seabass populations from Bulungan, North Kalimantan and Cenranae River estuary, Bone Regency; the lowest (0.086) was between the Bulungan and Maros populations. In the phylogenetic analysis, Gulf of Bone and Makassar Strait specimens formed separate clades. Commercial scale cross-breeding between Asian seabass from Makassar Strait and the Gulf of Bone may produce highly adaptable seed. These results will be helpful in future Asian seabass breeding programs as well as for optimising management and conservation strategies for wild Asian seabass populations.