Genetic Structures of Crassostrea ariakensis Generations Based on Partial Mitochondrial cox1 and rrnL Indicated a High Breeding Potential After Four-Years Successive Selections

With the rapid development of oyster farming and the emergence of new varieties, the identification and evaluation of genetic resources have become fundamental to the effective utilization of oyster germplasm resources. To evaluate the impact of selective breeding on the germplasm of <i>Crassostrea ariakensis</i>, this study conducted genetic structure analysis on five successive generations including four generations selected (F1 to F4) focusing on both fast growth and high glycogen content and one base population (F0) based on partial mitochondrial <i>cox1</i> and <i>rrnL</i> gene sequences. Results showed that the 649 bp <i>cox1</i> and 488 bp <i>rrnL</i> sequences exhibited (A+T)-biased composition and showed positive AT skew. A total of 12 haplotypes were found for the <i>cox1</i> sequences, while only three haplotypes were detected for the <i>rrnL</i> sequences. However, among the F1 to F4 populations, only three <i>cox1</i> haplotypes and two <i>rrnL</i> haplotypes were observed. Based on <i>cox1</i> sequences, the values of the haplotype diversity index, average number of nucleotide differences, and nucleotide diversity index all decreased progressively from F1 to F4, indicating a reduction in genetic variation due to selective breeding. All populations exhibited a low level of nucleotide diversity (<0.05). In addition, the intra-population genetic distance declined from F0 to F4, with significant genetic differentiation between F0 and F1, as well as between F0 and F4 (<i>p</i> < 0.05). In contrast, only the F0 and F4 population had multiple <i>rrnL</i> haplotypes, and no statistically significant genetic differentiations were observed based on <i>rrnL</i> fragments (<i>p</i> > 0.05). The AMOVA results showed that intra-population genetic variation exceeded inter-population variation, regardless of whether it was assessed using the <i>cox1</i> gene or the <i>rrnL</i> gene, indicating that substantial genetic diversity persists within populations despite multiple generations of selection, and complete genetic differentiation across generations has not been achieved. These findings indicate that the selectively bred lines retain considerable genetic potential and can serve as a valuable resource for future breeding programs.