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

TL;DR

Selective breeding of Crassostrea ariakensis over four generations reduced genetic diversity but still left enough variation for future breeding.

Contribution

The study shows that selective breeding in oysters leads to reduced genetic diversity but not complete homogenization.

Findings

Genetic diversity indices like haplotype diversity and nucleotide diversity decreased from F0 to F4.

Despite selective breeding, F4 maintained relatively high genetic diversity and showed no complete homogenization.

Intra-population variation remained higher than inter-population variation across generations.

Abstract

The genetic diversities of five successive generations, including the base population (F0) and four selective breeding populations (F1 to F4) of Crassostrea ariakensis, were analyzed based on both mitochondrial cox1 and rrnL gene sequence fragments. The cox1 gene sequences exhibited higher sequence variability compared to the rrnL. Based on the partial cox1 sequences, the genetic diversity indices, such as the haplotype diversity, average number of nucleotide differences, and nucleotide diversity, as well as the intra-population genetic distances, showed a decline across generations from F0 to F4, indicating a reduction in genetic variation due to selective breeding. Although the generations became more genetically conserved and very low genetic differentiation occurred as the selective breeding lasted, the F4 population still maintained relatively high levels of genetic diversity. These findings suggest that substantial within-populations variation persists even after multiple rounds of selection, and complete genetic homogenization across generations has not been achieved.

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 Crassostrea ariakensis, 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 cox1 and rrnL gene sequences. Results showed that the 649 bp cox1 and 488 bp rrnL sequences exhibited (A+T)-biased composition and showed positive AT skew. A total of 12 haplotypes were found for the cox1 sequences, while only three haplotypes were detected for the rrnL sequences. However, among the F1 to F4 populations, only three cox1 haplotypes and two rrnL haplotypes were observed. Based on cox1 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 (p < 0.05). In contrast, only the F0 and F4 population had multiple rrnL haplotypes, and no statistically significant genetic differentiations were observed based on rrnL fragments (p > 0.05). The AMOVA results showed that intra-population genetic variation exceeded inter-population variation, regardless of whether it was assessed using the cox1 gene or the rrnL 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.

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