Genetic Differences Between Wild Transplanted and Farmed Populations of Banggai Cardinalfish Pterapogon kauderni Based on Mitochondrial Control Region and SNP Polymorphism

Genetic diversity and population differentiation of an aquaculture population of Banggai cardinalfish (Pterapogon kauderni) introduced and maintained in Phang Nga province, Southern Thailand (A1, N = 45) was examined using control region (CR) polymorphism in comparison with three wild transplanted populations from Gilimanuk Bay (Bali), collected in 2019 (W1, N = 25), Banyuwangi (East Java), collected in 2024 (W2, N = 22), and Gilimanuk Bay (Bali), collected in 2024 (W3, N = 39). In total, 14 haplotypes were identified. Haplotype 3 was found in all populations, while haplotype 4 was found in wild transplanted but not in aquaculture populations. The remaining (12) haplotypes were private haplotypes. Of these, five private haplotypes (H5, H6, H7, H8 and H9) were found only in the A1 population. Moreover, genome-wide single nucleotide polymorphisms (SNPs) in P. kauderni from A1 (N = 21), W2 (N = 15) and W3 (N = 15) populations were also analyzed by Specific Locus Amplified Fragment-Sequencing (SLAF-Seq). In total, 648,378 SNPs were identified. By analyzing both mitochondrial DNA and SNP markers, significant genetic differences were clearly found between farmed and wild transplanted populations of P. kauderni. Reduced genetic diversity was found in a farmed population from genome-wide SNPs but not mtDNA analyses.